US20220220508A1 - Engineered casx systems - Google Patents

Abstract

Provided herein are engineered CasX systems and components thereof, including variant CasX proteins and variant guide nucleic acids (gNAs). The variant CasX proteins and variant gNAs of the disclosure display at least one improved characteristic when compared to a reference CasX protein or reference gNA of the disclosure. In some instances, the variants have one or more improved CasX ribonucleoprotein complex functions. Also provided are methods of making and using said variants.

Description

CROSS REFERENCE TO RELATED APPLICATION
• This application is a continuation of International Patent Application No. PCT/US2020/036505, filed on Jun. 5, 2020, which claims priority to U.S. Provisional Patent Application Nos. 62/858,750, filed on Jun. 7, 2019, 62/944,892, filed on Dec. 6, 2019 and 63/030,838, filed on May 27, 2020, the contents of each of which are incorporated herein by reference in their entireties.
INCORPORATION BY REFERENCE OF SEQUENCE LISTING
• This application contains a Sequence listing which has been submitted in ASCII format via EFS-WEB and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Dec. 3, 2021 is named SCRB_01_03US_SeqList_ST25.txt and is 3.64 MB in size.
BACKGROUND
• The CRISPR-Cas systems confer bacteria and archaea with acquired immunity against phage and viruses. Intensive research over the past decade has uncovered the biochemistry of these systems. CRISPR-Cas systems consist of Cas proteins, which are involved in acquisition, targeting and cleavage of foreign DNA or RNA, and a CRISPR array, which includes direct repeats flanking short spacer sequences that guide Cas proteins to their targets. Class 2 CRISPR-Cas are streamlined versions in which a single Cas protein hound to RNA is responsible for binding to and cleavage of a targeted sequence. The programmable nature of these minimal systems has facilitated their use as a versatile technology that is revolutionizing the field of genome manipulation.
• To date, only a few Class 2 CRISPR/Cas systems have been discovered that have been widely used. Thus, there is a need in the art for additional Class 2 CRISP/Cas systems (e.g., Cas protein plus guide RNA combinations) that have been optimized and/or offer improvements over earlier generation systems for utilization in a variety of therapeutic, diagnostic, and research applications.
SUMMARY
• In some aspects, the present disclosure provides variants of a reference CasX nuclease protein, wherein the CasX variant is capable of forming a complex with a guide nucleic acid (NA), and wherein the complex can hind a target DNA, wherein the target DNA comprises non-target strand and a target strand, and wherein the CasX variant comprises at least one modification relative to a domain of the reference CasX and exhibits one or more improved characteristics as compared to the reference CasX protein. The domains of the reference CasX protein include: (a) a non-target strand binding (NTSB) domain that binds to the non-target strand of DNA, wherein the NTSB domain comprises a four-stranded beta sheet; (b) a target strand loading (TSL) domain that places the target DNA in a cleavage site of the CasX variant, the TR, domain comprising three positively charged amino acids, wherein the three positively charged amino acids bind to the target strand of DNA, (c) a helical I domain that interacts with both the target DNA and a spacer region of a guide NA, wherein the helical I domain comprises one or more alpha helices; (d) a helical II domain that interacts with both the target DNA and a scaffold stein of the guide NA; (e) an oligonucleotide binding domain (OBD) that binds a triplex region of the guide NA; and (f) a RuvC DNA cleavage domain.
• In some aspects, the present disclosure provides variants of a reference guide nucleic acid (gNA) capable of binding a CasX protein, wherein the reference guide nucleic acid comprises at least one modification in a region compared to the reference guide nucleic acid sequence, and the variant exhibits one or more improved characteristics compared to the reference guide RNA. The regions of the scaffold of the gNA include: (a) an extended stem loop; (h) a scaffold stem loop; (c) a triplex; and (d) pseudoknot. In some cases, the scaffold stem of the variant gNA further comprises a bubble. In other cases, the scaffold of the variant gNA further comprises a triplex loop region. In other cases, the scaffold of the variant gNA further comprises a 5′ unstructured region.
• In some aspects, the present disclosure provides gene editing pairs comprising the CasX proteins and gNAs of any of the embodiments described herein.
• In some aspects, the present disclosure provides polynucleotides and vectors encoding the CasX proteins, gNAs and gene editing pairs described herein. In some embodiments, the vectors are viral vectors such as an Adeno-Associated Viral (AAV) vector or a lentiviral vector. In other embodiments, the vectors are non-viral particles such as virus-like particles or nanoparticles.
• In some aspects, the present disclosure provides cells comprising the polynucleotides, vectors, CasX proteins, gNAs and gene editing pairs described herein. In other aspects, the present disclosure provides cells comprising target DNA edited by the methods of editing embodiments described herein.
• In some aspects, the present disclosure provides kits comprising the polynucleotides. vectors, CasX proteins, gNAs and gene editing pairs described herein.
• In some aspects, the present disclosure provides methods of editing a target DNA, comprising contacting the target DNA with one or more of the gene editing pairs described herein, wherein the contacting results in editing of the target DNA.
• In other aspects, the disclosure provides methods of treatment of a subject in need thereof, comprising administration of the gene editing pairs or vectors comprising or encoding the gene editing pairs of any of the embodiments described herein.
• In another aspect, provided herein are gene editing pairs, compositions comprising gene editing pairs, or vectors comprising or encoding gene editing pairs, for use as a medicament.
• In another aspect, provided herein are gene editing pairs, compositions comprising gene editing pairs, or vectors comprising or encoding gene editing pairs, for use in a method of treatment, wherein the method comprises editing or modifying a target DNA; optionally wherein the editing occurs in a subject having a mutation in an allele of a gene wherein the mutation causes a disease or disorder in the subject, preferably wherein the editing changes the mutation to a wild type allele of the gene or knocks down or knocks out an allele of a gene causing a disease or disorder in the subject.
BRIEF DESCRIPTION OF THE DRAWINGS
• The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:
• FIG. 1 is a diagram showing an exemplary method of making CasX protein and guide RNA variants of the disclosure using Deep Mutational Evolution (DME). In some exemplary embodiments, DME builds and tests nearly every possible mutation, insertion and deletion in a bimolecule and combinations/multiples thereof, and provides a near comprehensive and unbiased assessment of the fitness landscape of a biomolecule and paths in sequence space towards desired outcomes. As described herein, DME can be applied to both CasX protein and guide RNA.
• FIG. 2 is a diagram and an example fluorescence activated cell sorting (FACS) plot illustrating an exemplary method for assaying the effectiveness of a reference CasX protein or single guide RNA (sgRNA), or variants thereof. A reporter (e.g. GFP reporter) coupled to a gRNA target sequence, complementary to the gRNA spacer, is integrated into a reporter cell line. Cells are transformed or transfected with a CasX protein and/or sgNA variant, with the spacer motif of the sgRNA complementary to and targeting the gRNA target sequence of the reporter. Ability of the CasX:sgRNA ribonucleoprotein complex to cleave the target sequence is assayed by FACS. Cells that lose reporter expression indicate occurrence of CasX:sgRNA ribonucleoprotein complex-mediated cleavage and indel formation.
• FIG. 3A and FIG. 3B are heat maps showing the results of an exemplary DME mutagenesis of the reference sgRNA encoded by SEQ ID NO: 5, as described in Example 3. FIG. 3A shows the effect of single base pair (single base) substitutions, double base pair (double base) substitutions, single base pair insertions, single base pair deletions, and a single base pair deletion plus at single base pair substitution at each position of the reference sgRNA shown at top. FIG. 3B shows the effect of double base pair insertions and a single base pair insertion plus a single base pair substitution at each position of the improved reference sgRNA. The reference sgRNA sequence of SEQ ID NO: 5 is shown at the top of FIG. 3A and bottom of FIG. 3B. In FIG. 3A and FIG. B, Log₂ fold enrichment of the variant in the DME library relative to the reference sgRNA following selection is indicated in grayscale. Enrichment is a proxy for activity, where greater enrichment is a more active molecule. The results show regions of the reference sgRNA that should not be mutated and key regions that are targeted for mutagenesis.
• FIG. 4A shows the results of exemplary DME experiments using a reference sgRNA, as described in Example 3. The improved reference sgNA (an sgRNA) with a sequence of SEQ II) NO: 5 is shown at top, and Log₂ fold enrichment of the variant in the DME library relative to the reference sgRNA following selection is indicated in grayscale. Enrichment is a proxy for activity, where greater enrichment is a more active molecule. The heat map shows an exemplary DME experiment showing four replicates of a library where every base pair in the reference sgRNA has been substituted with every possible alternative base pair.
• FIG. 4B is a series of 8 plots that compare biological replicates of different DME libraries. The Log₂ fold enrichment of individual variants relative to the reference sgRNA sequence for pairs of DME replicates are plotted against each other. Shown are plots for single deletion, single insertion and single substitution DME experiments, as well as wild type controls, and the plots indicate that there is a good amount of agreement for each replicate.
• FIG. 4C is a heat map of an exemplary DME experiment showing four replicates of a library where every location in the reference sgRNA has undergone a single base pair insertion. The DME experiment used a reference sgRNA of SEQ ID NO: 5 (at top), and was performed as described in Example 3. Log₂ fold enrichment of the variant in the DME library relative to the reference sgRNA following selection is indicated in grayscale,
• FIGS. 5A-5E are a series of plots showing that sgNA variants can improve gene editing by greater than two fold in an EGFP disruption assay, as described in Examples 2 and 3. Editing was measured by indel formation and GFP disruption in HEK293 cells carrying a GFP reporter. FIG. 5A shows the fold change in editing efficiency of a CasX sgRNA reference of SEQ ID NO: 4 and a variant of the reference which has a sequence of SEQ ID NO: 5, across 10 targets. When averaged across 10 targets, the editing efficiency of sgRNA SEQ ID NO: 5 improved 176% compared to SEQ ID NO: 4, FIG. 5B shows that further improvement of the sgRNA scaffold of SEQ ID NO: 5 is possible by swapping the extended stem loop sequence for additional sequences to generate the scaffolds whose sequences are shown in Table 2. Fold change in editing efficiency is shown on the Y-axis. FIG. 5C is a plot showing the fold improvement of sgNA variants (including a variant with SEQ ID NO: 17) generated. by DME mutations normalized to SEQ ID NO: 5 as the CasX reference sgRNA. FIG. 5D is a plot showing the fold improvement of sgNA variants of sequences listed in Table 2, which were generated by appending ribozyme sequences to the reference sgRNA sequence, normalized to SEQ ID NO: 5 as the CasX reference sgRNA. FIG. 5E is a plot showing the fold improvement normalized to the SEQ ID NO: 5 reference sgRNA of variants created by both combining (stacking) scaffold stem mutations showing improved cleavage, DME mutations showing improved cleavage, and using ribozyme appendages showing improved cleavage. The resulting sgNA variants yield 2 fold or greater improvement in cleavage compared to SEQ ID NO: 5 in this assay. EGFP editing assays were performed with spacer target sequences of E6 and E7.
• FIG. 6 shows a Hepatitis Delta Virus (HDV) genomic ribozyme used in exemplary gNA variants (SEQ ID NOs: 18-22).
• FIGS. 7A-7I are a series of heat maps showing the effect of single amino acid substitutions, single amino acid insertions, and deletions at each amino acid position in a reference CasX protein of SEQ ID NO: 2, as described in Example 4. Data were generated by a DME assay run at 37° C. The Y-axis shows each possible substitution or insertion (from top to bottom: R, H, K, D, E, S, T, N, Q, C, G, P, A, I, L, M, F, W, Y or V; boxes indicate the amino acid identity of the reference protein), the X-axis shows the amino acid position in the reference CasX protein. Log₂ fold enrichment of the CasX variant protein relative to the reference CasX protein of SEQ ID NO: 2 in a DME library following enrichment is indicated. As used herein, “enrichment” is a proxy for activity, where greater enrichment is a more active molecule. (*)s indicate active sites. FIGS. 7A-7D show the effect of single amino acid substitutions. FIGS. 7E-7H show the effect of single amino acid insertions. FIG. 7I shows the effect of single amino acid deletions.
• FIGS. 8A-8C are a series of heat maps showing the effect of single amino acid substitutions, single amino acid insertions and deletions at each amino acid position in a reference CasX protein of SEQ ID NO: 2, as described in Example 4. Data were generated by a DME assay run at 45° C. FIG. 8A shows the effect of single amino acid substitutions. FIG. 8B shows the effect of single amino acid insertions. FIG. 8C shows the effect of single amino acid deletions. For all of FIGS. 8A-8C, The Y-axis shows each possible substitution or insertion (from top to bottom: R, H, K, D, E, S, T, N, Q, C, G, P, A, I, L, M, F, W, Y or V; boxes indicate the amino acid identity of the reference protein), the X-axis shows the amino acid position in the reference CasX protein. Log₂ fold enrichment of the CasX variant protein relative to the reference CasX protein of SEQ ID NO: 2 in a DME library following enrichment is indicated in grayscale, where greater enrichment is a more active molecule. (*)s indicate active sites. Running this assay at 45° C. enriches for different variants than running the same assay at 37° C. (see FIGS. 7A-7I), thereby indicating which amino acid residues and changes are important for thermostability and folding.
• FIG. 9 shows a survey of the comprehensive mutational landscape of all single mutations of a reference CasX protein of SEQ ID NO: 2. On the Y-axis, fold enrichment of CasX variants relative to the reference CasX protein for single substitutions (top), single insertions (middle) or single deletions (bottom). On the X-axis, amino acid position in the reference CasX protein. Key regions that yield improved CasX variants are the initial helix region and regions in the RuvC domain bordering the target strand loading (TLS) domain, as well as others.
• FIG. 10 is a plot showing that the evaluated CasX variant proteins improved editing greater than three-fold relative to a reference CasX protein in the EGFP disruption assay, as described in Example 5. CasX proteins were tested for their ability to cleave an EGFP reporter at 2 different target sites in human HEK293 cells, and the normalized improvement in genome editing at these sites over the basic reference CasX protein of SEQ ID NO: 2 is shown. Variants, from left to right (indicated by the amino acid substitution, insertion or deletion at the given residue number) are: Y789T, [P793], Y789D, T72S, I546V, E552A, A636D, F536S, A708K, Y797L, L792G, A739V, G791M, {circumflex over ( )}G661, A788W, K390R, A751S, E385A, {circumflex over ( )}P696, {circumflex over ( )}M773, G695H, {circumflex over ( )}AS793, {circumflex over ( )}AS795, C477R, C477K, C479A, C479L, I55F, K210R, C233S, D231N, Q338E, Q338R, L379R, K390R, L481Q, F495, D600N, T886K, A739V, K460N, I199F, G492P, T153I, R591I, {circumflex over ( )}AS795, {circumflex over ( )}AS796, {circumflex over ( )}L889, E121D, S270W, E712Q, K942Q, E552K, K25Q, N47D, {circumflex over ( )}T696, L685I, N880D, Q102R, M734K, A724S, T704K, P224K, K25R, M29E, H152D, S5219R, E475K, G226R, A377K, E480K, K416E, H164R, K767R, I7F, M29R, H435R, E385Q, E385K, I279F, D489S, D732N, A739T, W885R, E53K, A238T, P283Q, E292K, Q628E, R388Q, G791M, L792K, L792E, M779N, G27D, K955R, S867R, R693I, F189Y, V635M, F399L, E498K, E386S, V254G, P793S, K188E, QT945KI, T620P, T946P, TT949PP, N952T, K682E, K975R, L212P, E292R, I303K, C349E, E385P, E386N, D387K, L404K, E466H, C477Q, C477H, C479A, D659H, T806V, K808S, {circumflex over ( )}AS797, V959M, K975Q, W974G, A708Q, V711K, D733T, L742W, V747K, F755M, M771A, M771Q, W782Q, G791F, L792D, L792K, P793Q, P793G, Q804A, Y966N, Y723N, Y857R, S890R, S932M, L897M, R624G, S603G, N737S, L307K, I658V {circumflex over ( )}PT688, {circumflex over ( )}SA794, S877R, N580T, V335G, T620S, W345G, T280S, L406P, A612D, A751S, E386R, V351M, K210N, D40A, E773G, H207L, T62A, T287P, T832A, A893S, {circumflex over ( )}V14, {circumflex over ( )}AG13, R11V, R12N, R13H, {circumflex over ( )}Y13, R12L, {circumflex over ( )}Q13,V15S, {circumflex over ( )}D17. {circumflex over ( )} indicate insertions, [] indicate deletions.
• FIG. 11 is a plot showing individual beneficial mutations can be combined (sometimes referred to as “stacked”) for even greater improvements in gene editing activity. CasX proteins were tested for their ability to cleave at 2 different target sites in human HEK293 cells using the E6 and E7 spacers targeting an EGFP reporter, as described in Example 5. The variants, from left to right, are: S794R+Y797L, K416E+A708K, A708K+[P793], [P793]+P793AS, Q367K+I425S, A708K+[P793]+A793V, Q338R+A339E, Q338R+A339K, S507G+G508R, L379R+A708K+[P793], C477K+A708K+[P793], L379R+C477K+A708K+[P793], L379R+A708K+[P793]+A739V, C477K+A708K+[P793]+A739V, L379R+C477K+A708K+[P793]+A739V, L379R+A708K+[P793]+M779N, L379R+A708K+[P793]+M771N, L379R+A708K+[P793]+D489S, L379R+A708K+[P793]+A739T, L379R+A708K+[P793]+D732N, L379R+A708K+[P793]+G791M, L379R+A708K+[P793]+Y797L, L379R+C477K+A708K+[P793]+M779N, L379R+C477K+A708K+[P793]+M771N, L379R+C477K+A708K+[P793]+D489S, L379R+C477K+A708K+[P793]+A739T, L379R+C477K+A708K+[P793]+D732N, L379R+C477K+A708K+[P793]+G791M, L379R+C477K+A708K+[P793]+Y797L, L379R+C477K+A708K+[P793]+T620P, A708K+[P793]+E386S, E386R+F399L+[P793] and R4581I+A739V of the reference CasX protein of SEQ ID NO: 2. [] refer to deleted amino acid residues at the specified position of SEQ ID NO: 2.
• FIG. 12A and FIG. 12B are a pair of plots showing that CasX protein and sgNA variants when combined, can improve activity more than 6-fold relative to a reference sgRNA and reference CasX protein pair. sgNA:protein pairs were assayed for their ability to cleave a GFP reporter in HEK293 cells, as described in Example 5. On the Y-axis, the fraction of cells in which expression of the GFP reporter was disrupted by CasX mediated gene editing are shown. FIG. 12A shows CasX protein and sgNAs that were assayed with the E6 spacer targeting GFP. FIG. 12B shows CasX protein and sgNAs that were assayed with the E7 spacer targeting GFP. iGFP stands for “inducible GFP.”
• FIG. 13A, FIG. 13B and FIG. 13C show that making and screening DME libraries has allowed for generation and identification of variants that exhibit a 1 to 81-fold improvement in editing efficiency, as described in Examples 1 and 3. FIG. 13A shows an RFP+ and GFP+ reporter in E. coli cells assayed for CRISPR interference repression of GFP with a reference nuclease dead CasX protein and sgNA. FIG. 13B shows the same reporter cells assayed for GFP repression with nuclease dead CasX variants screened from a DME library. FIG. 13C shows improved editing efficiency of a selected CasX protein and sgNA variant compared to the reference with 5 spacers targeting the endogenous B2M locus in FMK 293 human cells. The Y axis shows disruption in B2M staining by HLA1 antibody indicating gene disruption via CasX editing and indel formation. The improved CasX variants improved editing of this locus up to 81-fold over the reference in the case of guide spacer #43. CasX pairs with the reference sgRNA: protein pair of SEQ ID NO: 5 and SEQ ID NO: 2, and CasX variant protein of L379R+A708K+[P793] of SEQ ID NO: 2, assayed with the sgNA variant with a truncated stem. loop and a T10C substitution, which is encoded by a sequence of TACTGGCGCCTTTATCTCATTACTTTGAGAGCCATCACCAGCGACTATGTCGTATGG GTAAAGCGCTTACGGACTTCGGTCCGTAAGAAGCATCAAAG (SEQ ID NO: 23), are indicated. The following spacer sequences were used: #9: GTGTAGTACAAGAGATAGAA (SEQ ID NO: 24); #14: TGAAGCTGACAGCATTCGGG (SEQ ID NO: 25), #20: tagATCGAGACATGTAAGCA (SEQ ID NO: 26); 437: GGCCGAGATGTCTCGCTCCG (SEQ ID NO: 27) and #43: AGGCCAGAAAGAGAGAGTAG (SEQ ID NO: 28).
• FIGS. 14A-14F are a series of structural models of a prototypic CasX protein showing the location of mutations in CasX variant proteins of the disclosure which exhibit improved activity. FIG. 14A shows a deletion of P at 793 of SEQ ID NO: 2, with a deletion in a loop that nay affect folding, FIG. 14B shows a replacement of Alanine (A) by Lysine (K) at position 708 of SEQ ID NO: 2. This mutation is facing the gNA 5′ end plus a salt bridge to the gNA. FIG. 14C shows a replacement of Cysteine (C) by Lysine (K) at position 477 of SEQ ID NO: 2. This mutation is facing the gNA. There is salt bridge to the gNAbb (gNA phosphase backbone) at approximately base 14 that may be affected. This mutation removes a surface exposed cysteine. FIG. 14D shows a replacement of Leucine (L) with Arginine (R) at position 379 of SEQ ID NO: 2. There is a salt bridge to the target DNAbb (DNA phosphate backbone) towards base pairs 22-23 that may be affected. FIG. 14E shows one view of a combination of the deletion of P at 793 and the A708K substitution, FIG. 14F shows an alternate view, that shows that the effects of individual mutants are additive and single mutants can be combined (stacked) for even greater improvements. Arrows indicate the locations of mutations throughout FIG. 14A-14F.
• FIG. 15 is a plot showing the identification of optimal Planctomycetes CasX PAM and spacers for genes of interest, as described in Example 6. On the Y-axis, percent GFP negative cells, indicating cleavage of a GFP reporter, is shown. On the X-axis, different PAM sequences and spacers: ATC PAM, CTC PAM and ITC PAM. GTC. Trr and CTT PAMs were also tested and showed no activity.
• FIG. 16 is a plot showing that improved CasX variants generated by DME can edit both canonical and non-canonical PAMs more efficiently than reference CasX proteins, as described in Example 6. The Y-axis shows the average fold improvement in editing relative to a reference sgRNA: protein pair (SEQ ID NO:2, SEQ ID NO: 5) with 2 targets, N=6. Protein variants, from left to right for each set of bars were: A708K+[P793]+A739V; L379R+A708K+[P793]; C477K+A708K+[P793]; L379R+C477K+A708K+[P793]; L379R+A708K+[P793]+A739V; C477K+A708K+[P793]+A739V; and L379R+C477K+A708K+[P793]+A739V. Reference CasX and protein variants were assayed with a reference sgRNA scaffold of SEQ ID NO: 5 with DNA encoding spacer sequences of, from left to right, E6 (SEQ ID NO: 29) with a TTC PAM; E7 (SEQ ID NO: 30) with a TTC PAM; GFP8 (SEQ ID NO: 31) with a TTC PAM; B1 (SEQ ID NO: 32) with a CTC PAM and A7 (SEQ ID NO: 33) with an ATC PAM.
• FIGS. 17A-17F are a series of plots showing that a reference CasX protein and a reference sgRNA scaffold pair is highly specific for the target sequence, as described in Example 7. FIG. 17A and FIG. 17D, Streptococcus pyogenes Cas9 (SpyCas9) was assayed with two different gNA spacers and a 5′ PAM site (SEQ ID NOs: 34-65) and (SEQ ID NOs: 136-166) for its ability to edit templates with a target sequence complementary to the spacer sequence (arrow), or with 1, 2, 3 or 4 mutations in the target sequence relative to the spacer sequence. FIG. 17B and FIG. 17E, Staphylococcus aureus Cas9 (SauCas9) was assayed with two different gNA spacers and a 5′ PAM site (SEQ ID NOs: 66-103) and (SEQ ID NOs: 167-204) for its ability to edit templates with a target sequence complementary to the spacer sequence (arrow), or with 1, 2, 3 or 4 mutations in the target sequence relative to the spacer sequence. FIG. 17C and FIG. 17F, the reference Plm CasX protein and sgNA scaffold pair was assayed with two different gNA spacers and a 3′ PAM site (SEQ ID NOs: 104-135) and (SEQ ID NOs: 205-236) for its ability to edit templates with a target sequence complementary to the spacer sequence (arrow), or with 1, 2, 3 or 4 mutations in the target sequence relative to the spacer sequence. In all of FIG. 17A-17F, the X-axis shows the fraction of cells where gene editing at the target sequence occurred.
• FIG. 18 illustrates a scaffold stem loop of an exemplary reference sgRNA of the disclosure (SEQ ID NO: 237).
• FIG. 19 illustrates an extended stem loop sequence of an exemplary reference sgRNA of the disclosure (SEQ ID NO: 238).
• FIGS. 20A-20B are a pair of plots that demonstrate that specific subsets of changes discovered by DME of the CasX are more likely to predict improvements of activity, as described in Example 4. The plots represent data from the experiments described in FIG. 7 and FIG. 8. FIG. 20A shows that changing amino acids within a distance of 10 Angstroms (A) of the guide RNA to hydrophobic residues (A, V, I, L, M, F, Y, W) results in a significantly less active protein. FIG. 20B demonstrates that, in contrast, changing a residue within 10 A of the RNA to a positively charged amino acid (R, H, K) is likely to improve activity.
• FIG. 21 illustrates an alignment of two reference CasX protein sequences (SEQ ID NO: 1, top; SEQ ID NO: 2, bottom), with domains annotated.
• FIG. 22 illustrates the domain organization of a reference CasX protein of SEQ ID NO: 1. The domains have the following coordinates: non-target strand binding (NTSB) domain: amino acids 101-191; Helical I domain: amino acids 57-100 and 192-332, Helical II domain: 333-509; oligonucleotide binding domain (OBD): amino acids 1-56 and 510-660; RuvC DNA cleavage domain (RuvC): amino acids 551-824 and 935-986; target strand loading (TSL) domain: amino acids 825-934. Note that the Helical I, OBD and RuvC domains are non-contiguous.
• FIG. 23 illustrates an alignment of two CasX reference sgRNA scaffolds SEQ ID NO: 5 (top) and SEQ ID NO: 4 (bottom).
• FIG. 24 shows an SDS-PAGE gel of StX2 (CasX reference of SEQ ID NO: 2) purification fractions visualized by colloidal Coomassie staining, as described in Example 8. The lanes, from left to right, are: Pellet: insoluble portion following cell lysis, Lysate: soluble portion following cell lysis, Flow That: protein that did not bind the heparin column, Wash: protein that eluted from the column in wash buffer, Elution: protein eluted from the heparin column with elution buffer, Flow Thru: Protein that did not bind the StrepTactin column, Elution: protein eluted from the StrepTactin column with elution buffer, Injection: concentrated protein injected onto the s200 gel filtration column, Frozen: pooled fractions from the s200 elution that have been concentrated and frozen.
• FIG. 25 shows the chromatogram from a size exclusion chromatography assay of the StX2, as described in Example 8.
• FIG. 26 shows an SDS-PAGE gel of StX2 purification fractions visualized by colloidal Coomassie staining, as described in Example 8. From right to left: Injection sample, molecular weight markers, lanes 3 -9: samples from the indicated elution volumes.
• FIG. 27 shows the chromatogram from a size exclusion chromatography assay of the CasX 119, using of Superdex 200 16/600 pg gel filtration, as described in Example 8. The 67.47 mL peak corresponds to the apparent molecular weight of CasX variant 119 and contained the majority of CasX variant 119 protein.
• FIG. 28 shows an SDS-PAGE gel of CasX 119 purification fractions visualized by colloidal Coomassie staining, as described in Example 8. Samples from the indicated fractions were resolved by SDS-PAGE and stained with colloidal Coomassie. From right to left, Injection: sample of protein injected onto the gel filtration column, molecular weight markers, lanes 3 -10: samples from the indicated elution volumes.
• FIG. 29 shows an SDS-PAGE gel of purification samples of CasX 438, visualized on a Bio-Rad Stain-Free™ gel. The lanes, from left to right, are: Pellet: insoluble portion following cell lysis, Lysate: soluble portion following cell lysis. Flow Thru: protein that did not bind the heparin column, Elution: protein eluted from the heparin column with elution buffer, Flow Thru: Protein that did not bind the StrepTactin column, Elution: protein eluted from the StrepTactin column with elution buffer. Injection: concentrated protein injected onto the s200 gel filtration column, Pool: pooled CasX-containing fractions, Final: pooled fractions from the s200 elution that have been concentrated and frozen.
• FIG. 30 shows the chromatogram from a size exclusion chromatography assay of the CasX 438, using of Superdex 200 16/600 pg gel filtration, as described in Example 8. The 69.13 mL peak corresponds to the apparent molecular weight of CasX variant 438 and contained the majority of CasX variant 438 protein.
• FIG. 31 shows an SDS-PAGE gel of CasX 438 purification fractions visualized by colloidal Coomassie staining, as described in Example 8. Samples from the indicated fractions were resolved by SDS-PAGE and stained with colloidal Coomassie. From right to left, Injection: sample of protein injected onto the gel filtration column, molecular weight markers, lanes 3 -10: samples from the indicated elution volumes.
• FIG. 32 shows an SDS-PAGE gel of purification samples of CasX 457, visualized on a Bio-Rad Stain-Free™ gel. The lanes, from left to right, are: Pellet: insoluble portion following cell lysis, Lysate: soluble portion following cell lysis, Flow Thru: protein that did not bind the heparin column, Wash, Elution: protein eluted from the heparin column with elution buffer, Flow Thru: Protein that did not bind the StrepTactin column, Elution: protein eluted from the StrepTactin column with elution buffer, Injection: concentrated protein injected onto the s200 gel filtration column., Final: pooled fractions from the s200 elution that have been concentrated and frozen.
• FIG. 33 shows the chromatogram from a size exclusion chromatography assay of the CasX 457, using of Superdex 200 16/600 pg gel filtration, as described in Example 8. The 67.52 mL peak corresponds to the apparent molecular weight of CasX variant 457 and contained the majority of CasX variant 457 protein.
• FIG. 34 shows an SDS-PAGE gel of CasX 457 purification fractions visualized by colloidal Coomassie staining, as described in Example 8. Samples from the indicated fractions were resolved by SDS-PAGE and stained with colloidal Coomassie. From right to left, Injection: sample of protein injected onto the gel filtration column, molecular weight markers, lanes 3 -10: samples from the indicated elution volumes.
• FIG. 35 is a schematic showing the organization of the components in the pSTX34 plasmid used to assemble the CasX constructs, as described in Example 9.
• FIG. 36 is a schematic showing the steps of generating the CasX 119 variant, as described in Example 9.
• FIG. 37 is a graph of the results of an assay for the quantification of active fractions of RNP formed by sgRNA174 and the CasX variants 119 and 457, as described in Example 19. Equimolar amounts of RNP and target were co-incubated and the amount of cleaved target was determined at the indicated timepoints. Mean and standard deviation of three independent replicates are shown for each timepoint. The biphasic fit of the combined replicates is shown. “2” refers to the reference CasX protein of SEQ ID NO: 2.
• FIG. 38 is a graph of the results of an assay for quantification of active fractions of RNP formed by CasX2 and reference guide 2 the modified sgRNA guides 32, 64, and 174, as described in Example 19. Equimolar amounts of RNP and target were co-incubated and the amount of cleaved target was determined at the indicated timepoints. Mean and standard deviation of three independent replicates are shown for each timepoint. The biphasic fit of the combined replicates is shown. “2” refers to reference gRNAs SEQ ID NO: 5, respectively, and the identifying number of modified sgRNAs are indicated in Table 2.
• FIG. 39 is a graph of the results of an assay for quantification of cleavage rates of RNP formed by sgRNA174 and the CasX variants 119 and 457, as described in Example 19. Target DNA was incubated with a 20-fold excess of the indicated RNP and the amount of cleaved target was detemiined at the indicated time points. Mean and standard deviation of three independent replicates are shown for each timepoint. The monophasic fit of the combined replicates is shown.
• FIG. 40 is a graph of the results of an assay for quantification of cleavage rates of RNP formed by CasX2 and the sgRNA guide variants 2, 32, 64 and 174, as described in Example 19. Target DNA was incubated with a 20-fold excess of the indicated RNP and the amount of cleaved target was determined at the indicated time points. Mean and standard deviation of three independent replicates are shown for each timepoint. The monophasic fit of the combined replicates is shown.
• FIG. 41 is a graph of the results of an assay for quantification of initial velocities of RNP formed by CasX2 and the sgRNA guide variants 2, 32, 64 and 174, as described in Example 19. The first two time-points of the previous cleavage experiment were fit with a linear model to determine the initial cleavage velocity.
• FIG. 42 is a schematic showing an example of CasX protein and scaffold DNA sequence for packaging in adeno-associated virus (AAV), as described in Example 20. The DNA segment between the AAV inverted terminal repeats (ITRs), comprised of a CasX-encoding DNA and its promoter, and scaffold-encoding DNA and its promoter gets packaged within an AAV capsid during AAV production.
• FIG. 43 is a graph showing representative results of AAV titering by qPCR, as described in Example 20, During AAV purification, flow through (FT) and consecutive eluent fractions (1-6) are collected and titered by qPCR. Most virus, ˜1e14 viral genomes in this example, is found in the second elution fraction.
• FIG. 44 shows the results of an AAV-mediated gene editing experiment in the SOD1-GFP reporter cell line, as described in Example 21. CasX constructs (CasX 119 and guide 64 with SOD1 targeting spacer 2, ATGTTCATGAGTTTGGAGAT; SEQ ID NO: 239) and SauCas9 with SOD1 targeting spacer were packaged in AAV vectors and used to transduce SOD1-GFP reporter cells at a range of different multiplicity of infection (MOIs, no. of viral genomes/cell). Twelve days later, cells were assayed for GFP disruption via FACS. In this example, CasX and SauCas9 shows equivalent levels of editing, where 1-2% of the cells show GFP disruption at the highest MOIs, 1e7 or 1e6.
• FIG. 45 shows the results of a second AAV-mediated gene editing experiment in the SOD1-GFP reporter cell line, as described in Example 21. CasX constructs 119.64 with SOD1 targeting spacer (2, ATGTTCATGAGTTTGGAGAT; SEQ ID NO: 239) and SauCas9 with SOD1 targeting spacer were packaged in AAV vectors and used to transduce SOD1-GFP reporter cells at a range of different multiplicity of infection (MOIs, no. of viral genomes/cell). Twelve days later, cells were assayed for GFP disruption via FACS. In this example, CasX and SauCas9 shows equivalent levels of editing at the highest MOI, where ˜2-4% of the cells show GFP disruption.
• FIG. 46 shows the results of an AAV-mediated gene editing experiment in neural progenitor cells (NPCs) from the G93A mouse model of ALS, as described in Example 21. CasX constructs (CasX 119 and guide 64 with SOD1 targeting spacer 2, ATGTTCATGAGTTTGGAGAT; SEQ ID NO: 239) was packaged in an AAV vector and used to transduce G93A NPCs at a range of diMrent multiplicity of infection (MOIs, no. of viral genomes/cell). Twelve days later, cells were assayed for gene editing via T7E1 assay. Agarose gel image from the T7E1. assay shown here demonstrates successful editing of the SOD1 locus, Double arrows show the two DNA bands as a result of successful editing in cells.
• FIG. 47 shows the results of an editing assay of 6 target genes in HEK293T cells, as described in Example 23. Each dot represents results using an individual spacer.
• FIG. 48 shows the results of an editing assay of 6 target genes in HEK293T cells, with individual bars representing the results obtained with individual spacers, as described in Example 23.
• FIG. 49 shows the results of an editing assay of 4 target genes in HEK293T cells, as described in Example 23. Each dot represents results using an individual spacer utilizing a CTC (CTCV) PAM.
• FIG. 50 is a schematic showing the steps of Deep Mutational Evolution used to create libraries of genes encoding CasX variants, as described in Example 24, The pSTX1 backbone is minimal, composed of only a high-copy number origin and KanR resistance gene, making it compatible with the recombineering E. coli strain EcNR2. pSTX2 is a BsmbI destination plasmid for aTc-inducible expression in E. coli.
• FIG. 51 is dot plot graphs showing the results of CRISPRi screens for mutations in libraries D1, D2, and D3, as described in Example 24. In the absence of CRISPRi, E. coli constitutively express both GFP and RFP, resulting in intense fluorescence in both wavelengths, represented by dots in the upper-right region of the plot. CasX proteins resulting in CRISPRi of GFP can reduce green fluorescence by >10-fold, while leaving red fluorescence unaltered, and these cells fall within the indicated Sort Gate 1. The total fraction of cells exhibiting CRISPRi is indicated.
• FIG. 52 is photographs of colonies grown in the ccdB assay, as described in Example 24. 10-fold dilutions were assayed in the presence of glucose or arabinose to induce expression of the ccdB toxin, resulting in approximately a 1000-fold difference between functional and nonfunctional proteins. When grown in liquid culture, the resolving power was approximately 10,000-fold, as seen on the right-hand side.
• FIG. 53 is a graph of HEK iGFP genome editing efficiency testing CasX variants with sgRNA 2 (SEQ ID NO:5), with appropriate spacers, with data expressed as fold-improvement over the wild-type CasX protein (SEQ ID NO: 2) in the HEK iGFP editing assay, as described in Example 24. Single mutations are shown at the top, with groups of mutations shown at the bottom of the graph). Error bars combine internal measurement error (SD) and inter-experimental measurement error (SD across replicate experiments for those variants tested more than once), in at least triplicate assays.
• FIG. 54 is a scatterplot showing results of the SOD1-GFP reporter assay for CasX variants with sgRNA scaffold 2 utilizing two different spacers for GFP, as described in Example 24.
• FIG. 55 is a graph showing the results of the HEK293 iGFP genome editing assay assessing editing across four different PAM sequences comparing wild-type CasX (SEQ ID NO: 2) and CasX variant 119; both utilizing sgRNA scaffold I (SEQ ID NO: 4), with spacers utilizing four different PAM sequences, as described in Example 24.
• FIG. 56 is a graph showing the results of genome editing activity of CasX variant 119 and sgRNA 174 compared to wild-type CasX 2 and guide scaffold 1 in the iGFP lipofection assay utilizing two different spacers, as described in Example 24.
• FIG. 57 is a graph showing the results of genome editing activity of CasX variant 119 and sgRNA 174 compared to wild-type CasX and guide in the iGFP lentiviral transduction assay, using two different spacers, as described in Example 24.
• FIG. 58 is a graph showing the results of genome editing in the more stringent lentiviral assay to compare the editing activity of four CasX variants (119, 438, 488 and 491) and the optimized sgNA 174 and two different spacers, as described in Example 24. The results show the step-wise improvement in editing efficiency achieved by the additional modifications and domain swaps introduced to the starting-point 119 variant.
• FIGS. 59A-59B show the results of NGS analyses of the libraries of sgRNA, as described in Example 25, FIG. 59A shows the distribution of substitutions, deletions and insertions. FIG. 59B is a scatterplot showing the high reproducibility of variant representation in two separate library pools after the CRISPRi assay in the unsorted, naive population of cells. (Library pool D3 vs D2 are two different versions of the dCasX protein, and represent replicates of the CRISPRi assay.)
• FIGS. 60A-60B show the structure of wild-type CasX and RNA guide (SEQ ID NO:4). FIG. 60A depicts the CryoEM structure of Deltaproteobacteria CasX protein:sgRNA RNP complex (PDB id: 6YN2), including two stem loops, a pseudoknot, and a triplex. FIG. 60B depicts the secondary structure of the sgRNA was identified from the structure shown in (A) using the tool RNAPDBee 2.0 (mapdbee.cs.putpoznan.pl/, using the tools 3DNA/DSSR, and using the VARNA visualization tool). RNA regions are indicated. Residues that were not evident in the PDB crystal structure file are indicated by plain-text letters (i.e., not encircled), and are not included in residue numbering.
• FIGS. 61A-61C depict comparisons between two guide RNA scaffolds. FIG. 61A provides the sequence alignment between the single guide scaffold 1 (SEQ ID NO: 4) and scaffold 2 (SEQ ID NO: 5). FIG. 61B shows the predicted secondary structure of scaffold 1 (without the 5′ ACAUCU bases which were not in the cryoEM structure). Prediction was done using RNAfold (v 2.1.7), using a constraint that was derived from the base-pairing observed in the cryoEM structure (see FIGS. 60A-60B). This constraint required the base pairs observed in the cryoEM structure to be formed, and required the bases involved in triplex formation to be unpaired. This structure has distinct base pairing from the lowest-energy predicted structure at the 5′ end (i.e., the pseudoknot and triplex loop). FIG. 61C shows the predicted secondary structure of scaffold 2. Prediction was done for scaffold 1, using a similar constraint based on the sequence alignment.
• FIG. 62 shows a graph comparing GFP-knockdown capability of scaffold 1 versus scaffold 2 in GFP-lipofection assay, using four different spacers utilizing different PAM sequences, as described in Example 25. The results demonstrate the greater editing imparted by use of the modified scaffold 2 compared to the wild-type scaffold 1; the latter showing no editing with spacers utilizing GTC and CTC PAM sequences.
• FIGS. 63A-63C shows graphs depicting the enrichment of single variants across the scaffold, revealing mutable regions, as described in Example 25. FIG. 63A depicts substituted bases (A, T, G, or C; top to bottom), FIG. 63B depicts inserted bases (A, T, G, or C; top to bottom), and FIG. 63C depicts deletions at the individual nucleotide position (X-axis) across scaffold 2. Enrichment values were averaged across the three dead CasX versions, relative to the average WT value. Scaffolds with relative log2 enrichment>0 are considered ‘enriched’, as they were more represented in the sorted population relative to the naive population than the wildtype scaffold was represented. Error bars represent the confidence interval across the three catalytically dead CasX experiments.
• FIG. 64 are scatterplots showing that the enrichment values obtained across different dCasX variants are largely consistent, as described in Example 25. Libraries D2 and DDD have highly correlated enrichment scores, while D3 is more distinct.
• FIG. 65 shows a bar graph of cleavage activity of several scaffold variants in a more stringent lipofection assay at the SOD1-GFP locus, as described in Example 25.
• FIG. 66 shows a bar graph of cleavage activity for several scaffold variants using two different spacers; 8.2 and 8.4 that target SOD1-GFP locus (and a non-targeting spacer NT), with low-MOI lentiviral transduction using a p34 plasmid backbone, as described in Example 25.
• FIG. 67 is a schematic showing the secondary structure of single guide 174 on top and the linear structure on the bottom, with lines joining those segments associating by base-pairing or other non-covalent interactions. The scaffold stem (white, no fill) (and loop) and the extended stem (grey, no fill) (and loop) are adjacent from 5′ to 3′ in the sequence. However, the pseudoknot and extended stems are formed from strands that have intervening regions in the sequence. The triplex is formed, in the case of single guide 174, comprising nucleotides 5′-CUUUG′-3′ AND 5′-CAAAG-3′ that form a base-paired duplex and nucleotides 5′-UUU-3′ that associates with the 5′-AAA-3′ to form the triplex region.
• FIGS. 68A and 68B show comparisons between the highly-evolved single guide 174 and the scaffolds 1 and 2 that served as the starting points for the DME procedures described in Example 25. FIG. 68A shows a bar graph of cleavage activity of head-to-head comparisons of cleavage activity of the guide scaffolds with five different spacers in a plasmid lipofection assay at the GFP locus in HEK-GFP cells. FIG. 68B shows the sequence alignment between scaffold 2 and guide 174 (SEQ ID NO: 2238). Asterisks indicate point mutations, and the dotted box shows the entire extended stem swap.
• FIGS. 69A-69B shows scatterplots of HEK-iGFP cleavage assay for scaffolds sequences relative to WT scaffold with 2 spacers; 4.76 (FIG. 69A) and 4.77 (FIG. 69B), as described in Example 25.
• FIG. 70 shows a scatteiplot comparing the normalized cleavage activity of several scaffolds relative to WT with 2 spacers (4.76 and 4.77), as described in Example 25. Error bars combine internal measurement error (SD) and inter-experimental measurement error (SD across replicate experiments for those variants tested more than once), in quadrature.
• FIG. 71 shows a scatterplot comparing the normalized cleavage activity of multiple scaffolds relative to WT in the HEK-iGFP cleavage assay to the enrichments obtained from the CRISPRi comprehensive screen, as described in Example 25. Generally, scaffold mutations with high enrichment (>1.5) have cleavage activity comparable to or greater than WT. Two variants have high cleavage activity with low enrichment scores (C18G and T17G); interestingly, these substitutions are at the same position as several highly enriched insertions (FIGS. 63A-63C). Labels indicate the mutations for a subset of the comparisons.
• FIG. 72 shows the results of flow cytometry analysis of Cas-mediated editing at the RHO locus in APRE19 RHO-GFP cells 14 days post-transfection for the CasX variant constructs 438, 499 and 491, as described in Example 26. The points are the results of individual samples and the light dashed lines are upper and lower quartiles.
• FIG. 73 shows the quantification of cleavage rates of RNP formed by sgRNA174 and the CasX variants on targets with different PAMs. Target DNA was incubated with a 20-fold excess of the indicated RNP and the amount of cleaved target was determined at the indicated time points. The monophasic fit of the combined replicates is shown.
DETAILED DESCRIPTION
• While exemplary embodiments have been shown and described herein, it will he obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the inventions claimed herein. It should be understood that various alternatives to the embodiments described herein may be employed in practicing the embodiments of the disclosure. It is intended that the claims defne the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
Defintions
• Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present embodiments, suitable methods and materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention.
• The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, terms “polynucleotide” and “nucleic acid” encompass single-stranded DNA; double-stranded DNA; multi-stranded DNA; single-stranded RNA; double-stranded RNA; multi-stranded RNA; genomic DNA; cDNA; DNA-RNA hybrids; and a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.
• “Hybridizable” or “complementary” are used interchangeably to mean that a nucleic acid (e.g., RNA, DNA) comprises a sequence of nucleotides that enables it to non-covalently bind, i.e., form Watson-Crick base pairs and/or GIU base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence-specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and/or in vivo conditions of temperature and solution ionic strength. It is understood that the sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable; it can have at least about 70%, at least about 80%, or at least about 90%, or at least about 95% sequence identity and still hybridize to the target nucleic acid. Moreover, a polynucleotide may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure or hairpin structure, a ‘bulge’, ‘bubble’ and the like).
• A “gene,” for the purposes of the present disclosure, includes a DNA region encoding a gene product (e.g., a protein, RNA), as well as all DNA regions which regulate the production of the gene product, whether or not such regulatory sequences are adjacent to coding and/or transcribed sequences. Accordingly, a gene may include regulatory sequences including, but not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regions. Coding sequences encode a gene product upon transcription or transcription and translation; the coding sequences of the disclosure may comprise fragments and need not contain a full-length open reading frame. A gene can include both the strand that is transcribed, e.g. the strand containing the coding sequence, as well as the complementary strand.
• The term “downstream” refers to a nucleotide sequence that is located 3′ to a reference nucleotide sequence. In certain embodiments, downstream nucleotide sequences relate to sequences that follow the starting point of transcription. For example, the translation initiation codon of a gene is located downstream of the start site of transcription.
• The term “upstream” refers to a nucleotide sequence that is located 5′ to a reference nucleotide sequence. In certain embodiments, upstream nucleotide sequences relate to sequences that are located on the 5′ side of a coding region or starting point of transcription. For example, most promoters are located upstream of the start site of transcription.
• The term “regulatory element” is used interchangeably herein with the term “regulatory sequence,” and is intended to include promoters, enhancers, and other expression regulatory elements (e.g. transcription termination signals, such as polyadenylation signals and poly-U sequences), Exemplary regulatory elements include a transcription promoter such as, but not limited to, CMV, CMV+intron A, SV40, RSV, HIV-Ltr, elongation factor 1 alpha (EF1α), MMLV-ltr, internal ribosome entry site (IRES) or P2A peptide to permit translation of multiple germ's from a single transcript, metallothionein, a transcription enhancer element, a transcription termination signal, polyadenylation sequences, sequences for optimization of initiation of translation, and translation termination sequences. It will be understood that the choice of the appropriate regulatory element will depend on the encoded component to be expressed (e.g., protein or RNA) or whether the nucleic acid comprises multiple components that require different polymerases or are not intended to be expressed as a fusion protein.
• The term “promoter” refers to a DNA sequence that contains an RNA polymerase binding site, transcription start site, TATA box, and/or B recognition element and assists or promotes the transcription and expression of an associated transcribable polynucleotide sequence and/or gene (or transgene). A promoter can be synthetically produced or can be derived from a known or naturally occurring promoter sequence or another promoter sequence. A promoter can be proximal or distal to the gene to be transcribed. A promoter can also include a chimeric promoter comprising a combination of two or more heterologous sequences to confer certain properties. A promoter of the present disclosure can include variants of promoter sequences that are similar in composition, but not identical to, other promoter sequence(s) known or provided herein. A promoter can be classified according to criteria relating to the pattern of expression of an associated coding or transcribable sequence or gene operably linked to the promoter, such as constitutive, developmental, tissue-specific, inducible, etc.
• The term “enhancer” refers to regulatory element DNA sequences that, when bound by specific proteins called transcription factors, regulate the expression of an associated gene. Enhancers may be located in the intron of the gene, or 5′ or 3′ of the coding sequence of the gene. Enhancers may be proximal to the gene (i.e., within a few tens or hundreds of base pairs (bp) of the promoter), or may be located distal to the gene (i.e., thousands of bp. hundreds of thousands of bp, or even millions of by away from the promoter). A single gene may be regulated by more than one enhancer, all of which are envisaged as within the scope of the instant disclosure.
• “Recombinant,” as used herein, means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. Generally, DNA sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Such sequences can be provided in the form of an open reading frame uninterrupted by internal non-translated sequences, or introns, which are typically present in eukaryotic genes. Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5′ or 3′ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “enhancers” and “promoters”, above).
• The term “recombinant polynucleotide” or “recombinant nucleic acid” refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such can be done to replace a codon with a redundant codon encoding the same or a conservative amino acid, while typically introducing or removing a sequence recognition site. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.
• Similarly, the term “recombinant polypeptide” or “recombinant protein” refers to a polypeptide or protein which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of amino sequence through human intervention. Thus, e.g,, a protein that comprises a heterologous amino acid sequence is recombinant.
• As used herein, the term “contacting” means establishing a physical connection between two or more entities. For example, contacting a target nucleic acid with a guide nucleic acid means that the target nucleic acid and the guide nucleic acid are made to share a physical connection; e.g., can hybridize if the sequences share sequence similarity.
• “Dissociation constant”, or “K_d”, are used interchangeably and mean the affinity between a ligand “L” and a protein “P”; i.e., how tightly a ligand binds to a particular protein. It can be calculated using the formula K_d=[L][P]/[LP], where [P], [L] and [LP] represent molar concentrations of the protein, ligand and complex, respectively.
• The disclosure provides compositions and methods useful for editing a target nucleic acid sequence. As used herein “editing” is used interchangeably with “modifying” and includes but is not limited to cleaving, nicking, deleting, knocking in, knocking out, and the like.
• As used herein, “homology-directed repair” (NHEJ) refers to the form of DNA repair that takes place during repair of double-strand breaks in cells. This process requires nucleotide sequence homology, and uses a donor template to repair or knock-out a target DNA, and leads to the transfer of genetic information from the donor (e.g., such as the donor template) to the target. Homology-directed repair can result in an alteration of the sequence of the target nucleic acid sequence by insertion, deletion, or mutation if the donor template differs from the target DNA sequence and part or all of the sequence of the donor template is incorporated into the target DNA at the correct genomic locus.
• As used herein, “non-homologous end joining” (NHEJ) refers to the repair of double-strand breaks in DNA by direct ligation of the break ends to one another without the need for a homologous template (in contrast to homology-directed repair, which requires a homologous sequence to guide repair). NHEJ often results in indels; the loss (deletion) or insertion of nucleotide sequence near the site of the double-strand break.
• As used herein “micro-homology mediated end joining” (MMEJ) refers to a mutagenic DSB repair mechanism, which always associates with deletions flanking the break sites without the need for a homologous template (in contrast to homology-directed repair, which requires a homologous sequence to guide repair), MMEJ often results in the loss (deletion) of nucleotide sequence near the site of the double-strand break.
• A polynucleotide or polypeptide (or protein) has a certain percent “sequence similarity” or “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity (sometimes referred to as percent similarity, percent identity, or homology) can be determined in a number of different manners. To determine sequence similarity, sequences can be aligned using the methods and computer programs that are known in the art, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. Percent complementarity between particular stretches of nucleic acid sequences within nucleic acids can be determined using any convenient method. Example methods include BLAST programs (basic local alignment search tools) and PowerBLAST programs (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656) or by using the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), e.g., using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489).
• The terms “polypeptide,” and “protein” are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence.
• A “vector” or “expression vector” is a replicon, such as plasmid, phage, virus, or cosmid, to which another DNA segment, i.e., an “insert”, may be attached so as to bring about the replication or expression of the attached segment in a cell.
• The term “naturally-occurring” or “unmodified” or “wild-type” as used herein as applied to a nucleic acid, a polypeptide, a cell, or an organism, refers to a nucleic acid, polypeptide, cell, or organism that is found in nature.
• As used herein, a “mutation” refers to an insertion, deletion, substitution, duplication, or inversion of one or more amino acids or nucleotides as compared to a wild-type or reference amino acid sequence or to a wild-type or reference nucleotide sequence.
• As used herein the term “isolated” is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs. An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells.
• A “host cell,” as used herein, denotes a eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which cells are used as recipients for a nucleic acid (e.g., an expression vector), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector.
• The term “conservative amino acid substitution” refers to the interchangeability in proteins of amino acid residues having similar side chains. For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide-containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains consists of cysteine and methionine. Exemplary conservative amino acid substitution groups arc: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, and asparagine-glutamine.
• As used herein, “treatment” or “treating,” are used interchangeably herein and refer to an approach for obtaining beneficial or desired results, including but not limited to a therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant eradication or amelioration of the underlying disorder or disease being treated. A therapeutic benefit can also be achieved with the eradication or amelioration of one or more of the symptoms or an improvement in one or more clinical parameters associated with the underlying disease such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder.
• The terms “therapeutically effective amount” and “therapeutically effective dose”, as used herein, refer to an amount of a composition, vector, cells, etc., that is capable of having any detectable, beneficial effect on any symptom, aspect, measured parameter or characteristics of a disease state or condition when administered in one or repeated doses to a subject. Such effect need not be absolute to be beneficial. Such effect can be transient.
• As used herein, “administering” is meant as a method of giving a dosage of a composition of the disclosure to a subject.
• As used herein, a “subject” is a mammal. Mammals include, but are not limited to, domesticated animals, primates, non-human primates, humans, dogs, porcine (pigs), rabbits, mice, rats and other rodents.
• All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
I. General Methods
• The practice of the present invention employs, unless otherwise indicated, conventional techniques of immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA, which can be found in such standard textbooks as Molecular Cloning: A Laboratory Manual, 3rd Ed. (Sambrook et al., Harbor Laboratory Press 2001); Short Protocols in Molecular Biology, 4th Ed. (Ausubel et al. eds., John Wiley & Sons 1999); Protein Methods (Bollag et al., John Wiley & Sons 1996); Nonviral Vectors for Gene Therapy (Wagner et al. eds., Academic Press 1999); Viral Vectors (Kaplift & Loewy eds., Academic Press 1995); Immunology Methods Manual (I. Lefkovits ed., Academic Press 1997); and Cell and Tissue Culture: Laboratory Procedures in Biotechnology (Doyle & Griffiths, John Wiley & Sons 1998), the disclosures of which are incorporated herein by reference.
• Where a range of values is provided, it is understood that endpoints are included and that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included.
• Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
• It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.
• It will be appreciated that certain features of the disclosure, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. In other cases, various features of the disclosure, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. It is intended that all combinations of the embodiments pertaining to the disclosure are specifically embraced by the present disclosure and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically embraced by the present disclosure and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.
II. CasX:gNA Systems
• In a first aspect, the present disclosure provides CasX:gNA systems comprising a CasX protein and one or more guide nucleic acids (gNA) for use in modifying or editing a target nucleic acid, inclusive of coding and non-coding regions. The terms CasX protein and CasX are used interchangeably herein; the terms CasX variant protein and CasX variant are used interchangeably herein. The CasX protein and gNA of the CasX:gNA systems provided herein each independently may be a reference CasX protein, a CasX variant protein, a reference gNA, a gNA variant, or any combination of a reference CasX protein, reference gNA, CasX variant protein, or gNA variant. A gNA and a CasX protein, a gNA variant and CasX variant, or any combination thereof can form a complex and bind via non-covalent interactions, referred to herein as a ribonucleoprotein (RNP) complex. In some embodiments, the use of a pre-complexed CasX:gNA confers advantages in the delivery of the system components to a cell or target nucleic acid for editing of the target nucleic acid. In the RNP, the gNA can provide target specificity to the RNP complex by including a spacer sequence (targeting sequence) having a nucleotide sequence that is complementary to a sequence of a target nucleic acid. In the RNP, the CasX protein of the pre-complexed CasX:gNA provides the site-specific activity and is guided to a target site (and further stabilized at a target site) within a target nucleic acid sequence to be modified by virtue of its association with the gNA. The CasX protein of the RNP complex provides the site-specific activities of the complex such as binding, cleavage, or nicking of the target sequence by the CasX protein. Provided herein are compositions and cells comprising the reference CasX proteins, CasX variant proteins, reference gNAs, gNA variants, and CasX:gNA gene editing pairs of any combination of CasX and gNA, as well as delivery modalities comprising the CasX:gNA. In other embodiments, the disclosure provides vectors encoding or comprising the CasX:gNA pair and, optionally, donor templates for the production and/or delivery of the CasX:gNA systems. Also provided herein are methods of making CasX proteins and gNA, as well as methods of using the CasX and gNA, including methods of gene editing and methods of treatment. The CasX proteins and gNA components of the CasX:gNA and their features, as well as the delivery modalities and the methods of using the compositions are described more fully, below.
• The donor templates of the CasX:gNA systems are designed depending on whether they are utilized to correct mutations in a target gene or insert a transgene at a different locus in the genome (a “knock-in”), or are utilized to disrupt the expression of a gene product that is aberrant; e.g., it comprises one or more mutations reducing expression of the gene product or rendering the protein dysfunctional (a “knock-down” or “knock-out”). In some embodiments, the donor template is a single stranded. DNA template or a single stranded RNA template. In other embodiments, the donor template is a double stranded DNA template. In some embodiments, the CasX:gNA systems utilized in the editing of the target nucleic acid comprises a donor template having all or at least a portion of an open reading frame of a gene in the target nucleic acid for insertion of a corrective, wild-type sequence to correct a defective protein. In other cases, the donor template comprises all or a portion of a wild-type gene for insertion at a different locus in the genotne for expression of the gene product. In still other cases, a portion of the gene can be inserted upstream (′5) of the mutation in the target nucleic acid, wherein the donor template gene portion spans to the C-terminus of the gene, resulting, upon its insertion into the target nucleic acid, in expression of the gene product. In other embodiments, the donor template can comprise one or more mutations in an encoding sequence compared to a normal, wild-type sequence of the target gene utilized for insertion for either knocking out or knocking down (described more fully, below) the defective target nucleic acid sequence. In other embodiments, the donor template can comprise regulatory elements, an intron, or an intron-exon junction having sequences specifically designed to knock-down or knock-out a defective gene or, in the alternative, to knock-in a corrective sequence to permit the expression of a functional gene product. In some embodiments, the donor polynucleotide comprises at least about 10, at least about 20, at least about 50, at least about 100, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600. at least about 700, at least about 300, at least about 900, at least about 1000, at least about 10,000, at least about 15,000, at least about 25,000, at least about 50,000, at least about 100,000 or at least about 200,000 nucleotides. Provided that there are stretches of DNA sequence with sufficient numbers of nucleotides having sufficient homology flanking the cleavage site(s) of the target nucleic acid sequence targeted by the CasX:gNA (i.e., 5′ and 3′ to the cleavage site) to support homology-directed repair (the flanking regions being “homologous arms”), use of such donor templates can result in its integration into the target nucleic acid by HDR. In other cases, the donor template can be inserted by non-homologous end joining (NHEJ; which does not require homologous arms) or by microhomology-mediated end joining (MMEI; which requires short regions of homology on the 5′ and 3′ ends). In some embodiments, the donor template comprises homologous arms on the 5′ and 3′ ends, each having at least about 2, at least about 10, at least about 20, at least about 30, at least about 50, at least about 100, at least about 150, at least about 300, at least about 1000, at least about 1500 or more nucleotides having homology with the sequences flanking the intended cleave site(s) of the target nucleic acid. In some embodiments, the CasX:gNA systems utilize two or more gNA with targeting sequences complementary to overlapping or different regions of the target nucleic acid such that the defective sequence can be excised by multiple double-stranded breaks or by nicking in locations flanking the defective sequence and the donor template inserted by HDR to replace the excised sequence. In the foregoing, the gNA would be designed to contain targeting sequences that are 5′ and 3′ to the individual site or sequence to be excised. By such appropriate selection of the targeting sequences of the gNA, defined regions of the target nucleic acid can be edited using the CasX:gNA systems described herein.
III. Guide Nucleic Acids of the CasX:gNA Systems
• In other aspects, the disclosure provides guide nucleic acids (gNA) utilized in the CasX:gNA systems, and have utility in editing of a target nucleic acid. The present disclosure provides specifically-designed gNAs with targeting sequences (or “spacers”) that are complementary to (and are therefore able to hybridize with) the target nucleic acid as a component of the gene editing CasX:gNA systems. It is envisioned that in some embodiments, multiple gNAs (e.g., multiple gRNAs) are delivered by the CasX:gNA system for the modification of different regions of a gene, including regulatory elements, an exon, an intron, or an intron-exon junction. In some embodiments, the targeting sequence of the gNA is complementary to a sequence comprising one or more single nucleotide polymorphisms (SNPs) of the target nucleic. In other embodiments, the targeting sequence of the gNA is complementary to a sequence of an intergenic region. For example, when a deletion of a protein-encoding gene is desired, a pair of gNAs with targeting sequences to different or overlapping regions of the target nucleic acid sequence can be used in order to bind and cleave at two different sites within the gene that can then he edited by indel formation or homology-directed repair (HDR), which, in the case of HDR, utilizes a donor template that is inserted to replace the deleted sequence to complete the editing.
• a. Reference gNA and gNA Variants
• In some embodiments, a gNA of the present disclosure comprises a sequence of a naturally-occurring gNA (“reference gNA”). In other cases, a reference gNA of the disclosure may be subjected to one or more mutagenesis methods, such as the mutagenesis methods described herein, which may include Deep Mutational Evolution (DME), deep mutational scanning (DMS), error prone PCR, cassette mutagenesis, random mutagenesis, staggered extension PCR, gene shuffling, or domain swapping, in order to generate one or more gNA variants with enhanced or varied properties relative to the reference gNA. gNA variants also include variants comprising one or more exogenous sequences, for example fused to either the 5′ or 3′ end, or inserted internally. The activity of reference gNAs may be used as a benchmark against which the activity of gNA variants are compared, thereby measuring improvements in function or other characteristics of the gNA variants. In other embodiments, a reference gNA may be subjected to one or more deliberate, targeted mutations in order to produce a gNA variant, for example a rationally-designed variant. As used herein, the terms gNA, gRNA, and gDNA cover naturally-occurring molecules (reference molecules), as well as sequence variants.
• In some embodiments, the gNA is a deoxyribonucleic acid molecule (“gDNA”) sonic embodiments, the gNA is a ribonucleic acid molecule (“gRNA”), and in other embodiments, the gNA is a chimera, and comprises both DNA and RNA.
• The gNAs of the disclosure comprise two segments; a targeting sequence and a protein-binding segment (which constitutes the scaffold, discussed herein). The targeting segment of a gNA includes a nucleotide sequence (referred to interchangeably herein as a guide sequence, a spacer, a targeting sequence, or a targeting region) that is complementary to (and therefore hybridizes with) a specific sequence (a target site) within the target nucleic acid sequence (e.g., a target ssRNA, a target ssDNA, the complementary strand of a double stranded target DNA, etc.), described more fully below.
• The targeting sequence of a gNA is capable of binding to a target nucleic acid sequence, including a coding sequence, a complement of a coding sequence, a non-coding sequence, and to regulatory elements. The protein-binding segment (or “protein-binding sequence”) interacts with (e.g., binds to) a CasX protein. The protein-binding segment is alternatively referred to herein as a “scaffold”. In some embodiments, the targeting sequence and scaffold each include complementary stretches of nucleotides that hybridize to one another to form a double stranded duplex (e.g. dsRNA duplex for a gRNA). Site-specific binding and/or cleavage of a target nucleic acid sequence (e.g., genomic DNA) by the CasX:gNA can occur at one or more locations of a target nucleic acid, determined by base-pairing complementarity between the targeting sequence of the gNA and the target nucleic acid sequence.
• The gNA provides target specificity to the complex by having a nucleotide sequence that is complementary to a target sequence of a target nucleic acid. The CasX of the complex provides the site-specific activities of the complex such as binding, cleavage, or nicking of the target sequence of the target nucleic acid by the CasX nuclease and/or an activity provided by a fusion partner in case of a CasX containing fusion protein, described below. In some embodiments, the disclosure provides gene editing pairs of a CasX and gNA of any of the embodiments described herein that are capable of being bound together prior to their use for gene editing and, thus, are “pre-complexed” as the RNP. The use of a pre-complexed RNP confers advantages in the delivery of the system components to a cell or target nucleic acid sequence for editing of the target nucleic acid sequence. The CasX protein of the RNP provides the site-specific activity that is guided to a target site (e.g., stabilized at a target site) within a target nucleic acid sequence by virtue of its association with the guide RNA comprising a targeting sequence.
• In some embodiments, wherein the gNA is a gRNA, the term “targeter” or “targeter RNA” is used herein. to refer to a crRNA-like molecule (crRNA: “CRISPR RNA”) of a CasX dual guide RNA (dgRNA). In a single guide RNA (sgRNA), the “activator” and the “targeter” are linked together, e.g., by intervening nucleotides). Thus, for example, a guide RNA (dgRNA or sgRNA) comprises a guide sequence and a duplex-forming segment of a crRNA, which can also be referred to as a crRNA repeat. Because the targeter sequence of a guide sequence hybridizes with a specific target nucleic acid sequence, a targeter can be modified by a user to hybridize with a desired target nucleic acid sequence. In some embodiments, the sequence of a targeter may often be a non-naturally occurring sequence. The targeter and the activator each have a duplex-forming segment, where the duplex forming segment of the targeter and the duplex-forming segment of the activator have complementarity with one another and hybridize to one another to form a double stranded duplex (dsRNA duplex for a gRNA). In some embodiments, a targeter comprises both the guide sequence of the CasX guide RNA and a stretch of nucleotides that forms one half of the dsRNA duplex of the protein-binding segment of the gNA. A corresponding tracrRNA-like molecule (the activator “trans-acting CRISPR RNA”) also comprises a duplex-forming stretch of nucleotides that forms the other half of the dsRNA duplex of the protein-binding segment of the CasX guide RNA. In some cases the activator comprises one or more stem loops that can interact with CasX protein. Thus, a targeter and an activator, as a corresponding pair, hybridize to form a CasX dual guide NA, referred to herein as a “dual guide NA”, a “dgNA”, a “double-molecule guide NA”, or a “two-molecule guide NA”.
• In some embodiments, the activator and targeter of the reference gNA are covalently linked to one another and comprise a single molecule, referred to herein as a “single-molecule guide NA,” “one-molecule guide NA,” “single guide NA”, “single guide RNA”, a “single-molecule guide RNA,” a “one-molecule guide RNA”, a “single guide DNA”, a “single-molecule DNA,” or a “one-molecule guide DNA”, (“sgNA”, “sgRNA”, or a “sgDNA”). In some embodiments, the sgNA includes an “activator” or a “targeter” and thus can be an “activator-RNA” and a “targeter-RNA,” respectively.
• The reference gRNAs of the disclosure comprise four distinct regions, or domains: the RNA triplex, the scaffold stem, the extended stein, and the targeting sequence (specific for a target nucleic acid. The RNA triplex, the scaffold stem, and the extended stem, together, are referred to as the “scaffold” of the reference gNA, based upon which further gNA variants are generated.
• h. RNA Triplex
• In some embodiments of the guide NAs provided herein, the gNA comprises an RNA triplex, and the RNA triplex comprises the sequence of a UUU-Nx(∞4-15)-UUU stem loop (SEQ ID NO: 241) that ends with an AAAG after 2 intervening stem loops (the scaffold stem loop and the extended stem loop), forming a pseudoknot that may also extend past the triplex into a duplex pseudoknot. The UU-UUU-AAA sequence of the triplex forms as a nexus between the targeting sequence, scaffold stem, and extended stem. In exemplary gRNAs, the UUU-loop-UUU is coded for first, then the scaffold stem loop, and then the extended stem loop, which is linked by the tetraloop, and then an AAAG closes off the triplex before becoming the targeting sequence.
• c. Scaffold Stem Loop
• In some embodiments of gNAs of the disclosure, the triplex region is followed by the scaffold stem loop. The scaffold stem loop is a region of the gNA that is bound by CasX protein (such as a reference or CasX variant protein). In some embodiments, the scaffold stem loop is a fairly short and stable stem loop, and increases the overall stability of the gNA. In some cases, the scaffold stem loop does not tolerate many changes, and requires sonic form of an RNA bubble. In some embodiments, the scaffold stem is necessary for gNA function. While it is perhaps analogous to the nexus stem of Cas9 as being a critical stem loop, the scaffold stem of a gNA, in some embodiments, has a necessary bulge (RNA bubble) that is different from many other stem loops found in CRISPR/Cas systems. In some embodiments, the presence of this bulge is conserved across gNA that interact with different CasX proteins. An exemplary sequence of a scaffold stem loop sequence of a gNA comprises the sequence CCAGCGACUAUGUCGUAUGG (SEQ ID NO: 242). In other embodiments, the disclosure provides gNA variants wherein the scaffold stem loop is replaced with an RNA stem loop sequence from a heterologous RNA source with proximal 5′ and 3′ ends, such as, but not limited to stem loop sequences selected from MS2, Qβ, U1 hairpin II, Uvsx, or PP7 stem loops. In some cases, the heterologous RNA stem loop of the gNA is capable of binding a protein, an RNA structure, a DNA sequence, or a small molecule.
• d. Extended Stem Loop
• In some embodiments of the gNAs of the disclosure, the scaffold stem loop is followed by the extended stem loop. In some embodiments, the extended stem comprises a synthetic tracr and crRNA fusion that is largely unbound by the CasX protein. In some embodiments, the extended stem loop can be highly malleable. In some embodiments, a single guide gRNA is made with a GAAA tetraloop linker or a GAGAAA linker between the tracr and crRNA in the extended stem loop. In some cases, the targeter and activator of a sgNA are linked to one another by intervening nucleotides and the linker can have a length of from 3 to 20 nucleotides. In some embodiments of the sgNAs of the disclosure, the extended stem is a large 32-bp loop that sits outside of the CasX protein in the ribonucleoprotein complex. An exemplary sequence of an extended stem loop sequence of a sgNA comprises the sequence GCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGC (SEQ ID NO: 15). In some embodiments, the extended stem loop comprises a GAGAAA spacing sequence. In some embodiments, the disclosure provides gNA variants wherein the extended stem loop is replaced with an RNA stem loop sequence from a heterologous RNA source with proximal 5′ and 3′ ends, such as, but not limited to stem loop sequences selected from MS2, Qβ, U1 hairpin II, Uvsx, or PP7 stem loops. In such cases, the heterologous RNA stem loop increases the stability of the gNA. In other embodiments, the disclosure provides gNA variants having an extended stem loop region comprising at least 10, at least 100, at least 500, at least 1000, or at least 10,000 nucleotides.
• e. Targeting Sequence
• In some embodiments of the gNAs of the disclosure, the extended stem loop is followed by a region that forms part of the triplex, and then the targeting sequence (or “spacer”): The targeting sequence can be designed to target the CasX ribonucleoprotein holo complex to a specific region of the target nucleic acid sequence. Thus, the gNA targeting sequences of the gNAs of the disclosure have sequences complementarity to, and therefore can hybridize to, a portion of the target nucleic acid in a nucleic acid in a eukaryotic cell, (e.g., a eukaryotic chromosome, chromosomal sequence, a eukaryotic RNA, etc.) as a component of the RNP when any one of the PAM sequences TIC, ATC, GTC, or CTC is located 1 nucleotide 5′ to the non-target strand sequence complementary to the target sequence.
• In some embodiments, the disclosure provides a gNA wherein the targeting sequence of the gNA is complementary to a target nucleic acid sequence comprising one or more mutations compared to a wild-type gene sequence for purposes of editing the sequence comprising the mutations with the CasX:gNA systems of the disclosure. In some embodiments, the targeting sequence of a gNA is designed to be specific for an exon of the gene of the target nucleic acid. in other embodiments, the targeting sequence of a gNA is designed to be specific for an intron of the gene of the target nucleic acid. In other embodiments, the targeting sequence of the gNA is designed to he specific for an intron-exon junction of the gene of the target nucleic acid. In other embodiments, the targeting sequence of the gNA is designed to he specific for a regulatory element of the gene of the target nucleic acid. In some embodiments, the targeting sequence of the gNA is designed to be complementary to a sequence comprising one or more single nucleotide polymorphisms (SNPs) in a gene of the target nucleic acid. SNPs that are within the coding sequence or within non-coding sequences are both within the scope of the instant disclosure. In other embodiments, the targeting sequence of the gNA is designed to be complementary to a sequence of an intergenic region of the gene of the target nucleic acid.
• In some embodiments, the targeting sequence of a gNA is designed to be specific for a regulatory element that regulates expression of the gene product of the target nucleic acid. Such regulatory elements include, but are not limited to promoter regions, enhancer regions, intergenic regions, 5′ untranslated regions (5′ UTR), 3′ untranslated regions (3′ UTR), conserved elements, and regions comprising cis-regulatory elements. The promoter region is intended to encompass nucleotides within 5 kb of the initiation point of the encoding sequence or, in the case of gene enhancer elements or conserved elements, can be thousands of bp, hundreds of thousands of bp, or even millions of bp away from the encoding sequence of the gene of the target nucleic acid. In some embodiments of the foregoing, the targets are those in which the encoding gene of the target is intended to be knocked out or knocked down such that the encoded protein comprising mutations is not expressed or is expressed at a lower level in a cell.
• In some embodiments, the targeting sequence of a gNA has between 14 and 35 consecutive nucleotides. In some embodiments, the targeting sequence has 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 consecutive nucleotides. In some embodiments, the targeting sequence of the gNA consists of 20 consecutive nucleotides. In some embodiments, the targeting sequence consists of 19 consecutive nucleotides. In some embodiments, the targeting sequence consists of 18 consecutive nucleotides. In some embodiments, the targeting sequence consists of 17 consecutive nucleotides. In some embodiments, the targeting sequence consists of 16 consecutive nucleotides. In sonic embodiments, the targeting sequence consists of 15 consecutive nucleotides, in some embodiments, the targeting sequence has 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 consecutive nucleotides and the targeting sequence can comprise 0 to 5, 0 to 4, 0 to 3, or 0 to 2 mismatches relative to the target nucleic acid sequence and retain sufficient binding specificity such that the RNP comprising the gNA comprising the targeting sequence can form a complementary bond with respect to the target nucleic acid.
• In some embodiments, the CasX:gNA system comprises a first gNA and further comprises a second (and optionally a third, fourth, fifth, or more) gNA, wherein the second gNA or additional gNA has a targeting sequence complementary to a different or overlapping portion of the target nucleic acid sequence compared to the targeting sequence of the first gNA such that multiple points in the target nucleic acid are targeted, and for example, multiple breaks are introduced in the target nucleic acid by the CasX. It will he understood that in such cases, the second or additional gNA is complexed with an additional copy of the CasX protein. By selection of the targeting sequences of the gNA, defined regions of the target nucleic acid sequence bracketing a mutation can be modified or edited using the CasX:gNA systems described herein, including facilitating the insertion of a donor template.
• f. gNA Scaffolds
• With the exception of the targeting sequence region, the remaining regions of the gNA are referred to herein as the scaffold. In some embodiments, the gNA scaffolds are derived from naturally-occurring sequences, described below as reference gNA. In other embodiments, the gNA scaffolds are variants of reference gNA wherein mutations, insertions, deletions or domain substitutions are introduced to confer desirable properties on the gNA.
• In some embodiments, a reference gRNA comprises a sequence isolated or derived from Deltaproteobacteria. In some embodiments, the sequence is a CasX tracrRNA sequence. Exemplary CasX reference tracrRNA sequences isolated or derived from Deltaproteobacteria may include: ACAUCUGGCGCGUUUAUUCCAUUACUUUGGAGCCAGUCCCAGCGACUAUGUCGU AUGGACGAAGCGCUUAUUUAUCCGGAGA (SEQ ID NO: 6) and ACAUCUGGCGCGUUUAUUCCAUUACUUGGAGCCAGUCCCAGCGACUAUGUCGU AUGGACGAAGCGCUUAUUUAUCGG (SEQ ID NO: 7). Exemplary crRNA sequences isolated or derived from Deliaproteobacteria may comprise a sequence of CCGAUAAGUAAAACGCAUCAAAG (SEQ ID NO: 243). In some embodiments, a reference gNA comprises a sequence at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at leas 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical or 100% identical to a sequence isolated or derived from Deitaproteobacteria.
• In some embodiments, a reference guide RNA comprises a sequence isolated or derived from Planctomycetes. In some embodiments, the sequence is a CasX tracrRNA sequence. Exemplary reference tracrRNA sequences isolated or derived from Planctomycetes may include: UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUA UGGGUAAAGCGCUUAUUUAUCGGAGA (SEQ ID NO: 8) and UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUA UGGGUAAAGCGCUUAUUUAUCGG (SEQ ID NO: 9). Exemplary crRNA sequences isolated or derived from Planctomycetes may comprise a sequence of UCUCCGAUAAAUAAGAAGCAUCAAAG (SEQ ID NO: 244). In some embodiments, a reference gNA comprises a sequence at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical. at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical or 100% identical to a sequence isolated or derived from Planctomycetes.
• In some embodiments, a reference gNA comprises a sequence isolated or derived from Candidatus sungbacteria. In some embodiments, the sequence is a CasX tracrRNA sequence. Exemplary CasX reference tracrRNA sequences isolated or derived from Candidatus Sungbacteria may comprise sequences of: GUUUACACACUCCCUCUCAUAGGGU (SEQ ID NO: 10), GUUUACACACUCCCUCUCAUGAGGU (SEQ ID NO: 11), GUUUACAUACCCCCUCUCAUGGGAU (SEQ ID NO: 12) and GUUUACACACUCCCUCUCAUGGGGG (SEQ ID NO: 13). In some embodiments, a reference guide RNA comprises a sequence at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical. at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at leas 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical or 100% identical to a sequence isolated or derived from Candidatus sungbacteria.
• Table 1 provides the sequences of reference sRNA tracr, cr and scaffold sequences. In some embodiments, the disclosure provides gNA sequences wherein the gNA has a scaffold comprising a sequence having at least one nucleotide modification relative to a reference gNA sequence having a sequence of any one of SEQ ID NOS: 4-16 of Table 1. It will be understood that in those embodiments wherein a vector comprises a DNA encoding sequence for a gNA, or where a gNA is a gDNA or a chimera of RNA and DNA, that thymine (T) bases can be substituted for the uracil (U) bases of any of the gNA sequence embodiments described herein

• TABLE 1
  Reference gRNA tracr, c and scaffold sequences

  SEQ ID
  NO.	Nucleotide Sequence
  4	ACAUCUGGCGCGUUUAUUCCAUUACUUUGGAGCCAGUCCCAGCGACUAUGUCGUAUGGACGAAGC
  	GCUUAUUUAUCGGAGAGAAACCGAUAAGUAAAACGCAUCAAAG
  5	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAGCG
  	CUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  6	ACAUCUGGCGCGUUUAUUCCAUUACUUUGGAGCCAGUCCCAGCGACUAUGUCGUAUGGACGAAGC
  	GCUUAUUUAUCGGAGA
  7	ACAUCUGGCGCGUUUAUUCCAUUACUUUGGAGCCAGUCCCAGCGACUAUGUCGUAUGGACGAAGC
  	GCUUAUUUAUCGG
  8	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAGCG
  	CUUAUUUAUCGGAGA
  9	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAGCG
  	CUUAUUUAUCGG
  10	GUUUACACACUCCCUCUCAUAGGGU
  11	GUUUACACACUCCCUCUCAUGAGGU
  12	UUUUACAUACCCCCUCUCAUGGGAU
  13	GUUUACACACUCCCUCUCAUGGGGG
  14	CCAGCGACUAUGUCGUAUGG
  15	GCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGC
  16	GGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUA
  	UUUAUCGGA

• g. gNA Variants
• In another aspect, the disclosure relates to guide nucleic acid variants (referred to herein alternatively as “gNA variant” or “gRNA variant”), which comprise one or more modifications relative to a reference gRNA scaffold. As used herein, “scaffold” refers to all parts to the gNA necessary for gNA function with the exception of the spacer sequence.
• In some embodiments, a gNA variant comprises one or more nucleotide substitutions, insertions, deletions, or swapped or replaced regions relative to a reference gRNA sequence of the disclosure. In some embodiments, a mutation can occur in any region of a reference gRNA scaffold to produce a gNA variant. In some embodiments, the scaffold of the gNA variant sequence has at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, or at least 70%, at least 80%, at least 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity to the sequence of SEQ ID NO: 4 or SEQ ID NO: 5.
• In some embodiments, a gNA variant comprises one or more nucleotide changes within one or more regions of the reference gRNA scaffold that improve a characteristic of the reference gRNA. Exemplary regions include the RNA triplex, the pseudoknot, the scaffold stem loop, and the extended stem loop. In some cases, the variant scaffold stem further comprises a bubble. In other cases, the variant scaffold further comprises a triplex loop region. In still other cases, the variant scaffold further comprises a 5′ unstructured region. In some embodiments, the gNA variant scaffold comprises a scaffold stem loop having at least 60% sequence identity, at least 70% sequence identity, at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, or at least 99% sequence identity to SEQ ID NO: 14. In some embodiments, the gNA variant scaffold comprises a scaffold stem loop having at least 60% sequence identity to SEQ ID NO: 14. In other embodiments, the gNA variant comprises a scaffold stem loop having the sequence of CCAGCGACUAUGUCGUAGUGG (SEQ ID NO: 245). In other embodiments, the disclosure provides a gNA scaffold comprising, relative to SEQ ID NO:5, a C18G substitution, a G55 insertion, a gNA deletion, and a modified extended stem loop in which the original 6 nt loop and 13 most-loop-proximal base pairs (32 nucleotides total) are replaced by a Uvsx hairpin (4 nt loop and 5 loop-proximal base pairs; 14 nucleotides total) and the loop-distal base of the extended stem was converted to a fully base-paired stem contiguous with the new Uvsx hairpin by deletion of the A99 and substitution of G65 U. In the foregoing embodiment, the gNA scaffold comprises the sequence ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUGGUAAAGCUCCCUCUUCGGAG GGAGCAUCAAAG (SEQ ID NO: 2238).
• All gNA variants that have one or more improved characteristics, or add one or more new functions when the variant gNA is compared to a reference gRNA described herein, are envisaged as within the scope of the disclosure. A representative example of such a gNA variant is guide 174 (SEQ ID NO: 2238), the design of which is described in the Examples. In some embodim.ents, the gNA variant adds a new function to the RNP comprising the gNA variant. In some embodiments, the gNA variant has an improved characteristic selected from: improved stability; improved solubility; improved transcription of the gNA; improved resistance to nuclease activity; increased folding rate of the gNA; decreased side product formation during folding; increased productive folding; improved binding affinity to a CasX protein; improved binding affinity to a target DNA when complexed with a CasX protein; improved gene editing when complexed with a CasX protein; improved specificity of editing when complexed with a CasX protein; and improved ability to utilize a greater spectrum of one or more PAM sequences, including ATC, CTC. GTC, or TTC, in the editing of target DNA when complexed with a CasX protein, and any combination thereof. In some cases, the one or more of the improved characteristics of the gNA variant is at least about 1.1 to about 100,000-fold improved relative to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5. In other cases, the one or more improved characteristics of the gNA variant is at least about 1.1, at least about 10, at least about 100, at least about 1000, at least about 10,000, at least about 100,000-fold or more improved relative to the reference gNA of SEQ ID NO: 4 or SEQ II) NO: 5. In other cases, the one or more of the improved characteristics of the gNA variant is about 1.1 to 100,00-fold, about 1.1 to 10,00-fold, about 1.1 to 1,000-fold, about 1.1 to 500-fold, about 1.1 to 100-fold, about 1.1 to 50-fold, about 1.1 to 20-fold, about 10 to 100,00-fold, about 10 to 10,00-fold, about 10 to 1,000-fold, about 10 to 500-fold, about 10 to 100-fold, about 10 to 50-fold, about 10 to 20-fold, about 2 to 70-fold, about 2 to 50-fold, about 2 to 30-fold, about 2 to 20-fold, about 2 to 10-fold, about 5 to 50-fold, about 5 to 30-fold, about 5 to 10-fold, about 100 to 100,00-fold, about 100 to 10,00-fold, about 100 to 1,000-fold, about 100 to 500-fold, about 500 to 100,00-fold, about 500 to 10,00-fold, about 500 to 1,000-fold, about 500 to 750-fold, about 1,000 to 100,00-fold, about 10,000 to 100,00-fold, about 20 to 500-fold, about 20 to 250-fold, about 20 to 200-fold, about 20 to 100-fold, about 20 to 50-fold, about 50 to 10,000-fold, about 50 to 1,000-fold, about 50 to 500-fold, about 50 to 200-fold, or about 50 to 100-fold, improved relative to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5. In other cases, the one or more improved characteristics of the gNA variant is about 1.1-fold, 1.2-fold, 1. 3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, 15-fold, 16-fold, 17-fold, 18-fold, 19-fold, 20-fold, 25-fold, 30-fold, 40-fold, 45-fold, 50-fold, 55-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 110-fold, 120-fold, 130-fold, 140-fold, 150-fold, 160-fold, 170-fold, 180-fold, 190-fold, 200-fold, 210-fold, 220-fold, 230-fold, 240-fold, 250-fold, 260-fold, 270-fold, 280-fold, 290-fold, 300-fold, 310-fold, 320-fold, 330-fold, 340-fold, 350-fold, 360-fold, 370-fold, 380-fold, 390-fold, 400-fold, 425-fold, 450-fold, 475-fold, or 500-fold improved relative to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• In some embodiments, a gNA variant can be created by subjecting a reference gNA to a one or more mutagenesis methods, such as the mutagenesis methods described herein, below, which may include Deep Mutational Evolution (DME), deep mutational scanning (DMS), error prone PCR, cassette mutagenesis, random mutagenesis, staggered extension PCR, gene shuffling, or domain swapping, in order to generate the gNA variants of the disclosure. The activity of reference gNAs may be used as a benchmark against which the activity of gNA variants are compared, thereby measuring improvements in function of gNA variants. In other embodiments, a reference gNA may be subjected to one or more deliberate, targeted mutations, substitutions, or domain swaps in order to produce a gNA variant, for example a rationally designed variant. Exemplary gNA variants produced by such methods are described in the Examples and representative sequences of gNA scaffolds are presented in Table 2.
• In some embodiments, the gNA variant comprises one or more modifications compared to a reference guide nucleic acid scaffold sequence, wherein the one or more modification is selected from: at least one nucleotide substitution in a region of the reference gNA at least one nucleotide deletion in a region of the reference gNA; at least one nucleotide insertion in a region of the reference gNA ; a substitution of all or a portion of a region of the reference gNA; a deletion of all or a portion of a region of the reference gNA; or any combination of the foregoing. In some cases, the modification is a substitution of 1 to 15 consecutive or non-consecutive nucleotides in the reference gNA in one or more regions. In other cases, the modification is a deletion of 1 to 10 consecutive or non-consecutive nucleotides in the reference gNA in one or more regions. In other cases, the modification is an insertion of 1 to 10 consecutive or non-consecutive nucleotides in the reference gNA in one or more regions. In other cases, the modification is a substitution of the scaffold stem loop or the extended stem loop with an RNA stem loop sequence from a heterologous RNA source with proximal 5′ and 3′ ends. In some cases, a gNA variant of the disclosure comprises two or more modifications in one region relative to a reference gRNA. In other cases, a gNA variant of the disclosure comprises modifications in two or more regions. In other cases, a gNA variant comprises any combination of the foregoing modifications described in this paragraph. In some embodiments, exemplary modifications of gNA of the disclosure include the modifications of Table 24.
• In some embodiments, a 5′ G is added to a gNA variant sequence, relative to a reference gRNA, for expression in vivo, as transcription from a U6 promoter is more efficient and more consistent with regard to the start site when the +1 nucleotide is a G. In other embodiments, two 5′ Os are added to generate a gNA variant sequence for in vitro transcription to increase production efficiency, as 17 polymerase strongly prefers a 0 in the +1 position and a purine in the +2 position. In some cases, the 5′ G bases are added to the reference scaffolds of Table 1. In other cases, the 5′ G bases are added to the variant scaffolds of Table 2,
• Table 2 provides exemplary gNA variant scaffold sequences of the disclosure. In Table 2, (−) indicates a deletion at the specified position(s) relative to the reference sequence of SEQ ID NO: 5, (+) indicates an insertion of the specified base(s) at the position indicated relative to SEQ ID NO: 5, (:) indicates the range of bases at the specified start:stop coordinates of a deletion or substitution relative to SEQ ID NO: 5, and multiple insertions, deletions or substitutions are separated by commas; e.g., A14C, T170. In some embodiments, the gNA variant scaffold comprises any one of the sequences listed in Table 2, SEQ ID NOS: 2101-2280, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% sequence identity thereto. It will be understood that in those embodiments wherein a vector comprises a DNA encoding sequence for a gNA, or where a gNA is a gDNA or a chimera of RNA and DNA, that thymine (T) bases can be substituted for the uracil (U) bases of any of the gNA sequence embodiments described herein.

• TABLE 2
  Exemplary gNA Variant Scaffold Sequences

  SEQ
  ID	NAME or
  NO:	Modification	NUCLEOTIDE SEQUENCE
  2101	phage replication	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	stable	GGUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  2102	Kissing loop_b1	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUGCUCGACGCGUCCUCGAGCAGAAGCAUCAAAG
  2103	Kissing loop_a	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUGCUCGCUCCGUUCGAGCAGAAGCAUCAAAG
  2104	32, uvsX hairpin	GUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAU
  		GGGUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  2105	PP7	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCAGGAGUUUCUAUGGAAACCCUGAAGCAUCAAAG
  2106	64, trip mut,	GUACUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAU
  	extended stem	GGGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	truncation
  2107	hyperstable	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	tetraloop	GGUAAAGCGCUGCGCUUGCGCAGAAGCAUCAAAG
  2108	C18G	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2109	T17G	UACUGGCGCUUUUAUCGCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2110	CUUCGG loop	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGACUUCGGUCCGAUAAAUAAGAAGCAUCAAAG
  2111	MS2	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCACAUGAGGAUUACCCAUGUGAAGCAUCAAAG
  2112	-1, A2G, -78,	GCUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	G77T	GUAAAGCGCUUAUUUAUCGUGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2113	QB	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUGCAUGUCUAAGACAGCAGAAGCAUCAAAG
  2114	45, 44 hairpin	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCAGGGCUUCGGCCGAAGCAUCAAAG
  2115	U1A	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCAAUCCAUUGCACUCCGGAGUGAAGCAUCAAAG
  2116	A14C, T17G	UACUGGCGCUUUUCUCGCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2117	CUUCGG loop	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	modified	GGUAAAGCGCUUAUUUAUCGGACUUCGGUCCGAUAAAUAAGAAGCAUCAAAG
  2118	Kissing loop_b2	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUGCUCGUUUGCGGCUACGAGCAGAAGCAUCAAAG
  2119	-76:78, -83:87	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGAGAGAUAAAUAAGAAGCAUCAAAG
  2120	-4	UACGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  		GUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2121	extended stem	UACUGGCGCCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAU
  	truncated	GGGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2122	C55	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUC
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2123	trip mut	UACUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGACUUCGGUCCGAUAAAUAAGAAGCAUCAAAG
  2124	-76:78	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2125	-1:5	GCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAA
  		AGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2126	-83:87	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUC
  		GGUAAAGCGCUUAUUUAUCGGAGAGAGAUAAAUAAGAAGCAUCAAAG
  2127	=+G28, A82T,	UACUGGCGCUUUUAUCUCAUUACUUUGGAGAGCCAUCACCAGCGACUAUGUCGUAU
  	-84	GGGUAAAGCGCUUAUUUAUCGGAGAGUAUCCGAUAAAUAAGAAGCAUCAAAG
  2128	=+51T	UACUGGCGCUUUUAUCUCAGUACUUUGAGAGCCAUCACCAGCGACUAUGUUCGUAU
  		GGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2129	-1:4, +G5A,	AGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUA
  	+G86,	AAGCGCUUAUUUAUCGGAGAGAAAUGCCGAUAAAUAAGAAGCAUCAAAG
  2130	=+A94	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAAUAAGAAGCAUCAAAG
  2131	=+G72	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGGUUAUUGUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2132	shorten front,	GCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAA
  	CUUCGG loop	AGCGCUUAUUUAUCGGACUUCGGUCCGAUAAAUAAGCGCAUCAAAG
  	modified. extend
  	extended
  2133	A14C	UACUGGCGCUUUUCUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2134	-1:3, +G3	GUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGG
  		UAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2135	=+C45, T46	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACCUUAUGUCGUA
  		UGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2136	CUUCGG loop	GAUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	modified, fun	GUAAAGCGCUUAUUUAUCGGACUUCGGUCCGAUAAAUAAGAAGCAUCAAAG
  	start
  2137	-93:94	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAAGAAGCAUCAAAG
  2138	=+T45	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGAUCUAUGUCGUAU
  		GGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  3139	-69, -94	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGGCUUAUUUAUCGGAGAGAAAUCCGAUAAAAAGAAGCAUCAAAG
  2140	-94	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAAAGAAGCAUCAAAG
  2141	modified	UACUGGCGCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	CUUCGG,	GUAAAGCGCUUAUUUAUCGGACUUCGGUCCGAUAAAUAAGAAGCAUCAAAG
  	minus T in 1st
  	triplex
  2142	-1:4, +C4, A14C,	CGGCGCUUUUCUCGCAUUACUUJGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGU
  	T17G, +G72,	AAAGCGCUUAUUGUAUCGAGAGAUAAAUAAGAAGCAUCAAAG
  	-76:78, -83:87
  2143	T1C, -73	CACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2144	Scaffold uuCG,	UACUGGCGCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAUG
  	stem uuCG. Stem	GGUAAAGCGCUUAUGUAUCGGCUUCGGCCGAUACAUAAGAAGCAUCAAAG
  	swap, t shorten
  2145	Scaffold uuCG,	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAU
  	stem uuCG. Stem	GGGUAAAGCGCUUAUGUAUCGGCUUCGGCCGAUACAUAAGAAGCAUCAAAG
  	swap
  2146	=+G60	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUGAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2147	no stem Scaffold	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAU
  	uuCG	GGGUAAAG
  2148	no stem Scaffold	GAUGGGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAUGG
  	uuCG, fun start	GUAAAG
  2149	Scaffold uuCG,	GAUGGGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAUGG
  	stem uuCG, fun	GUAAAGCGCUUAUUUAUCGGCUUCGGCCGAUAAAUAAGAAGCAUCAAAG
  	start
  2150	Pseudoknots	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCGAUA
  		UACUUUGGAGUUUUAAAAUGUCUCUAAGUACAGAAGCAUCAAAG
  2151	Scaffold uuCG,	GGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAUGGGU
  	stem uuCG	AAAGCGCUUAUUUAUCGGCUUCGGCCGAUAAAUAAGAAGCAUCAAAG
  2152	Scaffold uuCG,	GCUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAUG
  	stem uuCG, no	GGUAAAGCGCUUAUGUAUCGGCUUCGGCCGAUAAAUAAGAAGCAUCAAAG
  	start
  2153	Scaffold uuCG	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUUCGGUCGUAU
  		GGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2154	=+GCTC36	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUGCUCCACCAGCGACUAUGUCG
  		UAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2155	G quadriplex	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	telomere basket +	GGUAAAGCGGGGUUAGGGUUAGGGUUAGGGAAGCAUCAAAG
  	ends
  2156	G quadriplex	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	M3q	GGUAAAGCGGAGGGAGGGAGGGAGAGGGAAAGCAUCAAAG
  2157	G quadriplex	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	telomere basket	GGUAAAGCGUUGGGUUAGGGUUAGGGUUAGGGAAAAGCAUCAAAG
  	no ends
  2158	45, 44 hairpin	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	(old version)	GGUAAAGCGC--------AGGGCUUCGGCCG---------GAAGCAUCAAAG
  2159	Sarcin-ricin loop	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCCUGCUCAGUACGAGAGGAACCGCAGGAAGCAUCAAAG
  2160	uvsX, C18G	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  2161	truncated stem	UACUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	loopm C18G, trip	GGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	mut (T10C)
  2162	short phage rep,	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	C18G	GGUAAAGCGCGGACGACCUCUCGGUCGUCCGAAGCAUCAAAG
  2163	phate rep loop,	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	C18G	GGUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  2164	=+G18, stacked	UACUGGCGCCUUUAUCUGCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAU
  	onto 64	GGGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2165	truncated stem	GCUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	loop, C18G, -1	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	A2G
  2166	phage rep loop,	UACUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	C18G, trip mut	GGUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  	(T10C)
  2167	short phage rep,	UACUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	C18G, trip mut	GGUAAAGCGCGGACGACCUCUCGGUCGUCCGAAGCAUCAAAG
  	(T10C)
  2168	uvsX, trip mut	UACUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	(T10C)	GGUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  2169	truncated stem	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	loop	GGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2170	=+A17, stacked	UACUGGCGCCUUUAUCAUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAU
  	onto 64	GGGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGAAUCAAAG
  2171	3′ HDV genomic	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	ribozyme	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGGGCC
  		GGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGU
  		CCCCUCGGUAAUGGCGAAUGGGACCC
  2172	phage rep loop,	UACUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	trip mut (T10C)	GGUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  2173	-79:80	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2174	short phage rep,	UACUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	trip mut (T10C)	GGUAAAGCGCGGACGACCUCUCGGUCGUCCGAAGCAUCAAAG
  2175	extra truncated	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	stem loop	GGUAAAGCGCCGGACUUCGGUCCGGAAGCAUCAAAG
  2176	T17G, C18G	UACUGGCGCUUUUAUCGGAUUACUUGGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUUGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2177	short phage rep	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCGGACGACCUCGCGGUCGUCCGAAGCAUCAAAG
  2178	uvsX, C18G, -1	GCUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	A2G	GUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  2179	uvsX, C18G, trip	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	mut (T10C), -1	GUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  	A2G, HDV -99
  	G65U
  2180	3′ HDV	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	antigenomic	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGGGGU
  	ribozyme	CGGCAUGGCAUCUCCACCUCCUCGCGGUCCGACCUGGGCAUCCGAAGGAGGACGCA
  		CGUCCACUCGGAUGGCUAAGGGAGAGCCA
  2181	uvsX, C18G, trip	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	mut (T10C), -1	GUAAAGCGCCCUCUUCGGAGGGCGCAUCAAAG
  	A2G, HDV
  	AA(98:99)C
  2182	3′ HDV ribozyme	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	(Lior Nissim,	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGUUUU
  	Timothy Lu)	GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUGCUUCGGCAU
  		GGCGAAUGGGACCCCGGG
  2183	TAC(1:3)GA,	GAUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	stacked onto 64	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2184	uvsX, -1 A2G	GCUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  		GUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  2185	truncated stem	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	loop, C18G, trip	GUAAAGCUCUUACGGACUUCGGUCCGUAAGAGCAUCAAAG
  	mut (T10C), -1
  	A2G, HDV -99
  	G65U
  2186	short phage rep,	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	C18G, trip mut	GUAAAGCUCGGACGACCUCUCGGUCGUCCGAGCAUCAAAG
  	(T10C), -1 A2G,
  	HDV -99 G65U
  2187	3′ sTRSV WT	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUC
  	viral	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGCCUC
  	Hammerhead	UCACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGUGAGGACGAAACAGG
  	ribozyme
  2188	short phage rep,	GCUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	C18G, -1 A2G	GUAAAGCGCGGACGACCUCUCGGUCGUCCGAAGCAUCAAAG
  2189	short phage rep,	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUATJGG
  	C18G, trip mut	GUAAAGCGCGGACGACCUCUCGGUCGUCCGAAGCAGCAAAG
  	(T10C), -1 A2G,
  	3′ genomic HDV
  2190	phage rep loop,	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	C18G, trip mut	GUAAAGCUCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAGCAUCAAAG
  	(T10C), -1 A2G,
  	HDV -99 G65U
  2191	3′ HDV ribozyme	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	(Owen Ryan,	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGGAUG
  	Jamie Cate)	GCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCUUCGGGUGGC
  		GAAUGGGAC
  2192	phage rep loop,	GCUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	C18G, -1 A2G	GUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  2193	0.14	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUACU
  		GGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2194	-78, G77T	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGUGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2195		GUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAU
  		GGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2196	short phage rep,	GCUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	-1 A2G	GUAAAGCGCGGACGACCUCUCGGUCGUCCGAAGCAUCAAAG
  2197	truncated stem	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	loop, C18G, trip	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	mut (T10C), -1
  	A2G
  2198	-1, A2G	GCUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  		GUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2199	truncated stem	GCUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	loop, trip mut	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	(T10C), -1 A2G
  2200	uvsX, C18G, trip	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	mut (T10C), -1	GUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  	A2G
  2201	phage rep loop.	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	-1 A2G	GUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  2202	phage rep loop,	GCUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	trip mut (T10C),	GUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  	-1 A2G
  2203	phage rep loop,	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	C18G, trip mut	GUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGAAGCAUCAAAG
  	(T10C), -1 A2G
  2204	truncated stem	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	loop, C18G	GGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2205	uvsX, trip mut	GCUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	(T10C), -1 A2G	GUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  2206	truncated stem	GCUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	loop, -1 A2G	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2207	short phage rep,	GCUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	trip mut (T10C),	GUAAAGCGCGGACGACCUCUCGGUCGUCCGAAGCAUCAAAG
  	-1 A2G
  2208	5′HDV ribozyme	GAUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCUUCGGG
  	(Owen Ryan,	UGGCGAAUGGGACUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCG
  	Jamie Cate)	ACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAA
  		GCAUCAAAG
  2209	5′HDV genomic	GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGA
  	ribozyme	CCGUCCCCUCGGUAAUGGCGAAUGGGACCCUACUGGCGCUUUUAUCUCAUUACUUU
  		GAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGA
  		AAUCCGAUAAAUAAGAAGCAGCAAAG
  2210	truncated stem	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	loop, C18G, trip	GUAAAGCGCUUACGGACUUCGGUCCGUAAGCGCAUCAAAG
  	mut (T10C), -1
  	A2G, HDV
  	AA(98:99)C
  2211	5′env25 pistol	CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUCUUCGGAUC
  	ribozyme (with	AGGUGCAAUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAU
  	an added	GUCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUC
  	CUUCGG loop)	AAAG
  2212	HDV	GGGUCGGCAUGGCAUCUCCACCUCCUCGCGGUCCGACCUGGGCAUCCGAAGGAGGA
  	antigenomic	CGCACGUCCACUCGGAUGGCUAAGGGAGAGCCAUACUGGCGCUUUUAUCUCAUUAC
  	ribozyme	UUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCGGAG
  		AGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2213	3′ Hammerhead	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	ribozyme (Lior	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGCCAG
  	Nissim, Timothy	UACUGAUGAGUCCGUGAGGACGAAACGAGUAAGCUCGUCUACUGGCGCUUUUAUCU
  	Lu) guide	CAU
  	scaffold scar
  2214	=+A27, stacked	UACUGGCGCCUUUAUCUCAUUACUUUAGAGAGCCAUCACCAGCGACUAUGUCGUAU
  	onto 64	GGGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2115	5′Hammerhead	CGACUACUGAUGAGUCCGUGAGGACGAAACGAGUAAGCUCGUCUAGUCGUACUGGC
  	ribozyme (Lior	GCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAG
  	Nissim, Timothy	CGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  	Lu) smaller scar
  2216	phage rep loop,	GCUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	C18G, trip mut	GUAAAGCGCAGGUGGGACGACCUCUCGGUCGUCCUAUCUGCGCAUCAAAG
  	(T10C), -1 A2G,
  	HDV
  	AA(98:99)C
  2217	-27, stacked onto	UACUGGCGCCUUUAUCUCAUUACUUUAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	64	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2218	3′ Hatchet	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACGAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGCAUU
  		CCUCAGAAAAUGACAAACCUGUGGGGCGUAAGUAGAUCUUCGGAUCUAUGAUCGUG
  		CAGACGUUAAAAUCAGGU
  2219	3′ Hammerhead	UACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	ribozyme (Lior	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGCGAC
  	Nissim, Timothy	UACUGAUGAGUCCGUGAGGACGAAACGAGUAAGCUCGUCUAGUCGCGUGUAGCGAA
  	Lu)	GCA
  2220	5′Hatchet	CAUUCCUCAGAAAAUGACAAACCUGUGGGGCGUAAGUAGAUCUUCGGAUCUAUGAU
  		CGUGCAGACGUUAAAAUCAGGUUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCA
  		UCACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAU
  		AAAUAAGAAGCAUCAAAG
  2221	5′HDV ribozyme	UUUUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUGCUUCG
  	(Lior Nissim,	GCAUGGCGAAUGGGACCCCGGGUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCA
  	Timothy Lu)	UCACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAU
  		AAAUAAGAAGCAUCAAAG
  2222		CGACUACUGAUGAGUCCGUGAGGACGAAACGAGUAAGCUCGUCUAGUCGCGUGUAG
  	ribozyme (Lior	CGAAGCAUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUG
  	Nissim, Timothy	UCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCA
  	Lu)	AAG
  2223	5′ HH15 Minimal	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	Hammerhead	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGGGGA
  	ribozyme	GCCCCGCUGAUGAGGUCGGGGAGACCGAAAGGGACUUCGGUCCCUACGGGGCUCCC
  2224	5′ RBMX	CCACCCCCACCACCACCCCCACCCCCACCACCACCCUACUGGCGCUUUUAUCUCAU
  	recruiting motif	UACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCG
  		GAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2225	3′ Hammerhead	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	ribozyme (Lior	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGCGAC
  	Nissim, Timothy	UACUGAUGAGUCCGUGAGGACGAAACGAGUAAGCUCGUCUAGUCG
  	Lu) smaller scar
  2226	3′ env25 pistol	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	ribozyme (with	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGCGUG
  	an added	GUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUCUUCGGAUCAGGU
  	CUUCGG loop)	GCAA
  2227	3′ Env-9 Twister	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  		GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGGGCA
  		AUAAAGCGGUUACAAGCCCGCAAAAAUAGCAGAGUAAUGUCGCGAUAGCGCGGCAU
  		UAAUGCAGCUUUAUUG
  2228	=+ATTATCTCA	UACUGGCGCUUUUAUCUCAUUACUAUUAUCUCAUUACUUUGAGAGCCAUCACCAGC
  	TTACT25	GACUAUGUCGUAUGGGUAAAGCGCUGAUUUAUCGGAGAGAAAUCCGAUAAAUAAGA
  		AGCAUCAAAG
  2229	5′Env-9 Twister	GGCAAUAAAGCGGUUACAAGCCCGCAAAAAUAGCAGAGUAAUGUCGCGAUAGCGCG
  		GCAUUAAUGCAGCUUUAUUGUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUC
  		ACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAA
  		AUAAGAAGCAUCAAAG
  2230	3′ Twisted Sister	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	1	GGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAGACCC
  		GCAAGGCCGACGGCAUCCGCCGCCGCUGGUGCAAGUCCAGCCGCCCCUUCGGGGGC
  		GGGCGCUCAUGGGUAAC
  2231	no stem	UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUC
  		GGUAAAG
  2232	5′HH15 Minimal	GGGAGCCCCGCUGAUGAGGUCGGGGAGACCGAAAGGGACUUCGGUCCCUACGGGGC
  	Hammerhead	UCCCUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCG
  	ribozyme	UAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAAAG
  2233	5′Hammerhead	CCAGUACUGAUGAGUCCGUGAGGACGAAACGAGUAAGCUCGUCUACUGGCGCUUUU
  	ribozyme (Lior	AUCUCAUUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUG
  	Nissim, Timothy	UCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCA
  	Lu) guide	AAG
  	scaffold scar
  2234	5′Twisted Sister	ACCCGCAAGGCCGACGGCAUCCGCCGCCGCUGGUGCAAGUCCAGCCGCCCCUUCGG
  	1	GGGCGGGCGCUCAUGGGUAACUACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAU
  		CACCAGCGACUAUGUCGUAUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUA
  		AAUAAGAAGCAUCAAAG
  2235	5′sTRSV WT	CCUGUCACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGUGAGGACGAAACAGGUACU
  	viral	GGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGGGUA
  	Hammerhead	AAGCGCUUAUUUAUCGGAGAGAAAGCCGAUAAAUAAGAAGCAUCAAAG
  	ribozyme
  2236	148, =+G55,	GUACUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAG
  	stacked onto 64	UGGGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2237	158,	GUACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAG
  	103 + 148(+G55)	UGGGUAAAGCUCCCUCUGCGGAGGGAGCAUCAAAG
  	-99, G65U
  2238	174, Uvsx	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	Extended stem	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  	with [A99]
  	G65U),
  	C18G, {circumflex over ( )}G55,
  	[GT-1]
  2239	175, extended	ACUGGCGCCUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	stem truncation,	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	T10C, [GT-1]
  2240	176, 174 with	GCUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	A1G substitution	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  	for T7
  	transcription
  2241	177, 174 with	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	bubble (+G55)	GUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  	removed
  2242	181, stem 42	ACUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	(truncated stem	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	loop);
  	T10C, C18G, [GT-1]
  	(95 + [GT-1]
  2243	182, stem 42	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	(truncated stem	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	loop);
  	C18G, [GT-1]
  2244	183, stem 42	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	(truncated stem	GGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	loop);
  	C18G, {circumflex over ( )}G55,
  	[GT-1]
  2242	184, stem 48	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUUG
  	(uvsx, -99 g65t);	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  	C18G, {circumflex over ( )}T55,
  	[GT-1]
  2246	185, stem 42	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUUG
  	(truncated stem	GGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	loop);
  	C18G, {circumflex over ( )}T55,
  	[GT-1]
  2247	186, stem 42	ACUGGCGCCUUUAUCAUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUG
  	(truncated stem	GGUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  	loop);
  	T10C, {circumflex over ( )}A17,
  	[GT-1]
  2248	187, stem 46	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	(uvsx);	GGUAAAGCGCCCUCUUCGGAGGGAAGCAUCAAAG
  	C18G, {circumflex over ( )}G55,
  	[GT-1]
  2249	188, stem 50	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	(ms2 U15C, -99,	GGUAAAGCUCACAUGAGGAUCACCCAUGUGAGCAUCAAAG
  	g65t);
  	C18G, {circumflex over ( )}G55,
  	[GT-1]
  2250	189, 174 +	ACUGGCACUUUUACCUGAUUACUUUGAGAGCCAACACCAGCGACUAUGUCGUAGUG
  	G48A; T15C; T35A	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2251	190, 174 + G8A	ACUGGCACUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2252	191, 174 + G8C	ACUGGCCCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2253	192, 174 + T15C	ACUGGCGCUUUUACCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2254	193, 174 + T35A	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAACACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2255	195, 175 + C18G +	ACUGGCACCUUUACCUGAUUACUUUGAGAGCCAACACCAGCGACUAUGUCGUAUGG
  	G8A; T15C; T35A	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2256	196, 175 + C18G +	ACUGGCACCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	G8A	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2257	197, 175 + C18G +	ACUGGCCCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG
  	G8C	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2258	198, 175 + C18G +	ACUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAACACCAGCGACUAUGUCGUAUGG
  	T35A	GUAAAGCGCUUACGGACUUCGGUCCGUAAGAAGCAUCAAAG
  2259	199, 174 + A2G	GCUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	(test G	GGUAAAGCUCCCUCuuCGGAGGGAGCAUCAAAG
  	transcription at
  	start; ccGCT...)
  2260	200, 174 + {circumflex over ( )}G1	GACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGU
  	(ccGACT...)	GGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2261	201, 174 +	ACUGGCGCCUUUAUCUGAUUACUUUGGAGAGCCAUCACCAGCGACUAUGUCGUAGU
  	T10C; {circumflex over ( )}G28	GGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2262	202, 174 +	ACUGGCGCAUUUAUCUGAUUACUUUGUGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	T10A; A28T	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2263	203, 174 + T10C	ACUGGCGCCUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2264	204, 174 + {circumflex over ( )}G28	ACUGGCGCUUUUAUCUGAUUACUUUGGAGAGCCAUCACCAGCGACUAUGUCGUAGU
  		GGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2265	205, 174 + T10A	ACUGGCGCAUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2266	206, 174 + A28T	ACUGGCGCUUUUAUCUGAUUACUUUGUGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2267	207, 174 + {circumflex over ( )}T15	ACUGGCGCUUUUAUUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGU
  		GGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2268	208, 174 + [T4]	ACGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUGG
  		GUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2269	209, 174 + C16A	ACUGGCGCUUUUAUAUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2270	210, 174 + {circumflex over ( )}T17	ACUGGCGCUUUUAUCUUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGU
  		GGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2271	211, 174 + T35G	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAGCACCAGCGACUAUGUCGUAGUG
  	(compare with	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  	174 + T35A
  	above)
  2272	212, 174 + U11G,	ACUGGCGCUGUUAUCUGAUUACUUCGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	A105G (A86G),	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCGAAG
  	U26C
  2273	213, 174 + U11C,	ACUGGCGCUCUUAUCUGAUUACUUCGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	A105G (A86G),	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCGAAG
  	U26C
  2274	214, 174 + U12G;	ACUGGCGCUUGUAUCUGAUUACUCUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	A106G (A87G),	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGAG
  	U25C
  2275	215, 174 + U12C;	ACUGGCGCUUCUAUCUGAUUACUCUGAGAGCCAUCACCAGCGACUAUGGCGUAGUG
  	A106G (A87G),	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGAG
  	U25C
  2276	216,	ACUGGCGCUUUGAUCUGAUUACCUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	174_tx11.G, 87.G,	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAGG
  	22.C
  2277	217,	ACUGGCGCUUUCAUCUGAUUACCUGGAGAGCCAGCACCAGCGACUAUGUCGUAGUG
  	174_tx11.c, 87.G,	GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAGG
  	22.C
  2278	218, 174 + U11G	ACUGGCGCUGUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG
  2279	219, 174 +	ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  	A105G (A86G)	GGUAAAGCUCCCUCUUCGGAGGGAGCAaCGAAG
  2280	220, 174 + U26C	ACUGGCGCUUUUAUCUGAUUACUUCGAGAGCCAUCACCAGCGACUAUGUCGUAGUG
  		GGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG

• In some embodiments, the gNA variant comprises a tracrRNA stem loop comprising the sequence -UUU-N4-25-UUU- (SEQ ID NO: 240). For example, the gNA variant comprises a scaffold stem loop or a replacement thereof, flanked by two triplet U motifs that contribute to the triplex region. In some embodiments, the scaffold stem loop or replacement thereof comprises at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 21 nucleotides, at least 22 nucleotides, at least 23 nucleotides, at least 24 nucleotides, or at least 25 nucleotides.
• In some embodiments, the gNA variant comprises a crRNA sequence with -AAAG- in a location 5′ to the spacer region. In some embodiments, the -AAAG- sequence is immediately 5′ to the spacer region.
• In some embodiments, the at least one nucleotide modification to a reference gNA to produce a gNA variant comprises at least one nucleotide deletion in the Cask variant gNA relative to the reference gRNA. In some embodiments, a gNA variant comprises a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 consecutive or non-consecutive nucleotides relative to a reference gNA. In some embodiments, the at least one deletion comprises a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 or more consecutive nucleotides relative to a reference gNA. In some embodiments, the gNA variant comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 or more nucleotide deletions relative to the reference gNA, and the deletions are not in consecutive nucleotides. In those embodiments where there are two or more non-consecutive deletions in the gNA variant relative to the reference gRNA, any length of deletions, and any combination of lengths of deletions, as described herein, are contemplated as within the scope of the disclosure. For example, in sonic embodiments, a gNA variant may comprise a first deletion of one nucleotide, and a second deletion of two nucleotides and the two deletions are not consecutive. In some embodiments, a gNA variant comprises at least two deletions in different regions of the reference gRNA. In some embodiments, a gNA variant comprises at least two deletions in the same region of the reference gRNA. For example, the regions may be the extended stem loop, scaffold stem loop, scaffold stem bubble, triplex loop, pseudoknot, triplex, ora 5′ end of the gNA variant. The deletion of any nucleotide in a reference gRNA is contemplated as within the scope of the disclosure.
• In some embodiments, the at least one nucleotide modification of a reference gRNA to generate a gNA variant comprises at least one nucleotide insertion. In some embodiments, a gNA variant comprises an insertion of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 consecutive or non-consecutive nucleotides relative to a reference gRNA. In some embodiments, the at least one nucleotide insertion comprises an insertion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 or more consecutive nucleotides relative to a reference gRNA. In some embodiments, the gNA variant comprises 2 or more insertions relative to the reference gRNA, and the insertions are not consecutive. In those embodiments where there are two or more non-consecutive insertions in the gNA variant relative to the reference gRNA, any length of insertions, and any combination of lengths of insertions, as described herein, are contemplated as within the scope of the disclosure. For example, in sonic embodiments, a gNA variant may comprise a first insertion of one nucleotide, and a second insertion of two nucleotides and the two insertions are not consecutive. In some embodiments, a gNA variant comprises at least two insertions in different regions of the reference gRNA. In some embodiments, a gNA variant comprises at least two insertions in the same region of the reference sRNA. For example, the regions may be the extended stem loop, scaffold stem loop, scaffold stem bubble, triplex loop, pseudoknot, triplex, or a 5′ end of the gNA variant. Any insertion of A, G, C, U (or T, in the corresponding DNA) or combinations thereof at any location in the reference gRNA is contemplated as within the scope of the disclosure.
• In some embodiments, the at least one nucleotide modification of a reference gRNA to genereate a gNA variant comprises at least one nucleic acid substitution. In some embodiments, a gNA variant comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 or more consecutive or non-consecutive substituted nucleotides relative to a reference gRNA. In some embodiments, a gNA variant comprises 1-4 nucleotide substitutions relative to a reference gRNA. In some embodiments, the at least one substitution comprises a substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 or more consecutive nucleotides relative to a reference gRNA. In some embodiments, the gNA variant comprises 2 or more substitutions relative to the reference gRNA, and the substitutions are not consecutive. In those embodiments where there are two or more non-consecutive substitutions in the gNA variant relative to the reference gRNA, any length of substituted nucleotides, and any combination of lengths of substituted nucleotides, as described herein, are contemplated as within the scope of the disclosure. For example, in some embodiments, a gNA variant may comprise a first substitution of one nucleotide, and a second substitution of two nucleotides and the two substitutions are not consecutive. In some embodiments, a gNA variant comprises at least two substitutions in different regions of the reference gRNA. In some embodiments, a gNA variant comprises at least two substitutions in the same region of the reference gRNA. For example, the regions may be the triplex, the extended stem loop, scaffold stem loop, scaffold stem bubble, triplex loop, pseudoknot, triplex, or a 5′ end of the gNA variant. Any substitution of A, G, C, U (or T, in the corresponding DNA) or combinations thereof at any location in the reference gRNA is contemplated as within the scope of the disclosure.
• Any of the substitutions, insertions and deletions described herein can be combined to generate a gNA variant of the disclosure. For example, a gNA variant can comprise at least one substitution and at least one deletion relative to a reference gRNA, at least one substitution and at least one insertion relative to a reference gRNA, at least one insertion and at least one deletion relative to a reference gRNA, or at least one substitution, one insertion and one deletion relative to a reference gRNA.
• In some embodiments, the gNA variant comprises a scaffold region at least 20% identical, at least 30% identical, at least 40% identical, at least 50% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical to any one of SEQ ID NOS: 4-16. In some embodiments, the gNA variant comprises a scaffold region at least 60% homologous (or identical) to any one of SEQ ID NOS: 4-16.
• In some embodiments, the gNA variant comprises a tracr stem loop at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical to SEQ ID NO: 14. In some embodiments, the gNA variant comprises a tracr stem loop at least 60% homologous (or identical) to SEQ II) NO: 14.
• In some embodiments, the gNA variant comprises an extended stem loop at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical to SEQ ID NO: 15. In some embodiments, the gNA variant comprises an extended stem loop at least 60% homologous (or identical) to SEQ ID NO: 15.
• In some embodiments, a gNA variant comprises a sequence of any one of SEQ ID NOs: 412-3295. In some embodiments, a gNA variant comprises a sequence of any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, or 2259-2280. In some embodiments, a gNA variant comprises a sequence of any one of SEQ ID NOS: 2236. 2237, 2238, 2241, 2244, 2248, 2249, or 2259-2280.
• In some embodiments, the gNA variant comprises an exogenous extended stem loop, with such differences from a reference gNA described as follows. In some embodiments, an exogenous extended stem loop has little or no identity to the reference stem loop regions disclosed herein (e.g., SEQ ID NO: 15). In some embodiments, an exogenous stem loop is at least 10 bp, at least 20 bp. at least 30 bp, at least 40 bp, at least 50 bp, at least 60 bp, at least 70 bp, at least 80 bp, at least 90 bp, at least 100 bp, at least 200 bp, at least 300 bp, at least 400 bp, at least 500 bp, at least 600 bp, at least 700 bp, at least 800 bp, at least 900 bp, at least 1,000 bp, at least 2,000 bp, at least 3,000 bp, at least 4,000 bp, at least 5,000 bp, at least 6,000 bp, at least 7,000 bp, at least 8,000 bp, at least 9,000 bp, at least 10,000 bp, at least 12,000 bp, at least 15,000 bp or at least 20,000 bp. In some embodiments, the gNA variant comprises an extended stem loop region comprising at least 10, at least 100, at least 500, at least 1000, or at least 10,000 nucleotides. In some embodiments, the heterologous stem loop increases the stability of the gNA. In some embodiments, the heterologous RNA stem loop is capable of binding a protein, an RNA structure, a DNA sequence, or a small molecule. In some embodiments, an exogenous stem loop region comprises an RNA stem loop or hairpin, for example a thermostable RNA such as MS2 (ACAUGAGGAUUACCCAUGU; SEQ ID NO: 4278), Qβ (UGCAUGUCUAAGACAGCA; SEQ ID NO: 4279), U1 hairpin II (AAUCCAUUGCACUCCGGAUU; SEQ ID NO:4280), Uvsx (CCUCUUCGGAGG; SEQ ID NO: 4281), PP7 (AGGAGUUUCUAUGGAAACCCU; SEQ ID NO: 4282), Phage replication loop (AGGUGGGACGACCUCUCGGUCGUCCUAUCU; SEQ ID NO: 4283), Kissing loop_a (UGCUCGCUCCGUUCGAGCA; SEQ ID NO: 4284), Kissing loop b1 (UGCUCGACGCGUCCUCGAGCA; SEQ ID NO: 4285). Kissing loop_b2 (UGCUCGUUUGCGGCUACGAGCA; SEQ ID NO: 4286), G quadriplex M3q (AGGGAGGGAGGGAGAGG; SEQ ID NO: 4287), G quadriplex telomere basket (GGUUAGGGUUAGGGUUAGG; SEQ ID NO: 4288). Sarcin-ricin loop (CUGCUCAGUACGAGAGGAACCGCAG; SEQ ID NO: 4289) or Pseudoknots (UACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGG AGUUUUAAAAUGUCUCUAAGUACA; SEQ ID NO: 4290). In some embodiments, an exogenous stem loop comprises an RNA scaffold. As used herein, an “RNA scaffold” refers to a multi-dimensional RNA structure capable of interacting with and organizing or localizing one or more proteins. In some embodiments, the RNA scaffold is synthetic or non-naturally occurring. In some embodiments, an exogenous stem loop comprises a long non-coding RNA (lncRNA). As used herein, a lncRNA refers to a non-coding RNA that is longer than approximately 200 bp in length. In some embodiments, the 5′ and 3′ ends of the exogenous stem loop are base paired, i.e., interact to form a region of duplex RNA. In some embodiments, the 5′ and 3′ ends of the exogenous stem loop are base paired, and one or more regions between the 5′ and 3′ ends of the exogenous stem loop are not base paired. In some embodiments, the at least one nucleotide modification comprises: (a) substitution of 1 to 15 consecutive or non-consecutive nucleotides in the gNA variant in one or more regions; (b) a deletion of 1 to 10 consecutive or non-consecutive nucleotides in the gNA variant in one or more regions; (c) an insertion of 1 to 10 consecutive or non-consecutive nucleotides in the gNA variant in one or more regions; (d) a substitution of the scaffold stem loop or the extended stem loop with an RNA stem loop sequence from a heterologous RNA source with proximal 5′ and 3′ ends; or any combination of (a)-(d).
• In some embodiments, a gNA variant comprises a sequence or subsequence of any one of SEQ ID NOs: 412-3295 and an a sequence of an exogenous stem loop. In some embodiments, a gNA variant comprises a sequence or subsequence of any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, or 2259-2280 and a sequence of an exogenous stem loop. In some embodiments, a gNA variant comprises a sequence or subsequence of any one of SEQ NOS: 2236, 2237, 2238. 2241, 2244, 2248. 2249, or 2259-2280 and a sequence of an exogenous stem loop.
• In some embodiments, the gNA variant comprises a scaffold stem loop having at least 60% identity to SEQ ID NO: 14. In some embodiments, the gNA variant comprises a scaffold stem loop having at least 60% identity, at least 70% identity, at least 80% identity, at least 90% identity, at least 95% identity, at least 98% identity or at least 99% identity to SEQ ID NO: 14. In some embodiments, the gNA variant comprises a scaffold stem loop comprising SEQ ID NO: 14.
• In some embodiments, the gNA variant comprises a scaffold stem loop sequence of CCAGCGACUAUGUCGUAGUGG (SEQ ID NO: 245). In some embodiments, the gNA variant comprises a scaffold stem loop sequence of CCAGCGACUAUGUCGUAGUGG (SEQ ID NO: 245) with at least 1, 2, 3, 4, or 5 mismatches thereto.
• In some embodiments, the gNA variant comprises an extended stem loop region comprising less than 32 nucleotides, less than 31 nucleotides, less than 30 nucleotides, less than 29 nucleotides, less than 28 nucleotides, less than 27 nucleotides, less than 26 nucleotides, less than 25 nucleotides, less than 24 nucleotides, less than 23 nucleotides, less than 22 nucleotides, less than 21 nucleotides, or less than 20 nucleotides. In some embodiments, the gNA variant comprises an extended stem loop region comprising less than 32 nucleotides. In some embodiments, the gNA variant further comprises a thermostable stem loop.
• In some embodiments, a sgRNA variant comprises a sequence of SEQ ID NO: 2104, 2106, SEQ II) NO: 2163, SEQ ID NO: 2107, SEQ NO: 2164, SEQ ID NO: :2165, SEQ NO: 2166, SEQ ID NO: 2103. SEQ ID NO: 2167, SEQ ID NO: 2105, SEQ ID NO: 2108, SEQ NO: 2112, SEQ ID NO: 2160, SEQ ID NO: 2170, SEQ ID NO: 2114, SEQ ID NO: 2171, SEQ ID NO: 2112. SEQ ID NO: 2173, SEQ ID NO: 2102. SEQ ID NO: 2174, SEQ ID NO: 2175, SEQ ID NO: 2109, SEQ ID NO: 2176, SEQ ID NO: 2238, SEQ ID NO: 2239, SEQ ID NO: 2240, or SEQ ID NO: 2241.
• In some embodiments, the gNA variant comprises one or more additional changes to a sequence of any one of SEQ ID NOs: 2201-2280. In some embodiments, the gNA variant comprises a sequence of any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249. or 2259-2280, or having at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In some embodiments, the gNA variant comprises one or more additional changes to a sequence of any one of SEQ ID NOs: 2201-2280. In some embodiments, the gNA variant comprises the sequence of any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, or 2259-2280.
• In some embodiments, a sgRNA variant comprises one or more additional changes to a sequence of SEQ ID NO: 2104. SEQ ID NO: 2163, SEQ ID NO: 2107, SEQ ID NO: 2164, SEQ NO: 2165, SEQ ID NO: 2166, SEQ ID NO: 2103, SEQ ID NO: 2167, SEQ ID NO: 2105, SEQ ID NO: 2108, SEQ ID NO: 2112, SEQ ID NO: 2160, SEQ ID NO: 2170, SEQ ID NO: 2114, SEQ NO: 2171, SEQ ID NO: 2112, SEQ 1D NO: 2173, SEQ ID NO: 2102, SEQ NO: 2174, SEQ ID NO: 2175, SEQ ID NO: 2109, SEQ ID NO: 2176, SEQ ID NO: 2238, SEQ ID NO: 2239, SEQ ID NO: 2240, or SEQ ID NO: 2241.
• In some embodiments of the gNA variants of the disclosure, the gNA variant comprises at least one modification, wherein the at least one modification compared to the reference guide scaffold of SEQ ID NO: 5 is selected from one or more of: (a) a C18G substitution in the triplex loop; (b) a G55 insertion in the stem bubble; (c) a U1 deletion; (d) a modification of the extended stem loop wherein (i) a 6 nt loop and 13 loop-proximal base pairs are replaced by a Uvsx hairpin; and (ii) a deletion of A99 and a substitution of G65U that results in a loop-distal base that is fully base-paired. In such embodiments, the gNA variant comprises the sequence of any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, or 2259-2280.
• In some embodiments, the scaffold of the gNA variant comprises the sequence of any one of SEQ ID NOS: 2201-2280 of Table 2. In some embodiments, the scaffold of the gNA consists or consists essentially of the sequence of any one of SEQ ID NOS: 2201-2280. In some embodiments, the scaffold of the gNA variant sequence is at least about 60% identical, at least about 65% identical, at least about 70% identical, at least about 75% identical, at least about 80% identical, at least about 85% identical, at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical or at least about 99% identical to any one of SEQ ID NOS: 2201 to 2280.
• In some embodiments, the gNA variant further comprises a spacer (or targeting sequence) region, described more fully, supra, which comprises at least 14 to about 35 nucleotides wherein the spacer is designed with a sequence that is complementary to a target DNA. In some embodiments, the gNA variant comprises a targeting sequence of at least 10 to 30 nucleotides complementary to a target DNA. In some embodiments, the targeting sequence has 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 nucleotides, In some embodiments, the gNA variant comprises a targeting sequence having 20 nucleotides. In some embodiments, the targeting sequence has 25 nucleotides. In some embodiments, the targeting sequence has 24 nucleotides. In some embodiments, the targeting sequence has 23 nucleotides. In some embodiments, the targeting sequence has 22 nucleotides. In some embodiments, the targeting sequence has 21 nucleotides. In some embodiments, the targeting sequence has 20 nucleotides. In some embodiments, the targeting sequence has 19 nucleotides. In some embodiments, the targeting sequence has 18 nucleotides. In some embodiments, the targeting sequence has 17 nucleotides. In some embodiments, the targeting sequence has 16 nucleotides. In some embodiments, the targeting sequence has 15 nucleotides. In some embodiments, the targeting sequence has 14 nucleotides.
• In some embodiments, the scaffold of the gNA variant is a variant comprising one or more additional changes to a sequence of a reference g,RNA that comprises SEQ ID NO: 4 or SEQ ID NO: 5. In those embodiments where the scaffold of the reference gRNA is derived from SEQ ID NO: 4 or SEQ ID NO: 5, the one or more improved or added characteristics of the gNA variant are improved compared to the same characteristic in SEQ ID NO: 4 or SEQ ID NO: 5.
• In some embodiments, the scaffold of the gNA variant is part of an RNP with a reference CasX protein comprising SEQ ID NO: 1. SEQ ID NO: 2, or SEQ ID NO: 3. In other embodiments, the scaffold of the gNA variant is part of an RNP with a CasX variant protein comprising any one of the sequences of Tables 3, 8, 9, 10 and 12, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto. In the foregoing embodiments, the gNA further comprises a spacer sequence.
• h. Chemically Modified gNAs
• In some embodiments, the disclosure provides chemically-modified gNAs. In some embodiments, the present disclosure provides a chemically-modified gNA that has guide NA functionality and has reduced susceptibility to cleavage by a nuclease. A gNA that comprises any nucleotide other than the four canonical ribonucleotides A, C, G, and U, or a deoxynucleotide, is a chemically modified gNA. In some cases, a chemically-modified gNA comprises any backbone or internucleotide linkage other than a natural phosphodiester internucleotide linkage. In certain embodiments, the retained functionality includes the ability of the modified gNA to bind to a CasX of any of the embodiments described herein. In certain embodiments, the retained functionality includes the ability of the modified gNA to bind to a. target nucleic acid sequence. In certain embodiments, the retained functionality includes targeting a CasX protein or the ability of a pre-complexed RNP to bind to a target nucleic acid sequence. In certain embodiments, the retained functionality includes the ability to nick a target polynucleotide by a CasX-gNA. In certain embodiments, the retained functionality includes the ability to cleave a target nucleic acid sequence by a CasX-gNA. In certain embodiments, the retained functionality is any other known function of a gNA in a recombinant system with a CasX chimera protein of the embodiments of the disclosure.
• In some embodiments, the disclosure provides a chemically-modified gNA in which a nucleotide sugar modification is incorporated into the gNA selected from the group consisting of 2′-O—C_1-4alkyl such as 2′-O-methyl (2′-OMe), 2′-deoxy (2′-H), 2′-O—C_1-3alkyl-O—C_1-3alkyl such as 2′-methoxyethyl (“2′-MOE”), 2′-fluoro (“2′-F”), 2′-amino (“2′-NH,”), 2′-arabinosyl (“2′-arabino”) nucleotide, 2′-F-arabinosyl (“2′-F-arabino”) nucleotide, 2′-locked nucleic acid (“LNA”) nucleotide, 2′-unlocked nucleic acid (“ULNA”) nucleotide, a sugar in L form (“L-sugar”), and 4′-thioribosyl nucleotide. In other embodiments, an internucleotide linkage modification incorporated into the guide RNA is selected from the group consisting of: phosphorothioate “P(S)” (P(S)), phosphonocarboxylate (P(CH₂)_nCOOR) such as phosphonoacetate “PACE” (P(CH₂COO—)), thiophosphonocarboxylate ((S)P(CH₂)_nCOOR) such as thiophosphonoacetate “thioPACE” ((S)P(CH₂)_nCOO—)), alkylphosphonate (P(C_1-3alkyl) such as methylphosphonate —P(CH₃), boranophosphonate (P(BH₃)), and phosphorodithioate (P(S)₂).
• In certain embodiments, the disclosure provides a chemically-modified gNA in which a nucleobase (“base”) modification is incorporated into the gNA selected from the group consisting of: 2-thiouracil (“2-thioU”), 2-thiocytosine (“2-thioC”), 4-thiouracil (“4-thioU”), 6-thioguanine (“6-thioG”), 2-aminoadenine (“2-aminoA”), 2-aminopurine, pseudouracil, hypoxanthine, 7-deazaguanine, 7-deaza-8-azaguanine, 7-deazaadenine, 7-deaza-8-azaadenine, 5-methylcytosine (“5-methylC”), 5-methyluracil (“5-methylU”), 5-hydroxymethylcytosine, 5-hydroxymethyluracil, 5,6-dehydrouracil, 5-propynylcytosine, 5-propynyluracil, 5-ethynylcytosine, 5-ethynyluracil, 5-arllyluracil (“5-allylU”), 5-allylcytosine (“5-allylC”), 5-aminoallyluracil (“5-aminoallylU”), 5-aminoallyl-cytosine (“5-aminoallylC”), an abasic nucleotide, Z base, P base, Unstructured Nucleic Acid (“UNA”), isoguanine (“isoG”), isocytosine (“isoC”), 5-methyl-2-pyrimidine, x(A,G,C,T) and y(A,G,C,T).
• In other embodiments, the disclosure provides a chemically-modified gNA in which one or more isotopic modifications are introduced on the nucleotide sugar, the nucleobase, the phosphodiester linkage and/or the nucleotide phosphates, including nucleotides comprising one or more ¹⁵N, ¹³C, ¹⁴C, deuterium, ³H, ³²P, ¹²⁵I, ¹³¹I atoms or other atoms or elements used as tracers.
• In some embodiments, an “end” modification incorporated into the gNA is selected. from the group consisting of: PEG (polyethyleneglycol), hydrocarbon linkers (including: heteroatom (O,S,N)-substituted hydrocarbon spacers; halo-substituted hydrocarbon spacers; keto-, carboxyl-, amido-, carbamoyl-, thionocarbamaoyl-containing hydrocarbon spacers), spermine linkers, dyes including fluorescent dyes (for example fluoresceins, rhodamines, cyanines) attached to linkers such as, for example 6-fluorescein-hexyl, quenchers (for example dabcyl, BHQ) and other labels (for example biotin, digoxigenin, acridine, streptavidin, avidin, peptides and/or proteins). In some embodiments, an “end” modification comprises a conjugation (or ligation) of the gNA to another molecule comprising an oligonucleotide of deoxynucleotides and/or ribonucleotides, a peptide, a protein, a sugar, an oligosaccharide, a steroid, a lipid, a folic acid, a vitamin and/or other molecule. In certain embodiments, the disclosure provides a chemically-modified gNA in which an “end” modification (described above) is located internally in the gNA sequence via a linker such as, for example, a 2-(4-butylamidoiluorescein)propane-1,3-diol bis(phosphodiester) linker, which is incorporated as a phosphodiester linkage and can he incorporated anywhere between two nucleotides in the gNA.
• In sonie embodiments, the disclosure provides a chemically-modified gNA having an end modification comprising a terminal functional group such as an amine, a thiol (or sulfhydryl), a hydroxyl, a carboxyl, carbonyl, thionyl, thiocarbonyl, a carbamoyl, a thiocarbanmoyl, a phoshoryl, art alkene, an alkyne, an halogen or a functional group-terminated linker that can be subsequently conjugated to a desired moiety selected from the group consisting of a fluorescent dye, a non-fluorescent label, a tag (for ¹⁴C, example biotin, avidin, streptavidin, or moiety containing an isotopic label such as ¹⁵N, ¹³C, deuterium, ³H, ³²P, ¹²⁵I and the like), an oligonucleotide (comprising deoxynucleotides and/or ribonucleotides, including an aptamer), an amino acid, a peptide, a protein, a sugar, an oligosaccharide, a steroid, a lipid, a folic acid, and a vitamin. The conjugation employs standard chemistry well-known in the art, including but not limited to coupling via N-hydroxysuccinimide, isothiocyanate, DCC (or DCI), and/or any other standard method as described in “Bioconjugate Techniques” by Greg T. Hermanson, Publisher Eslsevier Science, 3^rded. (2013), the contents of which are incorporated herein by reference in its entirety.
• i, Complex Formation with CasX Protein
• In some embodiments, a gNA variant has an improved ability to form a complex with a CasX protein (such as a reference CasX or a CasX variant protein) when compared to a reference gRNA. In some embodiments, a gNA variant has an improved affinity for a CasX protein (such as a reference or variant protein) when compared to a reference gRNA, thereby improving its ability to form a ribonucleoprotein (RNP) complex with the CasX protein, as described in the Examples. Improving ribonucleoprotein complex formation may, in some embodiments, improve the efficiency with which functional RNPs are assembled. In some embodiments, greater than 90%, greater than 93%, greater than 95%, greater than 96%, greater than 97%, greater than 98% or greater than 99% of RNPs comprising a gNA variant and a spacer are competent for gene editing of a target nucleic acid.
• Exemplary nucleotide changes that can improve the ability of gNA variants to form a complex with CasX protein may, in some embodiments, include replacing the scaffold stem with a thermostable stem loop. Without wishing to be bound by any theory, replacing the scaffold stem with a thermostable stem loop could increase the overall binding stability of the gNA variant with the CasX protein. Alternatively, or in addition, removing a large section of the stem loop could change the gNA variant folding kinetics and make a functional folded gNA easier and quicker to structurally-assemble, for example by lessening the degree to which the gNA variant can get “tangled” in itself. In some embodiments, choice of scaffold stem loop sequence could change with different spacers that are utilized for the gNA. In some embodiments, scaffold sequence can be tailored to the spacer and therefore the target sequence. Biochemical assays can be used to evaluate the binding affinity of CasX protein for the gNA variant to form the RINP, including the assays of the Examples. For example, a person of ordinary skill can measure changes in the amount of a fluorescently tagged gNA that is bound to an immobilized CasX protein, as a response to increasing concentrations of an additional unlabeled “cold competitor” gNA. Alternatively, or in addition, fluorescence signal can be monitored to or seeing how it changes as different amounts of fluorescently labeled gNA are flowed over immobilized CasX protein. Alternatively, the ability to form an RNP can be assessed using in vitro cleavage assays against a defined target nucleic acid sequence.
• j. gNA Stability
• In some embodiments, a gNA variant has improved stability when compared to a reference gRNA. Increased stability and efficient folding may, in some embodiments, increase the extent to which a gNA variant persists inside a target cell, which may thereby increase the chance of forming a functional RNP capable of carrying out CasX functions such as gene editing. Increased stability of gNA variants may also, in some embodiments, allow for a similar outcome with a lower amount of gNA delivered to a cell, which may in turn reduce the chance of off-target effects during gene editing.
• In other embodiments, the disclosure provides gNA in which the scaffold stem loop and/or the extended stem loop is replaced with a hairpin loop or a thermostable RNA stem loop in which the resulting gNA has increased stability and, depending on the choice of loop, can interact with certain cellular proteins or RNA. In some embodiments, the replacement RNA loop is selected from MS2, hairpin II, Uvsx, PP7. Phage replication loop, Kissing loop_a, Kissing loop_b1, Kissing loop b2, G quadriplex M3q, G quadriplex telomere basket, Sarcin-ricin loop and Pseudoknots. Sequences of gNA variants including such components are provided in Table 2.
• Guide NA stability can be assessed in a variety of ways, including for example in vitro by assembling the guide, incubating for varying periods of time in a solution that mimics the intracellular environment, and then measuring functional activity via the in vitro cleavage assays described herein. Alternatively, or in addition, gNAs can be harvested from cells at varying time points after initial transfection/transduction of the gNA to determine how long gNA variants persist relative to reference gRNAs.
• k. Solubility
• In some embodiments, a gNA variant has improved solubility when compared to a reference gRNA. In some embodiments, a gNA variant has improved solubility of the CasX protein:gNA RNP when compared to a reference gRNA. In some embodiments, solubility of the CasX protein:gNA RNP is improved by the addition of a ribozyme sequence to a 5′ or 3′ end of the gNA variant, for example the 5′ or 3′ of a reference sgRNA. Some ribozymes, such as the M1 ribozyme, can increase solubility of proteins through RNA mediated protein folding.
• Increased solubility of CasX RNPs comprising a gNA variant as described herein can be evaluated through a variety of means known to one of skill in the art, such as by taking densitometry readings on a gel of the soluble fraction of lysed E. coli in which the CasX and gNA variants are expressed.
• l. Resistance to Nuclease Activity
• In some embodiments, a gNA variant has improved resistance to nuclease activity compared to a reference gRNA. Without wishing to be bound by any theory, increased resistance to nucleases, such as nucleases found in cells, may for example increase the persistence of a variant gNA in an intracellular environment, thereby improving gene editing.
• Many nucleases are processive, and degrade RNA in a 3′ to 5′ fashion. Therefore, in some embodiments the addition of a nuclease resistant secondary structure to one or both termini of the gNA, or nucleotide changes that change the secondary structure of a sgNA, can produce gNA variants with increased resistance to nuclease activity. Resistance to nuclease activity may he evaluated through a variety of methods known to one of skill in the art. For example, in vitro methods of measuring resistance to nuclease activity may include for example contacting reference gNA and variants with one or more exemplary RNA nucleases and measuring degradation. Alternatively, or in addition, measuring persistence of a gNA variant in a cellular environment using the methods described herein can indicate the degree to which the gNA variant is nuclease resistant.
• m. Binding Affinity to a Target DNA
• In some embodiments, a gNA variant has improved affinity for the target DNA relative to a reference gRNA. In certain embodiments, a ribonucleoprotein complex comprising a gNA variant has improved affinity for the target DNA, relative to the affinity of an RNP comprising a reference gRNA. In some embodiments, the improved affinity of the RNP for the target DNA comprises improved affinity for the target sequence, improved affinity for the PAM sequence, improved ability of the RNP to search DNA for the target sequence, or any combinations thereof. In some embodiments, the improved affinity fbr the target DNA is the result of increased overall DNA binding affinity.
• Without wishing to be bound by theory, it is possible that nucleotide changes in the gNA variant that affect the function of the OBD in the CasX protein may increase the affinity of CasX variant protein binding to the protospacer adjacent motif (PAM), as well as the ability to bind or utilize an increased spectrum of PAM sequences other than the canonical TTC PAM recognized by the reference CasX protein of SEQ ID NO: 2, including PAM sequences selected from the group consisting of TTC, ATC, GTC, and CTC, thereby increasing the affinity and diversity of the CasX variant protein for target DNA sequences, thereby increasing the target nucleic acid sequences that can be edited and/or bound, compared to a reference CasX. As described more fully, below, increasing the sequences of the target nucleic acid that can be edited, compared to a reference CasX, refers to both the PAM and the protospacer sequence and their directionality according to the orientation of the non-target strand. This does not imply that the PAM sequence of the non-target strand, rather than the target strand, is determinative of cleavage or mechanistically involved in target recognition. For example, when reference is to a TTC PAM, it may in fact be the complementary GAA sequence that is required for target cleavage, or it may be some combination of nucleotides from both strands. In the case of the CasX proteins disclosed herein, the PAM is located 5′ of the protospacer with at least a single nucleotide separating the PAM from the first nucleotide of the protospacer. Alternatively, or in addition, changes in the gNA that affect function of the helical I and/or helical II domains that increase the affinity of the CasX variant protein for the target DNA strand can increase the affinity of the CasX RNP comprising the variant gNA for target DNA.
• ii. Adding or Changing gNA Function
• In some embodiments, gNA variants can comprise larger structural changes that change the topology of the gNA variant with respect to the reference gRNA, thereby allowing for different gNA functionality. For example, in some embodiments a gNA variant has swapped an endogenous stem loop of the reference gRNA scaffold with a previously identified stable RNA structure or a stem loop that can interact with a protein or RNA binding partner to recruit additional moieties to the CasX or to recruit CasX to a specific location, such as the inside of a viral capsid, that has the binding partner to the said RNA structure. In other scenarios the RNAs may be recruited to each other, as in Kissing loops, such that two CasX proteins can be co-localized for more effective gene editing at the target DNA sequence. Such RNA structures may include MS2, Qβ, U1 hairpin II, Uvsx, PP7, Phage replication loop, Kissing loop_a, Kissing loop_b1, Kissing loop_b2, G quadriplex M3q, G quadriplex telomere basket, Sarcin-ricin loop, or a Pseudoknot.
• In some embodiments, a gNA variant comprises a terminal fusion partner. The term gNA variant is inclusive of variants that include exogenous sequences such as terminal fusions, or internal insertions. Exemplary terminal fusions may include fusion of the gRNA to a self-cleaving ribozyme or protein binding motif. As used herein, a “ribozyme” refers to an RNA or segment thereof with one or more catalytic activities similar to a protein enzyme. Exemplary ribozyme catalytic activities may include, for example, cleavage and/or ligation of RNA, cleavage and/or ligation of DNA, or peptide bond formation. In some embodiments, such fusions could either improve scaffold folding or recruit DNA repair machinery. For example, a sRNA may in some embodiments be fused to a hepatitis delta virus (HDV) antienomic ribozyme, HDV genomic ribozyme, hatchet ribozyme (from metagenomic data), env25 pistol ribozyme (representative from Aliistipes putredinis), HH15 Minimal Hammerhead ribozyme, tobacco ringspot virus (TRSV) ribozyme, WT viral Hammerhead ribozyme (and rational variants), or Twisted Sister 1 or RBMX recruiting motif Hammerhead ribozymes are RNA motifs that catalyze reversible cleavage and ligation reactions at a specific site within an RNA molecule. Hammerhead ribozymes include type I, type II and type III hammerhead ribozymes. The HDV, pistol, and hatchet ribozymes have self-cleaving activities. gNA variants comprising one or more ribozymes may allow for expanded gNA function as compared to a gRNA reference. For example, gNAs comprising self-cleaving ribozymes can, in some embodiments, be transcribed and processed into mature gNAs as part of polycistronic transcripts. Such fusions may occur at either the 5′ or the 3′ end of the gNA. In some embodiments, a gNA variant comprises a fusion at both the 5′ and the 3′ end, wherein each fusion is independently as described herein. In some embodiments, a gNA variant comprises a phage replication loop or a tetraloop. In some embodiments, a gNA comprises a hairpin loop that is capable of binding a protein. For example, in some embodiments the hairpin loop is an MS2, Qβ, U2 hairpin II. Uvsx, or PP7 hairpin loop.
• In sonie embodiments, a gNA variant comprises one or more RNA aptamers. As used herein, an “RNA aptamer” refers to an RNA molecule that binds a target with high affinity and high specificity.
• In some embodiments, a gNA variant comprises one or more riboswitches. As used herein, a “riboswitch” refers to an RNA molecule that changes state upon binding a small molecule.
• In some embodiments, the gNA variant further comprises one or more protein binding motifs. Adding protein binding motifs to a reference gRNA or gNA variant of the disclosure may, in some embodiments, allow a CasX RNP to associate with additional proteins, which can for example add the functionality of those proteins to the CasX RNP.
IV. CasX Proteins for Modifying a Target Nucleic Add
• The term “CasX protein”, as used herein, refers to a family of proteins, and encompasses all naturally occurring CasX proteins, proteins that share at least 50% identity to naturally occurring CasX proteins, as well as CasX variants possessing one or more improved characteristics relative to a naturally-occurring reference CasX protein. Exemplary improved characteristics of the CasX variant embodiments include, but are not limited to improved folding of the variant, improved binding affinity to the gNA, improved binding affinity to the target nucleic acid, improved ability to utilize a greater spectrum of PAM sequences in the editing and/or binding of target DNA, improved unwinding of the target DNA, increased editing activity, improved editing efficiency, improved editing specificity, increased percentage of a eukaryotic genome that can be efficiently edited, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, improved protein stability, improved protein:gNA (RNP) complex stability, improved protein solubility, improved protein:gNA (RNP) complex solubility, improved protein yield, improved protein expression, and improved fusion characteristics, as described more fully, below. In the foregoing embodiments, the one or more of the improved characteristics of the CasX variant is at least about 1.1 to about 100,000-fold improved relative to the reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 when assayed in a comparable fashion. In other embodiments, the improvement is at least about 1.1-fold, at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 50-fold, at least about 100-fold, at least about 500-fold, at least about 1000-fold, at least about 5000-fold, at least about 10,000-fold, or at least about 100,000-fold compared to the reference CasX protein of SEQ ID NO: 1. SEQ ID NO: 2, or SEQ ID NO: 3 when assayed in a comparable fashion.
• The term CasX variant is inclusive of variants that are fusion proteins, i.e. the CasX is “fused to” a heterologous sequence. This includes CasX variants comprising CasX variant sequences and N-terminal, C-terminal, or internal fusions of the CasX to a heterologous protein or domain thereof.
• CasX proteins of the disclosure comprise at least one of the following domains: a non-target strand binding (NTSB) domain, a target strand loading (TSL) domain, a helical I domain, a helical II domain, an oligonucleotide binding domain (OBD), and a RuvC DNA cleavage domain (the last of which may be modified or deleted in a catalytically dead CasX variant), described more fully, below. Additionally, the CasX variant proteins of the disclosure have an enhanced ability to efficiently edit and/or bind target DNA utilizing PAM sequences selected from ITC, ATC, GTC, or CTC, compared to wild-type reference CasX proteins. In the foregoing, the PAM sequence is located at least 1 nucleotide 5′ to the non-target strand of the protospacer having identity with the targeting sequence of the gNA in a assay system compared to the editing efficiency and/or binding of an RNP comprising a reference CasX protein in a comparable assay system.
• In some cases, the CasX protein is a naturally-occurring protein (eg., naturally occurs in and is isolated from prokaryotic cells). In other embodiments, the CasX protein is not a naturally-occurring protein (e.g., the CasX protein is a CasX variant protein, a chimeric protein, and the like). A naturally-occurring CasX protein (referred to herein as a “reference CasX protein”) functions as an endonuclease that catalyzes a double strand break at a specific sequence in a targeted double-stranded DNA (dsDNA). The sequence specificity is provided by the targeting sequence of the associated gNA to which it is complexed, which hybridizes to a target sequence within the target nucleic acid.
• In some embodiments, a CasX protein can bind and/or modify (e.g., cleave, nick, methylate, demethylase, etc.) a target nucleic acid and/or a polypeptide associated with target nucleic acid (e.g., methylation or acetylation of a historic tail). In some embodiments, the CasX protein is catalytically dead (dCasX) but retains the ability to bind a target nucleic acid. An exemplary catalytically dead CasX protein comprises one or more mutations in the active site of the RuvC domain of the Cask protein. In some embodiments, a catalytically dead CasX protein comprises substitutions at residues 672, 769 and/or 935 of SEQ ID NO: 1. In one embodiment, a catalytically dead CasX protein comprises substitutions of D672A, E769A and/or D935A in a reference CasX protein of SEQ ID NO: 1. In other embodiments, a catalytically dead CasX protein comprises substitutions at amino acids 659. 756 and/or 922 in a reference CasX protein of SEQ ID NO: 2. In some embodiments, a catalytically dead CasX protein comprises D659A. E756A and/or D922A substitutions in a reference CasX protein of SEQ NO: 2. In further embodiments, a catalytically dead Cask protein comprises deletions of all or part of the RuvC domain of the CasX protein. It will be understood that the same foregoing substitutions can similarly be introduced into the CasX variants of the disclosure, resulting in a dCasX variant. In one embodiment, all or a portion of the RuvC domain is deleted from the CasX variant, resulting in a dCasX variant. Catalytically inactive dCasX variant proteins can, in some embodiments, be used for base editing or epigenetic modifications. With a higher affinity for DNA, in some embodiments, catalytically inactive dCasX variant proteins can, relative to catalytically active CasX, find their target nucleic acid faster, remain bound to target nucleic acid for longer periods of time, bind target nucleic acid in a more stable fashion, or a combination thereof, thereby improving the function of the catalytically dead CasX variant protein.
• a. Non-Target Strand Binding Domain
• The reference CasX proteins of the disclosure comprise a non-target strand binding domain (NTSBD). The NTSBD is a domain not previously found in any Cas proteins; for example this domain is not present in Cas proteins such as Cas9, Cas12a/Cpf1, Cas13, Cas14, CASCADE, CSM, or CSY. Without being bound to theory or mechanism, a NTSBD in a CasX allows for binding to the non-target DNA strand arid may aid in unwinding of the non-target and target strands. The NTSBD is presumed to be responsible for the unwinding, or the capture, of a non-target DNA strand in the unwound state. The NTSBD is in direct contact with the non-target strand in CryoEM model structures derived to date and may contain a non-canonical zinc finger domain. The NTSBD may also play a role in stabilizing DNA during unwinding, guide RNA invasion and R-loop formation. In some embodiments, an exemplary NTSBD comprises amino acids 101-191 of SEQ ID NO: 1 or amino acids 103-192 of SEQ ID NO: 2. In some embodiments, the NTSBD of a reference CasX protein comprises a four-stranded beta sheet.
• b. Target. Strand Loading Domain
• The reference CasX proteins of the disclosure comprise a Target Strand Loading (TSL) domain. The TSL domain is a domain not found in certain Cas proteins such as Cas9, CASCADE, CSM, or CSY. Without wishing to be bound by theory or mechanism, it is thought that the TSL domain is responsible for aiding the loading of the target DNA strand into the RuvC active site of a CasX protein. In some embodiments, the TSL acts to place or capture the target-strand in a folded state that places the scissile phosphate of the target strand DNA backbone in the RuvC active site. The TSL comprises a cys4 (CXXC (SEQ ID NO: 246, CXXC (SEQ ID NO: 246) zinc finger/ribbon domain that is separated by the bulk of the TSL. In some embodiments, an exemplary TSL comprises amino acids 825-934 of SEQ ID NO: 1 or amino acids 813-921 of SEQ D NO: 2.
• c. Helical I Domain
• The reference CasX proteins of the disclosure comprise a helical 1 domain. Certain Cas proteins other than CasX have domains that may be named in a similar way. However, in some embodiments, the helical I domain of a CasX protein comprises one or more unique structural features, or comprises a unique sequence, or a combination thereof, compared to non-CasX proteins. For example, in some embodiments, the helical I domain of a CasX protein comprises one or more unique secondary structures compared to domains in other Cas proteins that may have a similar name. For example, in some embodiments the helical I domain in a CasX protein comprises one or more alpha helices of unique structure and sequence in arrangement, number and length compared to other CR1SPR proteins. In certain embodiments, the helical I domain is responsible for interacting with the bound DNA and spacer of the guide RNA. Without wishing to be bound by theory, it is thought that in some cases the helical I domain may contribute to binding of the protospacer adjacent motif (PAM). In some embodiments, an exemplary helical I domain comprises amino acids 57-100 and 192-332 of SEQ ID NO: 1, or amino acids 59-102 and 193-333 of SEQ ID NO: 2. In some embodiments, the helical I domain of a reference CasX protein comprises one or more alpha helices.
• d. Helical H Domain
• The reference CasX proteins of the disclosure comprise a helical II domain. Certain Cas proteins other than CasX have domains that may be named in a similar way. However, in some embodiments, the helical II domain of a CasX protein comprises one or more unique structural features, or a unique sequence, or a combination thereof, compared to domains in other Cas proteins that may have a similar name. For example, in some embodiments, the hellcat H domain comprises one or more unique structural alpha helical bundles that align along the target DNA:guide RNA channel. In some embodiments, in a CasX comprising a helical II domain, the target strand and guide RNA interact with helical H (and the helical I domain, in sonic embodiments) to allow RuvC domain access to the target DNA. The helical II domain is responsible for binding to the guide RNA scaffold stem loop as well as the bound DNA. In some embodiments, an exemplary helical H domain comprises amino acids 333-509 of SEQ ID NO: 1, or amino acids 334-501 of SEQ ID NO: 2.
• e. Oligonucleotide Binding Domain
• The reference CasX proteins of the disclosure comprise an Oligonucleotide Binding Domain (OBD). Certain Cas proteins other than CasX have domains that may be named in a similar way. However, in some embodiments, the OBD comprises one or more unique functional features, or comprises a sequence unique to a CasX protein, or a combination thereof For example, in some embodiments the bridged helix (BH), helical I domain, helical II domain, and Oligonucleotide Binding Domain (OBD) together are responsible for binding of a CasX protein to the guide RNA. Thus, for example, in some embodiments the OBD is unique to a CasX protein in that it interacts functionally with a helical I domain, or a helical II domain, or both, each of which may be unique to a CasX protein as described herein. Specifically, in CasX the OBD largely binds the RNA triplex of the guide RNA scaffold. The OBD may also be responsible for binding to the protospacer adjacent motif (PAM). An exemplary OBD domain comprises amino acids 1-56 and 510-660 of SEQ ID NO: 1. or amino acids 1-58 and 502-647 of SEQ ID NO: 2.
• f. RuvC DNA Cleavage Domain
• The reference CasX proteins of the disclosure comprise a RuvC domain, that includes 2 partial RuvC domains (RuvC-I and RuvC-H). The RuvC domain is the ancestral domain of all type 12 CRISPR proteins. The RuvC domain originates from a TNPB (transposase B) like transposase. Similar to other RuvC domains, the CasX RuvC domain has a DED catalytic triad that is responsible for coordinating a magnesium (Mg) ion and cleaving DNA. In some embodiments, the RuvC has a DED motif active site that is responsible for cleaving both strands of DNA (one by one, most likely the non-target strand first at 1144 nucleotides (nt) into the targeted sequence and then the target strand next at 2-4 nucleotides after the target sequence). Specifically in CasX, the RuvC domain is unique in that it is also responsible for binding the guide RNA scaffold stem loop that is critical for CasX function. An exemplary RuvC domain comprises amino acids 661-824 and 935-986 of SEQ ID NO: 1, or amino acids 648-812 and 922-978 of SEQ ID NO: 2.
• g. Reference CasX Proteins
• The disclosure provides reference CasX proteins. In some embodiments, a reference CasX protein is a naturally-occurring protein. For example, reference CasX proteins can be isolated from naturally occurring prokaryotes, such as Deltaproteobacteria, Planctomycetes, or Candidatus sungbacteria species. A reference CasX protein (sometimes referred to herein as a reference CasX polypeptide) is a type II CRISPR/Cas endonuclease belonging to the CasX (sometimes referred to as Cas12e) family of proteins that is capable of interacting with a guide NA to form a ribonucleoprotein (RNP) complex. In some embodiments, the RNP complex comprising the reference CasX protein can be targeted to a particular site in a target nucleic acid via base pairing between the targeting sequence (or spacer) of the gNA and a target sequence in the target nucleic acid. In some embodiments, the RNP comprising the reference CasX protein is capable of cleaving target DNA. In some embodiments, the RNP comprising the reference CasX protein is capable of nicking target DNA. In some embodiments, the RNP comprising the reference CasX protein is capable of editing target DNA, for example in those embodiments where the reference CasX protein is capable of cleaving or nicking DNA, followed by non-homologous end joining (NHEJ), homology-directed repair (HDR), homology-independent targeted integration (HITI). micro-homology mediated end joining (MMEJ), single strand annealing (SSA) or base excision repair (BER). In some embodiments, the RNP comprising the CasX protein is a catalytically dead (is catalytically inactive or has substantially no cleavage activity) CasX protein (dCasX), but retains the ability to bind the target DNA, described more fully, supra.
• In some cases, a reference CasX protein is isolated or derived from Deltaproteobacteria. In some embodiments, a CasX protein comprises a sequence at least 50% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at leas 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical or 100% identical to a sequence of:

• (SEQ ID NO: 1)

  1	MEKRINKIRK KLSADNATKP VSRSGPMKTL LVRVMTDDLK KRLEKRRKKP EVMPQVISNN
  61	AANNLRMLLD DYTKMKEAIL QVYWQEFKDD HVGLMCKFAQ PASKKIDQNK LKPEMDEKGN
  121	LTTAGFACSQ CGQPLFVYKL EQVSEKGKAY TNYFGRCNVA EHEKLILLAQ LKPEKDSDEA
  181	VTYSLGKFGQ RALDFYSIGV TKESTHPVKP LAQIAGNRYA SGPVGKALSD ACMGTIASFL
  241	SKYQDIIIEH QKVVKGNQKR LESLRELAGK ENLEYPSVTL PPQPGTKEGV DAYNEVIARV
  301	RMWVNLNLWQ LKLKSRDDAK PLLRLKGFPS FPVVERRENE VDWWNTINEV KKLIDAKRDM
  361	GRVFWSGVTA EKRNTILEGY NYLPNENDHK KREGSLENPK KPAKRQFGDL LLYLEKKYAG
  421	DWGKVFDEAW ERIDKKIAGL TSHIEREEAR NAEDAQSKAV LTDWLRAKAS FVLERLKEMD
  481	EKEFYACEIQ LQKWYGDLRG NPFAVEAENR VVDISGFSIG SDGHSIQYRN LLAWKYLENG
  541	KREFYLLMNY GKKGRIRFTD GTDIKKSGKW QGLLYGGGKA KVIDLTFDPD DEQLIILPLA
  601	PGTRQGREFI WNDLLSLETG LIKLANGRVI EKTIYNKKIG RDEPALFVAL TFERREVVDP
  661	SNIKPVNLIG VDRGENIPAV IALTDPEGCP LPEFKDSSGG PTDILRIGEG YKEKQRAIAQ
  721	AKEVEQRRAG GYSRKFASKS RNLADDMVRN SARDLFYHAV THDAVLVFEN LSRGFGRQGK
  781	FTFMTERQYT KMEDWLTAKL AYEGLTSKTY LSKTLAQYTS KTCSNCGFTI TTADYDGMLV
  841	RLKKTSDGWA TTLNNKELKA EGQITYYNRY KRQTVEKELS AELDRLSEES GNNDISKWTK
  901	GRRDEALFLL KKRFSHRPVQ EQFVCLDCGH EVHADEQAAL NIARSWLFLN SNSTEFKSYK
  961	SGKQPFVGAW QAFYKRRLKE WVKPNA.

• In some cases, a reference CasX protein is isolated or derived from Planctomycetes. In some embodiments, a CasX protein comprises a sequence at least 50% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical. at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical or 100% identical to a sequence of:

• (SEQ ID NO: 2)

  1	MQEIKRINKI RRRLVKDSNT KKAGKTGPMK TLLVRVMTPD LRERLENLRK KPENIPQPIS
  61	NTSRANLNKL LTDYTEMKKA ILHVYWEEFQ KDPVGLMSRV AQPAPKNIDQ RKLIPVKDGN
  121	ERLTSSGFAC SQCCQPLYVY KLEQVNDKGK PHTNYFGRCN VSEHERLILL SPHKPEANDE
  181	LVTYSLGKFG QRALDFYSIH VTRESNHPVK PLEQIGGNSC ASGPVGKALS DACMGAVASF
  241	LTKYQDIILE HQKVIKKNEK RLANLKDIAS ANGLAFPKIT LPPQPHTKEG IEAYNNVVAQ
  301	IVIWVNLNLW QKLKIGRDEA KPLQRLKGFP SFPLVERQAN EVDWWDMVCN VKKLINEKKE
  361	DGKVFWQNLA GYKRQEALLP YLSSEEDRKK GKKFARYQFG DLLLHLEKKH GEDWGKVYDE
  421	AWERIDKKVE GLSKHIKLEE ERRSEDAQSK AALTDWLRAK ASFVIEGLKE ADKDEFCRCE
  481	LKLQKWYGDL RGKPFAIEAE NSILDISGFS KQYNCAFIWQ KDGVKKLNLY LIINYFKGGK
  541	LRFKKIKPEA FEANRFYTVI NKKSGEIVPM EVNFNFDDPN LIILPLAFGK RQGREFIWND
  601	LLSLETGSLK LANGRVIEKT LYNRRTRQDE PALFVALTFE RREVLDSSNI KPMNLIGIDR
  661	GENIPAVIAL TDPEGCPLSR FKDSLGNPTH ILRIGESYKE KQRTIQAAKE VEQRRAGGYS
  721	RKYASKAKNL ADDMVRNTAR DLLYYAVTQD AMLIFENLSR GFGRQGKRTF MAERQYTRME
  781	DWLTAKLAYE GLPSKTYLSK TLAQYTSKTC SNCGFTITSA DYDRVLEKLK KTATGWMTTI
  841	NGKELKVEGQ ITYYNRYKRQ NVVKDLSVEL DRLSEESVNN DISSWTKGRS GEALSLLKKR
  901	FSHRPVQEKF VCLNCGFETH ADEQAALNIA RSWLFLRSQE YKKYQTNKTT GNTDKRAFVE
  961	TWQSFYRKKL KEVWKPAV.

• In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 2, or at least 60% similarity thereto. In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 2, or at least 80% similarity thereto. In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 2, or at least 90% similarity thereto. In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 2, or at least 95% similarity thereto. In some embodiments, the CasX protein consists of the sequence of SEQ ID NO: 2, In some embodiments, the CasX protein comprises or consists of a sequence that has at least 1, at least 2, at least 3, at least 4, at least 5. at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 30, at least 40 or at least 50 mutations relative to the sequence of SEQ ID NO: 2. These mutations can be insertions, deletions, amino acid substitutions, or any combinations thereof.
• In some cases, a reference CasX protein is isolated or derived from Candidatus sungbacteria. In some embodiments, a CasX protein comprises a sequence at least 50% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical or 100% identical to a sequence of

• (SEQ ID NO: 3)

  1	MDNANKPSTK SLVNTTRISD HFGVTPGQVT RVFSFGIIPT KRQYAIIERW FAAVEAARER
  61	LYGMLYAHFQ ENPPAYLKEK FSYETFFKGR PVLNGLRDID PTIMTSAVFT ALRHKAEGAM
  121	AAFHTNHRRL FEEARKKMRE YAECLKANEA LLRGAADIDW DKIVNALRTR LNTCLAPEYD
  181	AVIADFGALC AFRALIAETN ALKGAYNHAL NQMLPALVKV DEPEEAEESP RLRFFNGRIN
  241	DLPKFPVAER ETPPDTETII RQLEDMARVI PDTAEILGYI HRIRHKAARR KPGSAVPLPQ
  301	RVALYCAIRM ERNPEEDPST VAGHFLGEID RVCEKRRQGL VRTPFDSQIR ARYMDIISFR
  361	ATLAHPDRWT EIQFLRSNAA SRRVRAETIS APFEGFSWTS NRTNPAPQYG MALAKDANAP
  421	ADAPELCICL SPSSAAFSVR EKGGDLIYMR PTGGRRGKDN PGKEITWVPG SFDEYPASGV
  481	ALKLRLYFGR SQARRMLTNK TWGLLSDNPR VFAANAELVG KKRNPQDRWK LFFHMVISGP
  541	PPVEYLDFSS DVRSRARTVI GINRGEVNPL AYAVVSVEDG QVLEEGLLGK KEYIDQLIET
  601	RRRISEYQSR EQTPPRDLRQ RVRHLQDTVL GSARAKIHSL IAFWKGILAI ERLDDQFHGR
  661	EQKIIPKKTY LANKTGFMNA LSFSGAVRVD KKGNPWGGMI EIYPGGISRT CTQCGTVWLA
  721	RRPKNPGHRD AMVVIPDIVD DAAATGFDNV DCDAGTVDYG ELFTLSREWV RLTPRYSRVM
  781	RGTLGDLERA IRQGDDRKSR QMLELALEPQ PQWGQFFCHR CGFNGQSDVL AATNLARRAI
  841	SLIRRLPDTD TPPTP.

• In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 3, or at least 60% similarity thereto. In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 3, or at least 80% similarity thereto. In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 3, or at least 90% similarity thereto. In some embodiments, the CasX protein comprises the sequence of SEQ ID NO: 3, or at least 95% similarity thereto. In some embodiments, the CasX protein consists of the sequence of SEQ NO: 3. In some embodiments, the CasX protein comprises or consists of a sequence that has at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 30, at least 40 or at least 50 mutations relative to the sequence of SEQ ID NO: 3. These mutations can be insertions, deletions, amino acid substitutions, or any combinations thereof.
• h. CasX Variant Proteins
• The present disclosure provides variants of a reference CasX protein (interchangeably referred to herein as “CasX variant” or “CasX variant protein”), wherein the CasX variants comprise at least one modification in at least one domain relative to the reference CasX protein, including but not limited to the sequences of SEQ NOS:1-3. In some embodiments, the CasX variant exhibits at least one improved characteristic compared to the reference CasX protein. All variants that improve one or more functions or characteristics of the CasX variant protein when compared to a reference CasX protein described herein are envisaged as being within the scope of the disclosure. In some embodiments, the modification is a mutation in one or more amino acids of the reference CasX. In other embodiments, the modification is a substitution of one or more domains of the reference CasX with one or more domains from a different CasX. In some embodiments, insertion includes the insertion of a part or all of a domain from a different Cask protein. Mutations can occur in any one or more domains of the reference CasX protein, and may include, for example, deletion of part or all of one or more domains, or one or more amino acid substitutions, deletions, or insertions in any domain of the reference CasX protein. The domains of CasX proteins include the non-target strand binding (NTSB) domain, the target strand loading (TSL) domain, the helical I domain, the helical II domain, the oligonucleotide binding domain (OBD), and the RuvC DNA cleavage domain. Any change in amino acid sequence of a reference CasX protein that leads to an improved characteristic of the CasX protein is considered a CasX variant protein of the disclosure. For example, CasX variants can comprise one or more amino acid substitutions, insertions, deletions, or swapped domains, or any combinations thereof, relative to a reference CasX protein sequence.
• In some embodiments, the CasX variant protein comprises at least one modification in at least each of two domains of the reference CasX protein, including the sequences of SEQ ID NOS: 1-3. In some embodiments, the CasX variant protein comprises at least one modification in at least 2 domains, in at least 3 domains, at least 4 domains or at least 5 domains of the reference CasX protein. In some embodiments, the CasX variant protein comprises two or more modifications in at least one domain of the reference CasX protein. In some embodiments, the CasX variant protein comprises at least two modifications in at least one domain of the reference CasX protein, at least three modifications in at least one domain of the reference CasX protein or at least four modifications in at least one domain of the reference CasX protein. In some embodiments, wherein the CasX variant comprises two or more modifications compared to a reference CasX protein, each modification is made in a domain independently selected from the group consisting of a NTSBD, TSLD, helical I domain, helical II domain, OBD, and RuvC DNA cleavage domain.
• In some embodiments, the at least one modification of the CasX variant protein comprises a deletion of at least a portion of one domain of the reference CasX protein. In some embodiments, the deletion is in the NTSBD, ISM, helical I domain, helical II domain, OBD, or RuvC DNA cleavage domain.
• Suitable mutagenesis methods for generating CasX variant proteins of the disclosure may include, for example, Deep Mutational Evolution (DME), deep mutational scanning (DMS), error prone PCR, cassette mutagenesis, random mutagenesis, staggered extension PCR. gene shuffling, or domain swapping. Exemplary methods for the generation of CasX variants with improved characteristics are provided in the Examples, below. In some embodiments, the CasX variants are designed, for example by selecting one or more desired mutations in a reference CasX. In certain embodiments, the activity of a reference CasX protein is used as a benchmark against which the activity of one or more CasX variants are compared, thereby measuring improvements in function of the CasX variants. Exemplary improvements of CasX variants include, but are not limited to, improved folding of the variant, improved binding affinity to the gNA, improved binding affinity to the target DNA, improved ability to utilize a greater spectrum of PAM sequences in the editing or binding of target DNA, improved unwinding of the target DNA, increased editing activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, improved protein stability, improved CasX:gNA (RNP) complex stability, improved protein solubility, improved CasX:gNA (RNP) complex solubility, improved protein yield, improved protein expression, and improved fusion characteristics, as described more fully, below.
• In some embodiments of the CasX variants described herein, the at least one modification comprises: (a) a substitution of 1 to 100 consecutive or non-consecutive amino acids in the CasX variant; (b) a deletion of 1 to 100 consecutive or non-consecutive amino acids in the CasX variant: (c) an insertion of 1 to 100 consecutive or non-consecutive amino acids in the CasX; or (d) any combination of (a)-(c). In some embodiments, the at least one modification comprises: (a) a substitution of 5-10 consecutive or non-consecutive amino acids in the CasX variant; (b) a deletion of 1-5 consecutive or non-consecutive amino acids in the CasX variant; (c) an insertion of 1-5 consecutive or non-consecutive amino acids in the CasX; or (d) any combination of (a)-(c).
• In some embodiments, the CasX variant protein comprises or consists of a sequence that has at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 30, at least 40 or at least 50 mutations relative to the sequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. These mutations can be insertions, deletions, amino acid substitutions, or any combinations thereof.
• In some embodiments, the CasX variant protein comprises at least one amino acid substitution in at least one domain of a reference CasX protein. In some embodiments, the CasX variant protein comprises at least about 1-4 amino acid substitutions, 1-10 amino acid substitutions, 1-20 amino acid substitutions, 1-30 amino acid substitutions. 1-40 amino acid substitutions, 1-50 amino acid substitutions, 1-60 amino acid substitutions, 1-70 amino acid substitutions, 1-80 amino acid substitutions, 1-90 amino acid substitutions, 1-100 amino acid substitutions, 2-10 amino acid substitutions, 2-20 amino acid substitutions, 2-30 amino acid substitutions, 3-10 amino acid substitutions, 3-20 amino acid substitutions, 3-30 amino acid substitutions, 4-10 amino acid substitutions, 4-20 amino acid substitutions, 3-300 amino acid substitutions, 5-10 amino acid substitutions, 5-20 amino acid substitutions, 5-30 amino acid substitutions. 10-50 amino acid substitutions, or 20-50 amino acid substitutions, relative to a reference CasX protein. In some embodiments, the CasX variant protein comprises at least about 100 amino acid substitutions relative to a reference CasX protein. In some embodiments, the CasX variant protein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid substitutions relative to a reference CasX protein. In some embodiments, the CasX variant protein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid substitutions in a single domain relative to the reference CasX protein. In some embodiments, the amino acid substitutions are conservative substitutions. In other embodiments, the substitutions are non-conservative; e.g., a polar amino acid is substituted for a non-polar amino acid, or vice versa.
• In some embodiments, a CasX variant protein comprises 1 amino acid substitution, 2-3 consecutive amino acid substitutions, 2-4 consecutive amino acid substitutions, 2-5 consecutive amino acid substitutions, 2-6 consecutive amino acid substitutions, 2-7 consecutive amino acid substitutions, 2-8 consecutive amino acid substitutions, 2-9 consecutive amino acid substitutions, 2-10 consecutive amino acid substitutions. 2-20 consecutive amino acid substitutions, 2-30 consecutive amino acid substitutions, 2-40 consecutive amino acid substitutions, 2-50 consecutive amino acid substitutions, 2-60 consecutive amino acid substitutions, 2-70 consecutive amino acid substitutions, 2-80 consecutive amino acid substitutions, 2-90 consecutive amino acid substitutions, 2-100 consecutive amino acid substitutions, 3-10 consecutive amino acid substitutions, 3-20 consecutive amino acid substitutions, 3-30 consecutive amino acid substitutions. 4-10 consecutive amino acid substitutions, 4-20 consecutive amino acid substitutions, 3-300 consecutive amino acid substitutions, 5-10 consecutive amino acid substitutions, 5-20 consecutive amino acid substitutions, 5-30 consecutive amino acid substitutions, 10-50 consecutive amino acid substitutions or 20-50 consecutive amino acid substitutions relative to a reference CasX protein. In some embodiments, a CasX variant protein comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 consecutive amino acid substitutions. In some embodiments, a CasX variant protein comprises a substitution of at least about 100 consecutive amino acids. As used herein “consecutive amino acids” refer to amino acids that are contiguous in the primary sequence of a polypeptide.
• In some embodiments, a CasX variant protein comprises two or more substitutions relative to a reference CasX protein, and the two or more substitutions are not in consecutive amino acids of the reference CasX sequence. For example, a first substitution may be in a first domain of the reference CasX protein, and a second substitution may be in a second domain of the reference CasX protein. In some embodiments, a CasX variant protein comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 non-consecutive substitutions relative to a reference CasX protein. In some embodiments, a CasX variant protein comprises at least 20 non-consecutive substitutions relative to a reference CasX protein. Each non-consecutive substitution may be of any length of amino acids described herein, e.g., 1-4 amino acids, 1-10 amino acids, and the like. In some embodiments, the two or more substitutions relative to the reference CasX protein are not the same length, for example, one substitution is one amino acid and a second substitution is three amino acids. In some embodiments, the two or more substitutions relative to the reference CasX protein are the same length, for example both substitutions are two consecutive amino acids in length.
• Any amino acid can be substituted for any other amino acid in the substitutions described herein. The substitution can be a conservative substitution (e.g., a basic amino acid is substituted for another basic amino acid). The substitution can be a non-conservative substitution (e.g., a basic amino acid is substituted for an acidic amino acid or vice versa). For example, a proline in a reference CasX protein can be substituted for any of arginine, histidine, lysine, aspartic acid, glutamic acid, serine, threonine, asparagine, glutamine, cysteine, glycine, alanine, isoleucine, leucine:, methionine, phenylalanine, tryptophan, tyrosine or valine to generate a CasX variant protein of the disclosure.
• In some embodiments, a CasX variant protein comprises at least one amino acid deletion relative to a reference CasX protein. In some embodiments, a CasX variant protein comprises a deletion of 1-4 amino acids, 1-10 amino acids, 1-20 amino acids, 1-30 amino acids, 1-40 amino acids, 1-50 amino acids, 1-60 amino acids, 1-70 amino acids, 1-80 amino acids, 1-90 amino acids, 1-100 amino acids, 2-10 amino acids, 2-20 amino acids, 2-30 amino acids, 3-10 amino acids, 3-20 amino acids, 3-30 amino acids, 4-10 amino acids, 4-20 amino acids, 3-300 amino acids, 5-10 amino acids, 5-20 amino acids, 5-30 amino acids, 10-50 amino acids or 20-50 amino acids relative to a reference CasX protein. In some embodiments, a CasX variant comprises a deletion of at least about 100 consecutive amino acids relative to a reference CasX protein. In some embodiments, a CasX variant protein comprises a deletion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50 or 100 consecutive amino acids relative to a reference CasX protein. In some embodiments, a CasX variant protein comprises a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 consecutive amino acids.
• In some embodiments, a CasX variant protein comprises two or more deletions relative to a reference CasX protein, and the two or more deletions are not consecutive amino acids. For example, a first deletion may be in a first domain of the reference CasX protein, and a second deletion may be in a second domain of the reference CasX protein. In some embodiments, a CasX variant protein comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 non-consecutive deletions relative to a reference CasX protein. In some embodiments, a CasX variant protein comprises at least 20 non-consecutive deletions relative to a reference CasX protein. Each non-consecutive deletion may be of any length of amino acids described herein, e.g., 1-4 amino acids, 1-10 amino acids, and the like.
• In some embodiments, the CasX variant protein comprises at least one amino acid insertion. In some embodiments, a CasX variant protein comprises an insertion of 1 amino acid, an insertion of 2-3 consecutive amino acids, 2-4 consecutive amino acids, 2-5 consecutive amino acids, 2-6 consecutive amino acids, 2-7 consecutive amino acids, 2-8 consecutive amino acids, 2-9 consecutive amino acids, 2-10 consecutive amino acids, 2-20 consecutive amino acids, 2-30 consecutive amino acids, 2-40 consecutive amino acids, 2-50 consecutive amino acids, 2-60 consecutive amino acids, 2-70 consecutive amino acids, 2-80 consecutive amino acids, 2-90 consecutive amino acids, 2400 consecutive amino acids, 340 consecutive amino acids, 3-20 consecutive amino acids, 3-30 consecutive amino acids, 4-10 consecutive amino acids, 4-20 consecutive amino acids, 3-300 consecutive amino acids, 5-10 consecutive amino acids, 5-20 consecutive amino acids, 5-30 consecutive amino acids, 10-50 consecutive amino acids or 20-50 consecutive amino acids relative to a reference CasX protein. In some embodiments, the CasX variant protein comprises an insertion of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 consecutive amino acids. In some embodiments, a CasX variant protein comprises an insertion of at least about 100 consecutive amino acids.
• In some embodiments, a CasX variant protein comprises two or more insertions relative to a reference CasX protein, and the two or more insertions are not consecutive amino acids of the sequence. For exainpie, a first insertion may be in a first domain of the reference CasX protein, and a second insertion may be in a second domain of the reference CasX protein. in some embodiments, a CasX variant protein comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 non-consecutive insertions relative to a reference CasX protein. In some embodiments, a CasX variant protein comprises at least 10 to about 20 or more non-consecutive insertions relative to a reference CasX protein. Each non-consecutive insertion may be of any length of amino acids described herein, e.g., 1-4 amino acids, 1-10 amino acids, and the like.
• Any amino acid, or combination of amino acids, can be inserted as described herein. For example, a proline, arginine, histidine, lysine, aspartic acid, glutamic acid, serine, threonine, asparagine, glutamine, cysteine, glycine, alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, tyrosine or valine or any combination thereof can be inserted into a reference CasX protein of the disclosure to generate a CasX variant protein.
• Any permutation of the substitution, insertion and deletion embodiments described herein can be combined to generate a CasX variant protein of the disclosure. For example, a CasX variant protein can comprise at least one substitution and at least one deletion relative to a reference CasX protein sequence, at least one substitution and at least one insertion relative to a reference CasX protein sequence, at least one insertion and at least one deletion relative to a reference CasX protein sequence, or at least one substitution, one insertion and one deletion relative to a reference CasX protein sequence.
• In some embodiments, the CasX variant protein has at least about 60% sequence similarity, at least 70% similarity, at least 80% similarity, at least 85% similarity, at least 86% similarity, at least 87% similarity, at least 88% similarity, at least 89% similarity, at least 90% similarity, at least 91% similarity, at least 92% similarity, at least 93% similarity, at least 94% similarity, at least 95% similarity, at least 96% similarity, at least 97% similarity, at least 98% similarity, at least 99% similarity, at least 99.5% similarity, at least 99.6% similarity, at least 99.7% similarity, at least 99.8% similarity or at least 99.9% similarity to one of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• In some embodiments, the CasX variant protein has at least about 60% sequence similarity to SEQ ID NO: 2 or a portion thereof. In some embodiments, the CasX variant protein comprises a substitution of Y789T of SEQ ID NO: 2, a deletion of P793 of SEQ II) NO: 2, a substitution of Y789D of SEQ ID NO: 2, a substitution of T72S of SEQ ID NO: 2, a substitution of I546V of SEQ ID NO: 2, a substitution of E552A of SEQ ID NO: 2, a substitution of A636D of SEQ ID NO: 2, a substitution of F536S SEQ ID NO: 2, a substitution of A708K ref SEQ ID NO: 2, a substitution of Y797L of SEQ ID NO: 2, a substitution of L792G SEQ ID NO: 2, a substitution of A739V of SEQ ID NO: 2, a substitution of G791M of SEQ ID NO: 2, an insertion of A at position 661 of SEQ ID NO: 2, a substitution of A788W of SEQ ID NO: 2, a substitution of K390R of SEQ ID NO: 2, a substitution of A751S of SEQ ID NO: 2, a substitution of E385A of SEQ ID NO: 2, an insertion of P at position 696 of SEQ ID NO: 2, an insertion of M at position 773 of SEQ ID NO: 2, a substitution of G695H of SEQ ID NO: 2, an insertion of AS at position 793 of SEQ ID NO: 2, an insertion of AS at position 795 of SEQ ID NO: 2, a substitution of C477R of SEQ ID NO: 2, a substitution of C477K of SEQ ID NO: 2, a substitution of C479A of SEQ ID NO: 2, a substitution of C479L, of SEQ ID NO: 2, a substitution of I55F of SEQ ID NO: 2, a substitution of K210R of SEQ ID NO: 2, a substitution of C2335 of SEQ ID NO: 2, a substitution of D23IN of SEQ ID NO: 2, a substitution of Q338E of SEQ ID NO: 2, a substitution of Q338R of SEQ ID NO: 2, a substitution of L379R of SEQ ID NO: 2, a substitution of K390R of SEQ ID NO: 2, a substitution of L481Q of SEQ ID NO: 2, a substitution of F495S of SEQ ID NO:2, a substitution of D600N of SEQ ID NO: 2, a substitution of T886K of SEQ ID NO: 2, a substitution of A739V of SEQ ID NO: 2, a substitution of K460N of SEQ ID NO: 2, a substitution of I199F of SEQ ID NO: 2, a substitution of G492P of SEQ ID NO: 2, a substitution of T153I of SEQ ID NO: 2, a substitution of R591I of SEQ ID NO: 2, an insertion of AS at position 795 of SEQ ID NO: 2, an insertion of AS at position 796 of SEQ ID NO:2, an insertion of L at position 889 of SEQ ID NO: 2, a substitution of E121D of SEQ m NO: 2, a substitution of S270W of SEQ ID NO: 2, a substitution of E712Q of SEQ ID NO: 2, a substitution of K942Q of SEQ ID NO: 2, a substitution of E552K of SEQ ID NO:2, a substitution of K25Q of SEQ ID NO: 2, a substitution of N47D of SEQ ID NO: 2. an insertion of T at position 696 of SEQ ID NO: 2, a substitution of L685I of SEQ ID NO: 2, a substitution of N880D of SEQ ID NO: 2, a substitution of Q102R of SEQ ID NO: 2, a substitution of M734K of SEQ II) NO: 2. a substitution of A724S of SEQ ID NO: 2, a substitution of T704K of SEQ NO: 2, a substitution of P224K of SEQ ID NO: 2, a substitution of K25R of SEQ ID NO: 2, a substitution of M29E of SEQ ID NO: 2, a substitution of H152D of SEQ ID NO: 2, a substitution of S219R of SEQ ID NO: 2, a substitution of E475K of SEQ ID NO: 2, a substitution of G226R of SEQ ID NO: 2, a substitution of A.3 77K of SEQ ID NO: 2, a substitution of E480K of SEQ ID NO: 2, a substitution of K416E of SEQ ID NO: 2, a substitution of H164R of SEQ ID NO: 2, a substitution of K767R of SEQ ID NO: 2, a substitution of 17F cif SEQ ID NO: 2, a substitution of M29R of SEQ ID NO: 2, a substitution of H435R of SEQ II) NO: 2. a substitution of E385Q of SEQ ID NO: 2, a substitution of E385K of SEQ ID NO: 2, a substitution of I279F of SEQ ID NO: 2, a substitution of D4895 of SEQ ID NO: 2, a substitution of D732N of SEQ ID NO: 2, a substitution of A739T of SEQ ID NO: 2, a substitution of W885R of SEQ ID NO: 2, a substitution of E53K of SEQ ID NO: 2, a substitution of A238T of SEQ ID NO: 2, a substitution of P283Q of SEQ ID NO: 2, a substitution of E292K of SEQ ID NO: 2, a substitution of Q628E of SEQ ID NO: 2, a substitution of R388Q of SEQ ID NO: 2, a substitution of G791M of SEQ ID NO: 2, a substitution of L792K of SEQ ID NO: 2, a substitution of L792E of SEQ ID NO: 2, a substitution of M779N of SEQ ID NO: 2, a substitution of G27D of SEQ ID NO: 2, a substitution of K955R of SEQ ID NO: 2, a substitution of S867R of SEQ ID NO: 2, a substitution of R693I of SEQ ID NO: 2, a substitution of F189Y of SEQ ID NO: 2, a substitution of V635M of SEQ ID NO: 2, a substitution of F399L of SEQ ID NO: 2, a substitution of E498K of SEQ ID NO: 2, a substitution of E386R of SEQ ID NO: 2, a substitution of V254G of SEQ ID NO: 2, a substitution of P793S of SEQ ID NO: 2, a substitution of K188E of SEQ ID NO: 2, a substitution of QT945KI of SEQ ID NO: 2, a substitution of T620P of SEQ ID NO: 2, a substitution of T946P of SEQ ID NO: 2, a substitution of TT949PP of SEQ ID NO: 2, a substitution of N952T of SEQ ID NO: 2, a substitution of K682E cif SEQ ID NO: 2, a substitution of K975R of SEQ ID NO: 2, a substitution of L212P of SEQ ID NO: 2, a substitution of E292R of SEQ ID NO: 2, a substitution of I303K of SEQ ID NO: 2, a substitution of C349E of SEQ ID NO: 2, a substitution of E385P of SEQ ID NO: 2, a substitution of E386N of SEQ ID NO: 2, a substitution of D387K of SEQ ID NO: 2, a substitution of L404K of SEQ ID NO: 2, a substitution of E466H of SEQ ID NO: 2, a substitution of C477Q of SEQ ID NO: 2, a substitution of C477H of SEQ ID NO: 2, a substitution of C479A of SEQ ID NO: 2, a substitution of D659H of SEQ ID NO: 2, a substitution of T806V of SEQ ID NO: 2, a substitution of K808S of SEQ ID NO: 2, an insertion of AS at position 797 of SEQ ID NO: 2, a substitution of V959M of SEQ ID NO: 2, a substitution of K975Q of SEQ ID NO: 2, a substitution of W974G of SEQ ID NO: 2, a substitution of A708Q of SEQ ID NO: 2, a substitution of V711K of SEQ ID NO: 2, a substitution of D733T of SEQ ID NO: 2, a substitution of L742W of SEQ ID NO: 2, a substitution of V747K of SEQ ID NO: 2, a substitution of F755M of SEQ ID NO: 2, a substitution of M771A of SEQ ID NO: 2, a substitution of M771Q of SEQ ID NO: 2, a substitution of W782Q of SEQ ID NO: 2, a substitution of G791F, cif SEQ ID NO: 2 a substitution of L792D of SEQ ID NO: 2, a substitution of L792K of SEQ ID NO: 2, a substitution of P793Q of SEQ ID NO: 2, a substitution of P793G of SEQ ID NO: 2, a substitution of Q804A of SEQ ID NO: 2, a substitution of Y966N of SEQ ID NO: 2, a substitution of Y723N of SEQ II) NO: 2, a substitution of Y857R of SEQ II) NO: 2, a substitution of S890R of SEQ ID NO: 2, a substitution of S932M of SEQ ID NO: 2, a substitution of L897M of SEQ ID NO: 2, a substitution of R624G of SEQ ID NO: 2, a substitution of S603G of SEQ ID NO: 2, a substitution of N737S ref SEQ ID NO: 2, a substitution of L307K of SEQ ID NO: 2, a substitution of I658V of SEQ ID NO: 2, an insertion of PT at position 688 of SEQ ID NO: 2, an insertion of SA at position 794 of SEQ ID NO: 2, a substitution of S877R of SEQ ID NO: 2, a substitution of N580T of SEQ ID NO: 2, a substitution of V335G of SEQ NO: 2, a substitution of T620S of SEQ ID NO: 2, a substitution of W345G of SEQ ID NO: 2, a substitution of T280S of SEQ ID NO: 2, a substitution of L406P of SEQ ID NO: 2, a substitution of A612D of SEQ ID NO: 2, a substitution of A751S of SEQ ID NO: 2, a substitution of E386R of SEQ ID NO: 2, a substitution of V351M of SEQ ID NO: 2, a substitution of K210N of SEQ ID NO: 2, a substitution of D40A of SEQ ID NO: 2, a substitution of E773R of SEQ ID NO: 2, a substitution of H207L of SEQ ID NO: 2, a substitution of T62A SEQ ID NO: 2, a substitution of T287P of SEQ ID NO: 2, a substitution of T832A of SEQ ID NO: 2, a substitution of A893S of SEQ NO: 2, an insertion of V at position 14 of SEQ ID NO: 2, an insertion of AG at position 13 of SEQ ID NO: 2, a substitution of R11V of SEQ ID NO: 2, a substitution of R12N of SEQ ID NO: 2, a substitution of R13H of SEQ ID NO: 2, an insertion of Y at position 13 of SEQ ID NO: 2, a substitution of R 12 L of SEQ ID NO: 2, an insertion of Q at position 13 of SEQ ID NO: 2, an substitution of V15S of SEQ ID NO: 2, an insertion of D at position 17 of SEQ ID NO: 2 or a combination thereof.
• In some embodiments, the CasX variant comprises at least one modification in the NTSB domain.
• In some embodiments, the CasX variant comprises at least one modification in the TSL domain. In some embodiments, the at least one modification in the TSL domain comprises an amino acid substitution of one or more of amino acids Y857, S890, or S932 of SEQ ID NO: 2.
• In some embodiments, the CasX variant comprises at least one modification in the helical I domain. In some embodiments, the at least one modification in the helical I domain comprises an amino acid substitution of one or more of amino acids S219, L249, E259, Q252, E292, L307, or D318 of SEQ ID NO: 2.
• In some embodiments, the CasX variant comprises at least one modification in the helical II domain. In some embodiments, the at least one modification in the helical II domain comprises an amino acid substitution of one or more of amino acids D361, L379, E385, E386, D387, F399, L404, R458, C477, or D489 of SEQ ID NO: 2.
• In some embodiments, the CasX variant comprises at least one modification in the OBD domain. In some embodiments, the at least one modification in the OBD comprises an amino acid substitution of one or more of amino acids F536, E552, T620, or I658 of SEQ ID NO: 2.
• In some embodiments, the CasX variant comprises at least one modification in the RuvC DNA cleavage domain. In some embodiments, the at least one modification in the RuvC DNA cleavage domain comprises an amino acid substitution of one or more of amino acids K682, G695, A708, V711, D732, A739, D733, L742, V747, F755, M771, M779, W782, A788, G791, L792, P793, Y797, M799, Q804, S819, or Y857 or a deletion of amino acid P793 of SEQ ID NO: 2.
• In some embodiments, the CasX variant comprises at least one modification compared to the reference CasX sequence of SEQ ID NO: 2 is selected from one or more of: (a.) an amino acid substitution of L379R; (h) an amino acid substitution of A708K; (c) an amino acid substitution of T620P; (d) an amino acid substitution of E385P; (e) an amino acid substitution of Y857R; (f) an amino acid substitution of I658V; (g) an amino acid substitution of F399L; (h) an amino acid substitution of Q252K; (i) an amino acid substitution of L404K; and (j) an amino acid deletion of P793.
• In some embodiments, a CasX variant protein comprises at least two amino acid changes to a reference CasX protein amino acid sequence. The at least two amino acid changes can be substitutions, insertions, or deletions of a reference CasX protein amino acid sequence, or any combination thereof. The substitutions, insertions or deletions can be any substitution, insertion or deletion in the sequence of a reference CasX protein described herein. In some embodiments, the changes are contiguous, non-contiguous, or a combination of contiguous and non-contiguous amino acid changes to a reference CasX protein sequence. In some embodiments, the reference CasX protein is SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises at least 2, at least 3, at least 4, at least 5. at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95 or at least 100 amino acid changes to a. reference CasX protein sequence. In some embodiments, a CasX variant protein comprises 1-50, 3-40, 5-30, 5-20, 5-15, 5-10, 10-50, 10-40, 10-30, 10-20, 15-50, 15-40, 15-30, 2-25, 2-24, 2-22, 2-23, 2-22, 2-21, 2-20, 2-19, 2-18, 2-17, 2-16, 2-15, 2-14, 2-12, 2-11, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4, 2-3, 3-25, 3-24, 3-22, 3-23, 3-22, 3-21, 3-20, 3-19, 3-18, 3-17, 3-16, 3-15, 3-14, 3-12, 3-11, 3-10, 3-9, 3-8, 3-7, 3-6, 3-5, 3-4, 4-25, 4-24, 4-22, 4-23, 4-22, 4-21, 4-20, 4-19, 4-18, 4-17, 4-16, 4-15, 4-14, 4-12, 4-11, 4-10, 4-9, 4-8, 4-7, 4-6, 4-5, 5-25, 5-24, 5-22, 5-23, 5-22, 5-21, 5-20, 5-19, 5-18, 5-17, 5-16, 5-15, 5-14, 5-12 5-11, 5-10, 5-9, 5-8, 5-7 or 5-6 amino acid changes to a reference CasX protein sequence. In some embodiments, a CasX variant protein comprises 15-20 changes to a reference CasX protein sequence. In some embodiments, a CasX variant protein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 amino acid changes to a reference CasX protein sequence. In some embodiments, the at least two amino acid changes to the sequence of a reference CasX variant protein are selected from the group consisting of a substitution of Y789T of SEQ ID NO: 2, a deletion of P793 of SEQ ID NO: 2, a substitution of Y789D of SEQ ID NO: 2, a substitution of T72S of SEQ ID NO: 2, a substitution of I546V of SEQ ID NO: 2, a substitution of E552A of SEQ ID NO: 2, a substitution of A636D of SEQ ID NO: 2, a substitution of F536S of SEQ ID NO:2, a substitution of A708K of SEQ ID NO: 2, a substitution of Y797L of SEQ ID NO: 2, a substitution of L792G SEQ ID NO: 2, a substitution of A739V of SEQ ID NO: 2. a substitution of G791M of SEQ ID NO: 2, an insertion of A at position 661of SEQ ID NO: 2, a substitution of A788W SEQ ID NO: 2, a substitution of K390R of SEQ ID NO: 2, a substitution of A751S of SEQ ID NO: 2, a substitution of E385A of SEQ ID NO: 2, an insertion of P at position 696 of SEQ ID NO: 2, an insertion of M at position 773 of SEQ ID NO: 2, a substitution of G695H of SEQ ID NO: 2, an insertion of AS at position 793 of SEQ ID NO: 2, an insertion of AS at position 795 of SEQ ID NO: 2, a substitution of C477R of SEQ ID NO: 2, a substitution of C477K of SEQ ID NO: 2, a substitution of C479A of SEQ ID NO: 2, a substitution of C479L of SEQ ID NO: 2, a substitution of I55F of SEQ ID NO: 2, a substitution of K210R of SEQ ID NO: 2, a substitution of C233S of SEQ ID NO: 2, a substitution of D23 IN of SEQ ID NO: 2, a substitution of Q338E of SEQ ID NO: 2, a substitution of Q338R of SEQ ID NO: 2, a substitution of L379R of SEQ ID NO: 2, a substitution of K390R of SEQ ID NO: 2, a substitution of L481Q of SEQ ID NO: 2, a substitution of F495S of SEQ ID NO:2, a substitution of D600N of SEQ ID NO: 2, a substitution of1886K of SEQ ID NO: 2, a substitution of A739V of SEQ ID NO: 2, a substitution of K460N of SEQ ID NO: 2, a substitution of I199F of SEQ ID NO: 2, a substitution of G492P of SEQ ID NO: 2, a substitution of T153I of SEQ ID NO: 2, a substitution of R5911 of SEQ ID NO: 2, an insertion of AS at position 795 of SEQ ID NO: 2, an insertion of AS at position 796 of SEQ ID NO:2, an insertion of L at position 889 of SEQ ID NO: 2, a substitution of E121D of SEQ ID NO: 2, a substitution of S270W of SEQ ID NO: 2, a substitution of E712Q of SEQ ID NO: 2, a substitution of K942Q of SEQ ID NO: 2, a substitution of E552K of SEQ ID NO:2, a substitution of K25Q of SEQ ID NO: 2, a substitution of N47D of SEQ ID NO: 2, an insertion of T at position 696 of SEQ ID NO: 2, a substitution of L685I of SEQ ID NO: 2, a substitution of N880D of SEQ ID NO: 2, a substitution of Q102R of SEQ ID NO: 2, a substitution of M734K of SEQ ID NO: 2, a substitution of A724S of SEQ ID NO: 2, a substitution of T704K of SEQ ID NO: 2, a substitution of P224K of SEQ ID NO: 2, a substitution of K25R of SEQ ID NO: 2, a substitution of M29E of SEQ ID NO: 2, a substitution of H152D of SEQ ID NO: 2, a substitution of S219R of SEQ ID NO: 2, a substitution of E475K of SEQ ID NO: 2, a substitution of G226R of SEQ ID NO: 2, a substitution of A377K of SEQ ID NO: 2, a substitution of E480K of SEQ ID NO: 2, a substitution of K416E of SEQ II) NO: 2, a substitution of II164R of SEQ ID NO: 2, a substitution of K767R of SEQ ID NO: 2, a substitution of I7F of SEQ ID NO: 2, a substitution of M29R of SEQ ID NO: 2, a substitution of H435R of SEQ ID NO: 2. a substitution of E385Q of SEQ ID NO: 2, a substitution of E385K of SEQ ID NO: 2, a substitution of I279F of SEQ NO: 2, a substitution of D4895 of SEQ ID NO: 2, a substitution of D732N of SEQ ID NO: 2, a substitution of A739T of SEQ ID NO: 2, a substitution of W885R of SEQ ID NO: 2, a substitution of E53K of SEQ ID NO: 2. a substitution of A238T of SEQ ID NO: 2, a substitution of P283Q of SEQ ID NO: 2, a substitution of E292K of SEQ ID NO: 2, a substitution of Q628E of SEQ ID NO: 2, a substitution of R388Q of SEQ ID NO: 2, a substitution of G79IM of SEQ ID NO: 2, a substitution of L792K of SEQ ID NO: 2, a substitution of L792E of SEQ ID NO: 2, a substitution of M779N of SEQ ID NO: 2, a substitution of G27D of SEQ ID NO: 2, a substitution of K955R of SEQ ID NO: 2, a substitution of S867R of SEQ ID NO: 2, a substitution of R693I of SEQ ID NO: 2, a substitution of F189Y of SEQ ID NO: 2, a substitution of V635M of SEQ ID NO: 2, a substitution of F399L of SEQ ID NO: 2, a substitution of E498K of SEQ ID NO: 2, a substitution of E386R of SEQ ID NO: 2, a substitution of V254G of SEQ ID NO: 2, a substitution of P793S of SEQ ID NO: 2, a substitution of K188E of SEQ ID NO: 2, a substitution of QT945KI of SEQ ID NO: 2, a substitution of T620P of SEQ ID NO: 2, a substitution of T946P of SEQ ID NO: 2, a substitution of TT949PP of SEQ ID NO: 2, a substitution of N952T of SEQ ID NO: 2, a substitution of K682E of SEQ ID NO: 2, a substitution of K975R of SEQ ID NO: 2, a substitution of L212P of SEQ ID NO: 2, a substitution of E292R of SEQ ID NO: 2, a substitution of 1303K of SEQ ID NO: 2, a substitution of C349E of SEQ ID NO: 2, a substitution of E385P of SEQ ID NO: 2, a substitution of E386N of SEQ ID NO: 2, a substitution of D387K of SEQ ID NO: 2, a substitution of L404K of SEQ ID NO: 2, a substitution of E466H cif SEQ ID NO: 2, a substitution of C4177Q of SEQ ID NO: 2, a substitution of C477H of SEQ ID NO: 2, a substitution of C479A of SEQ ID NO: 2, a substitution of D659H of SEQ ID NO: 2, a substitution of T806V of SEQ ID NO: 2, a substitution of K808S of SEQ ID NO: 2, an insertion of AS at position 797 of SEQ ID NO: 2, a substitution of V959M of SEQ ID NO: 2, a substitution of K975Q of SEQ ID NO: 2, a substitution of W974G of SEQ ID NO: 2, a substitution of A708Q of SEQ ID NO: 2, a substitution of V711K of SEQ ID NO: 2, a substitution of D733T of SEQ ID NO: 2, a substitution of L742W of SEQ ID NO: 2, a substitution of V747K of SEQ ID NO: 2, a substitution of F755M of SEQ ID NO: 2, a substitution of M771A of SEQ ID NO: 2, a substitution of M771Q of SEQ ID NO: 2, a substitution of W782Q of SEQ ID NO: 2, a substitution of G791F, of SEQ ID NO: 2 a substitution of L792D of SEQ ID NO: 2, a substitution of L792K of SEQ ID NO: 2, a substitution of P793Q of SEQ ID NO: 2, a substitution of P793G of SEQ ID NO: 2, a substitution of Q804A of SEQ ID NO: 2, a substitution of Y966N of SEQ ID NO: 2, a substitution of Y723N of SEQ ID NO: 2, a substitution of Y857R of SEQ ID NO: 2, a substitution of S890R of SEQ ID NO: 2, a substitution of S932I of SEQ ID NO; 2, a substitution of L897M of SEQ ID NO: 2, a substitution of R624G of SEQ ID NO: 2, a substitution of S603G of SEQ ID NO: 2, a substitution of N7375 of SEQ ID NO: 2, a substitution of L307K of SEQ ID NO: 2, a substitution of I658V SEQ ID NO: 2, an insertion of PT at position 688 of SEQ ID NO: 2, an insertion of SA at position 794 of SEQ ID NO: 2, a substitution of S877R of SEQ ID NO: 2, a substitution of N580T of SEQ ID NO: 2, a substitution of V335G of SEQ ID NO: 2, a substitution of T620S of SEQ ID NO: 2, a substitution of W345G of SEQ ID NO: 2, a substitution of T280S of SEQ ID NO: 2, a substitution of L406P of SEQ ID NO: 2, a substitution of A612D of SEQ ID NO: 2, a substitution of A751S of SEQ ID NO: 2, a substitution of E386R. of SEQ ID NO: 2, a substitution of V351M of SEQ ID NO: 2, a substitution of K210N of SEQ ID NO: 2, a substitution of D40A of SEQ II) NO: 2, a substitution of E773G of SEQ ID NO: 2, a substitution of H207L of SEQ ID NO: 2, a substitution of T62A SEQ ID NO: 2, a substitution of T287P of SEQ ID NO: 2, a substitution of T832A of SEQ ID NO: 2, a substitution of A893S of SEQ ID NO: 2, an insertion of V at position 14 of SEQ ID NO: 2, an insertion of AG at position 13 of SEQ ID NO: 2, a substitution of R11V of SEQ ID NO: 2, a substitution of R12N of SEQ ID NO: 2, a substitution of R13H of SEQ ID NO: 2, an insertion of Y at position 13 of SEQ ID NO: 2, a substitution of R12L of SEQ ID NO: 2, an insertion of Q at position 13 of SEQ ID NO: 2, an substitution of V15S of SEQ ID NO: 2 and an insertion of D at position 17 of SEQ ID NO: 2. In some embodiments, the at least two amino acid changes to a reference CasX protein are selected from the amino acid changes disclosed in the sequences of Table 3. In some embodiments, a CasX variant comprises any combination of the foregoing embodiments of this paragraph.
• In some embodiments, a CasX variant protein comprises more than one substitution, insertion and/or deletion of a reference CasX protein amino acid sequence. In some embodiments, the reference CasX protein comprises or consists essentially of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of S794R and a substitution of Y797L of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of K416E and a substitution of A708K of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of A708K and a deletion of P793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a deletion of P793 and an insertion of AS at position 795 SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of Q367K and a substitution of I425S of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of A708K, a deletion of P position 793 and a substitution A793V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of Q338R and a substitution of A339E of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of Q338R and a substitution of A339K of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of S507G and a substitution of G508R of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of C477K, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K and a deletion of P at position of 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of M779N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of M771N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of 708K, a deletion of P at position 793 and a substitution of D489S of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of A739T of SEQ ID NO: 2. in some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of D732N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of G791M of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of 708K, a deletion of P at position 793 and a substitution of Y797L of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a. substitution of M779N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of M771N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of D489S of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of A739T of SEQ ID NO: :2. in some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of D732N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of G791M of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of Y797L of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of T620P of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of A708K, a deletion of P at position 793 and a substitution of E386S of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of E386R, a substitution of F399L and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of R581I and A739V of SEQ ID NO: 2. In some embodiments, a CasX variant comprises any combination of the foregoing embodiments of this paragraph.
• In some embodiments, a CasX variant protein comprises more than one substitution, insertion and/or deletion of a reference CasX protein amino acid sequence. In some embodiments, a CasX variant protein comprises a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of C477K, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of C477K, substitution of A708K, a deletion of P at position 793 and a substitution of A739 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of T620P of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of M771A of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of D732N of SEQ ID NO: 2. In some embodiments, a CasX variant comprises any combination of the foregoing embodiments of this paragraph.
• In some embodiments, a CasX variant protein comprises a substitution of W782Q of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of M771Q of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of R458I and a substitution of A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution oft:379R, a substitution of A708K, a deletion of P at position 793 and a substitution of M771N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of A739T of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a. deletion of P at position 793 and a substitution of D489S of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of D732N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of V711K of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of Y797L of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of M771N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of A708K, a substitution of P at position 793 and a substitution of E386S SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477K, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L792D of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of G791F of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ II) NO: 2. In some embodiments, a CasX variant protein comprises a substitution of C477K, a substitution of A708K and a substitution of P at position 793 of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L249I and a substitution of M77 IN of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of V747K of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of L379R, a substitution of C477, a substitution of A708K, a deletion of P at position 793 and a substitution of M779N of SEQ ID NO: 2. In some embodiments, a CasX variant protein comprises a substitution of F755M. In some embodiments, a CasX variant comprises any combination of the foregoing embodiments of this paragraph.
• In some embodiments, a CasX variant protein comprises at least one modification compared to the reference CasX sequence of SEQ ID NO: 2, wherein the at least one modification is selected from one or more of: an amino acid substitution of L379R; an amino acid substitution of A708K; an amino acid substitution of T620P; an amino acid substitution of E385P; an amino acid substitution of Y857R an amino acid substitution of I658V; an amino acid substitution of F399L; an amino acid substitution of Q252K; an amino acid substitution of L404K; and an amino acid deletion of [P793]. In other embodiments, a CasX variant protein comprises any combination of the foregoing substitutions or deletions compared to the reference CasX sequence of SEQ ID NO: 2. in other embodiments, the CasX variant protein can, in addition to the foregoing substitutions or deletions, further comprise a substitution of an NTSB and/or a helical 1b domain from the reference CasX of SEQ D NO: 1.
• In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 3498-3501, 3505-3520 and 3540-3549.
• In some embodiments, a CasX variant comprises one or modifications to any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, a CasX variant comprises one or modifications to any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, a CasX variant comprises one or modifications to any one of SEQ ID NOS: 3498-3501, 3505-3520 and 3540-3549.
• In some embodiments, the CasX variant protein comprises between 400 and 2000 amino acids, between 500 and 1500 amino acids, between 700 and 1200 amino acids, between 800 and 1100 amino acids or between 900 and 1000 amino acids.
• In some embodiments, the CasX variant protein comprises one or more modifications in a region of non-contiguous residues that form a channel in which gNA:target DNA complexing occurs. In some embodiments, the CasX variant protein comprises one or more modifications comprising a region of non-contiguous residues that form an interface which hinds with the gNA. For example, in some embodiments of a reference CasX protein, the helical I, helical II and OBD domains all contact or are in proximity to the gNA:target DNA complex, and one or more modifications to non-contiguous residues within any of these domains may improve function of the CasX variant protein.
• In some embodiments, the CasX variant protein comprises one or more modifications in a region of non-contiguous residues that form a channel which binds with the non-target strand DNA. For example, a CasX variant protein can comprise one or more modifications to non-contiguous residues of the NTSBD. In some embodiments, the CasX variant protein comprises one or more modifications in a region of non-contiguous residues that form an interface which binds with the PAM. For example, a CasX variant protein can comprise one or more modifications to non-contiguous residues of the helical I domain or OBD. In some embodiments, the CasX variant protein comprises one or more modifications comprising a region of non-contiguous surface-exposed residues. As used herein, “surface-exposed residues” refers to amino acids on the surface of the CasX protein, or amino acids in which at least a portion of the amino acid, such as the backbone or a part of the side chain is on the surface of the protein. Surface exposed residues of cellular proteins such as CasX, which are exposed to an aqueous intracellular environment, are frequently selected from positively charged hydrophilic amino acids, for example arginine, asparagine, aspartate, glutamine, glutamate, histidine, serine, and threonine. Thus, for example, in some embodiments of the variants provided herein, a region of surface exposed residues comprises one or more insertions, deletions, or substitutions compared to a reference CasX protein. In some embodiments, one or more positively charged residues are substituted for one or more other positively charged residues, or negatively charged residues, or uncharged residues, or any combinations thereof. In some embodiments, one or more amino acids residues for substitution are near bound nucleic acid, for example residues in the RuvC domain or helical I domain that contact target DNA, or residues in the OBD or helical II domain that hind the gNA, can be substituted for one or more positively charged or polar amino acids.
• In some embodiments, the CasX variant protein comprises one or more modifications in a region of non-contiguous residues that form a core through hydrophobic packing in a domain of the reference CasX protein. Without wishing to be bound by any theory, regions that form cores through hydrophobic packing are rich in hydrophobic amino acids such as valine, isoleucine, leucine, methionine, phenylalanine, tryptophan, and cysteine. For example, in some reference CasX proteins, RuvC domains comprise a hydrophobic pocket adjacent to the active site. In some embodiments, between 2 to 15 residues of the region are charged, polar, or base-stacking. Charged amino acids (sometimes referred to herein as residues) may include, for example, arginine, lysine, aspartic acid, and glutamic acid, and the side chains of these amino acids may form salt bridges provided a bridge partner is also present (see FIG. 14). Polar amino acids may include, for example, glutamine, asparagine, histidine, serine, threonine, tyrosine, and cysteine. Polar amino acids can, in some embodiments, form hydrogen bonds as proton donors or acceptors, depending on the identity of their side chains. As used herein, “base-stacking” includes the interaction of aromatic side chains of an amino acid residue (such as tryptophan, tyrosine, phenylalanine, or histidine) with stacked nucleotide bases in a nucleic acid. Any modification to a region of non-contiguous amino acids that are in close spatial proximity to form a functional part of the CasX variant protein is envisaged as within the scope of the disclosure.
• i. CasX Variant Proteins with Domains from Multiple Source Proteins
• In certain embodiments, the disclosure provides a chimeric CasX protein comprising protein domains from two or more different CasX proteins, such as two or more naturally occurring CasX proteins, or two or more CasX variant protein sequences as described herein. As used herein, a “chimeric CasX protein” refers to a CasX containing at least two domains isolated or derived from different sources, such as two naturally occurring proteins, which may, in some embodiments, be isolated from different species. For example, in sonic embodiments, a chimeric CasX protein comprises a first domain from a first CasX protein and a second domain from a second, different CasX protein. In some embodiments, the first domain can be selected from the group consisting of the NTSB, TSL, helical I, helical II, OBD and RuvC domains. In some embodiments, the second domain is selected from the group consisting of the NTSB, TSL, helical I, helical II, OBD and RuvC domains with the second domain being different from the foregoing first domain. For example, a chimeric CasX protein may comprise an NTSB, TSL, helical I, helical II, OBD domains from a CasX protein of SEQ ID NO: 2, and a RuvC domain from a CasX protein of SEQ ID NO: 1, or vice versa. As a further example, a chimeric CasX protein may comprise an NTSB, TSL, helical II, OBD and RuvC domain from CasX protein of SEQ ID NO: 2, and a helical I domain from a CasX protein of SEQ ID NO: 1, or vice versa. Thus, in certain embodiments, a chimeric CasX protein may comprise an NTSB, TSL, helical OBD and RuvC domain from a first CasX protein, and a helical I domain from a second CasX protein. In some embodiments of the chimeric CasX proteins, the domains of the first CasX protein are derived from the sequences of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3, and the domains of the second CasX protein are derived from the sequences of SEQ ID NO: 1, SEQ II) NO: 2 or SEQ ID NO: 3, and the first and second CasX proteins are not the same. In some embodiments, domains of the first CasX protein comprise sequences derived from SEQ ID NO: 1 and domains of the second CasX protein comprise sequences derived from SEQ ID NO: 2. In some embodim.ents, domains of the first CasX protein comprise sequences derived from SEQ ID NO: 1 and domains of the second CasX protein comprise sequences derived from SEQ m NO: 3. In some embodiments, domains of the first CasX protein comprise sequences derived from SEQ ID NO: 2 and domains of the second CasX protein comprise sequences derived from SEQ ID NO: 3. In some embodiments, the CasX variant is selected of group consisting of CasX variants with sequences of SEQ ID NO: 328, SEQ ID NO: 3540, SEQ ID NO: 4413, SEQ ID NO: 4414, SEQ ID NO: 4415, SEQ ID NO: 329, SEQ ID NO: 3541, SEQ ID NO: 330, SEQ ID NO: 3542, SEQ ID NO: :331, SEQ ID NO: 3543, SEQ ID NO: 332, SEQ ID NO: 3544, SEQ ID NO: 333, SEQ ID NO: 3545, SEQ ID NO: 334, SEQ ID NO: 3546, SEQ ID NO: 335, SEQ ID NO: 3547, SEQ ID NO: 336 and SEQ ID NO: 3548. In some embodiments, the CasX variant comprises one or more additional modifications to any one of SEQ ID NO: 328, SEQ ID NO: 3540, SEQ ID NO: 4413, SEQ ID NO: 4414, SEQ ID NO: 4415, SEQ ID NO: 329, SEQ ID NO: 3541, SEQ ID NO: 330, SEQ ID NO: 3542, SEQ ID NO: 331, SEQ ID NO: 3543, SEQ ID NO: 332, SEQ ID NO: 3544, SEQ ID NO: 333, SEQ ID NO: 3545, SEQ ID NO: 334, SEQ ID NO: 3546, SEQ ID NO: 335, SEQ ID NO: 3547, SEQ ID NO: 336 or SEQ ID NO: 3548. In some embodiments, the one or more additional modifications comprises an insertion, substitution or deletion as described herein.
• In some embodiments, a CasX variant protein comprises at least one chimeric domain comprising a first part from a first CasX protein and a second part from a second, different CasX protein. As used herein, a “chimeric domain” refers to a domain containing at least two parts isolated or derived from different sources, such as two naturally occurring proteins or portions of domains from two reference CasX proteins. The at least one chimeric domain can be any of the NTSB, TSL, helical I, helical II, OBD or RuvC domains as described herein. In some embodiments, the first portion of a CasX domain comprises a sequence of SEQ ID NO: 1 and the second portion of a CasX domain comprises a sequence of SEQ ID NO: 2. In some embodiments, the first portion of the CasX domain comprises a sequence of SEQ ID NO: 1 and the second portion of the CasX domain comprises a sequence of SEQ ID NO: 3. In some embodiments, the first portion of the CasX domain comprises a sequence of SEQ ID NO: 2 and the second portion of the CasX domain comprises a sequence of SEQ ID NO: 3. In some embodiments, the at least one chimeric domain comprises a chimeric RuvC domain. As an example of the thregoing, the chimeric RuvC domain comprises amino acids 661 to 824 of SEQ ID NO: 1 and amino acids 922 to 978 of SEQ ID NO: 2. As an alternative example of the foregoing, a chimeric RuvC domain comprises amino acids 648 to 812 of SEQ ID NO: 2 and amino acids 935 to 986 of SEQ ID NO: 1. In some embodiments, a CasX protein comprises a first domain from a first CasX protein and a second domain from a second CasX protein, and at least one chimeric domain comprising at least two parts isolated from different CasX proteins using the approach of the embodiments described in this paragraph. In the foregoing embodiments, the chimeric CasX proteins having domains or portions of domains derived from SEQ ID NOS: 1, 2 and 3, can further comprise amino acid insertions, deletions, or substitutions of any of the embodiments disclosed herein,
• In some embodiments, a CasX variant protein comprises a sequence set forth in Tables 3, 8, 9, 10 or 12. In other embodiments, a CasX variant protein comprises a sequence at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to a sequence set forth in Tables 3, 8, 9, 10 or 12. In other embodiments, a CasX variant protein comprises a sequence set forth in Table 3, and further comprises one or more NIS disclosed herein on either the N-terminus, the C-terminus, or both. It will be understood that in some cases. the N-terminal methionine of the CasX variants of the Tables is removed from the expressed CasX variant during post-translational modification.

• TABLE 3
  CasX Variant Sequences

  Description*	Amino Acid Sequence
  TSL, Helical I, Helical II, OBD and RuvC domains from SEQ ID NO: 2 and an NTSB	SEQ ID NO: 247
  domain from SEQ ID NO: 1
  NTSB, Helical I, Helical II, OBD and RuvC domains from SEQ ID NO: 2 and a TSL	SEQ ID NO: 248
  domain from SEQ ID NO: 1.
  TSL, Helical I, Helical II, OBD and RuvC domains from SEQ ID NO: 1 and an NTSB	SEQ ID NO: 249
  domain from SEQ ID NO: 2
  NTSB, Helical I, Helical II, OBD and RuvC domains from SEQ ID NO: 1 and an TSL	SEQ ID NO: 250
  domain from SEQ ID NO: 2,
  NTSB, TSL, Helical I, Helical II and OBD domains SEQ ID NO: 2 and an exogenous	SEQ ID NO: 251
  RuvC domain or a portion thereof from a second CasX protein.
  No description	SEQ ID NO: 252
  NTSB, TSL, Helical II, OBD and RuvC domains from SEQ ID NO: 2 and a Helical I	SEQ ID NO: 253
  domain from SEQ ID NO: 1
  NTSB, TSL, Helical I, OBD and RuvC domains from SEQ. ID NO: 2 and a Helical II	SEQ ID NO: 254
  domain from SEQ ID NO: 1
  N'I'SB, TSL, Helical I, Helical II and RuvC domains from a first CasX protein and an	SEQ ID NO: 255
  exogenous OBD or a part thereof from a second CasX :protein
  No description	SEQ ID NO: 256
  No description	SEQ ID NO: 257
  substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of	SEQ ID NO: 258
  P at position 793 and a substitution of T620P of SEQ ID NO: 2
  substitution of M771A of SEQ ID NO: 2.	SEQ ID NO: 259
  substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a	SEQ ID NO: 260
  substitution of D732N of SEQ ID NO: 2.
  substitution of W782Q of SEQ ID NO: 2.	SEQ ID NO: 261
  substitution of M771Q of SEQ ID NO: 2	SEQ ID NO: 262
  substitution of R458I and a substitution of A739V of SEQ ID NO: 2.	SEQ ID NO: 263
  L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of	SEQ ID NO: 264
  M771N of SEQ ID NO: 2
  substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a	SEQ ID NO: 265
  stibstitution of A739T of SEQ ID NO: 2
  substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of	SEQ ID NO: 266
  P at position 793 and a substitution of D4895 of SEQ ID NO: 2.
  substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of	SEQ ID NO: 267
  P at position 793 and a substitution of D732N of SEQ, ID NO: 2.
  substitution of V711K of SEQ ID NO: 2.	SEQ ID NO: 268
  substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of	SEQ ID NO: 269
  P at position 793 and a substitution of Y797L of SEQ ID NO: 2.
  119, substitution of L379R, a substitution of A708K and a deletion of P at position 793	SEQ ID NO: 270
  of SEQ ID NO: 2.
  substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of	SEQ ID NO: 271
  P at position 793 and a substitution of M771N of SEQ ID NO: 2.
  substitution of A708K, a deletion of P at position 793 and a substitution of E386S of	SEQ ID NO: 272
  SEQ ID NO: 2.
  substitution of L379R, a substitution of C477K, a substitution of A708K and a deletion	SEQ ID NO: 273
  of P at position 793 of SEQ ID NO: 2.
  substitution of L792D of SEQ ID NO: 2.	SEQ ID NO: 274
  substitution of G791F of SEQ ID NO: 2.	SEQ ID NO: 275
  substitution of A708K, a deletion of P at position 793 and a substitution of A739V of	SEQ ID NO: 276
  SEQ ID NO: 2,
  substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a	(SEQ ID NO: 277
  substitution of A739V of SEQ ID NO: 2.
  substitution of C477K., a substitution of A708K and a deletion of P at position 793 of	SEQ ID NO: 278
  SEQ ID NO: 2.
  substitution of L249I and a substitution of M771N of SEQ ID NO: 2.	SEQ ID NO: 279
  substitution of V747K of SEQ ID NO: 2.	SEQ ID NO: 280
  substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of	SEQ ID NO: 281
  P at position 793 and a substitution of M779N of SEQ ID NO: 2.
  L379R, F755M	SEQ ID NO: 282
  429, L379R, A708K, P793_, Y857R	SEQ ID NO: 283
  430, L379R, A708K, P793_, Y857R, I658V	SEQ ID NO: 284
  431, L379R, A708K, P793_, Y857R, I658V, E386N	SEQ ID NO: 285
  432, L379R, A708K, P793_, Y857R, I658V, L404K	SEQ ID NO: 286
  433, L379R, A708K, P793_, Y857R, I658V, AV192	SEQ ID NO: 287
  434, L379R, A708K, P793_, Y857R, I658V, L404K, E386N	SEQ ID NO: 288
  435, L379R, A708K, P793_, Y857R, I658V, F399L	SEQ ID NO: 289
  436, L379R, A708K, P793_, Y857R, I658V, F399L, E386N	SEQ ID NO: 290
  437, L379R, A708K, P793_, Y857R, I658V, F399L, C477S	SEQ ID NO: 291
  438, L379R, A708K, P793_, Y857R, I658V, F399L, L404K	SEQ ID NO: 292
  439, L379R, A708K, P793_, Y857R, I658V, F399L, E386N, C4775, L404K	SEQ ID NO: 293
  440, L379R, A708K, P793_, Y857R, I658V, F399L, Y797L	SEQ ID NO: 294
  441, L379R, A708K, P793_ , Y857R, I658V, F399L, Y797L, E386N	SEQ ID NO: 295
  442, L379R, A708K, P793_, Y857R, I658V, F399L, Y797L, E386N, C477S, L404K	SEQ ID NO: 296
  443, L379R, A708K, P793_, Y857R, I658V, Y797L	SEQ ID NO: 297
  444, 1,379R, A708K, P793_, Y857R, I658V, Y797L, L404K	SEQ ID NO: 298
  445, L379R, A708K, P793_, Y857R, I658V, Y797L, E386N	SEQ ID NO: 299
  446, L379R, A708K, P793_, Y857R, I658V, Y797L, E386N, C4775, L404K	SEQ ID NO: 300
  447, L379R, A708K, P793_, Y857R, E386N	SEQ ID NO: 301
  448, L379R, A708K, P793_ , Y857R, E386N, L404K	SEQ ID NO: 302
  449, L379R, A708K, P793_, D732N, E385P, Y857R	SEQ ID NO: 303
  450, L379R, A708K, P793_, D732N, E385P, Y857R, I651W	SEQ ID NO: 304
  451, L379R, A708K, P793_, D732N, E385P, Y857R, I651W, F399L	SEQ ID NO: 305
  452, L379R, A708K, P793_, D732N, E385P, Y857R, I658V, E386N	SEQ ID NO: 306
  453, L379R, A708K, P793_, D732N, E385P, Y857R, I658V, L404K	SEQ ID NO: 307
  454, L379R, A708K, P793_, T620P, E385P, Y857R, Q252K	SEQ ID NO: 308
  455, L379R, A708K, P793_, T620P, E385P, Y857R, I658V, Q252K	SEQ ID NO: 309
  456, L379R, A708K, P793_, T620P, E385P, Y857R, I658V, E386N, Q252K	SEQ ID NO: 310
  457, L379R, A708K, P793_, T620P, E385P, Y857R, I658V, F399L, Q252K	SEQ ID NO: 311
  458, L379R, A708K, P793_, T620P, E385P, Y857R, I658V, L404K, Q252K	SEQ ID NO: 312
  459, L379R, A708K, P793_, T620P, Y857R, I658V, E386N	SEQ ID NO: 313
  460, L379R, A708K, P793_ , T620P, E385P, Q252K	SEQ ID NO: 314
  278	SEQ ID NO: 315
  279	SEQ ID NO: 316
  280	SEQ ID NO: 317
  285	SEQ ID NO: 318
  286	SEQ ID NO: 319
  287	SEQ ID NO: 320
  288	SEQ ID NO: 321
  290	SEQ ID NO: 322
  291	SEQ ID NO: 323
  293	SEQ ID NO: 324
  300	SEQ ID NO: 325
  492	SEQ ID NO: 326
  493	SEQ ID NO: 327
  387, NTSB swap from SEQ ID NO: 1	SEQ ID NO: 328
  395, Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 329
  485, Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 330
  486, Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 331
  487, Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 332
  488, NTSB and Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 333
  489, NTSB and Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 334
  490, NTSB and Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 335
  491, NTSB and Helical 1B swap from SEQ ID NO: 1	SEQ ID NO: 336
  494, NTSB swap from SEQ ID NO: 1	SEQ ID NO: 337
  328, S867G	SEQ ID NO: 4412
  388, L379R + A708K+ [P793] + X1 Helical2 swap	SEQ ID NO: 4413
  389, L379R + [P793] +X1 RuvC1 swap	SEQ ID NO: 4144
  390, L3791R + A708K + [P793] + X1 RuvC2 swap	SEQ ID NO: 4415
  * Strain indicated numerically; changes, where indicated, are relative to SEQ ID NO: 2

• In some embodiments, the CasX variant protein has one or more improved characteristics when compared to a reference CasX protein, for example a reference protein of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3. In some embodiments, an improved characteristic of the CasX variant is at least about 1.1. to about 100,000-fold improved relative to the reference protein. In some embodiments, an improved characteristic of the CasX variant is at least about 1.1 to about 10,000-fold improved, at least about 1.1 to about 1,000-fold improved, at least about 1.1 to about 500-fold improved, at least about 1.1 to about 400-fold improved, at least about 1.1 to about 300-fold improved, at least about 1.1 to about 200-fold improved, at least about 1.1 to about 100-fold improved, at least about 1.1 to about 50-fold improved, at least about 1.1 to about 40-fold improved, at least about 1.1 to about 30-fold improved, at least about 1.1 to about 20-fold improved, at least about 1.1 to about 10-fold improved, at least about 1.1 to about 9-fold improved, at least about 1.1 to about 8-fold improved, at least about 1.1 to about 7-fold improved, at least about 1.1 to about 6-fold improved, at least about 1.1 to about 5-fold improved, at least about 1.1 to about 4-fold improved, at least about 1.1 to about 3-fold improved, at least about 1.1 to about 2-fold improved, at least about 1.1 to about 1.5-fold improved, at least about 1.5 to about 3-fold improved, at least about 1.5 to about 4-fold improved, at least about 1.5 to about 5-fold improved, at least about 1.5 to about 10-fold improved, at least about 5 to about 10-fold improved, at least about 10 to about 20-fold improved, at least 10 to about 30-fold improved, at least 10 to about 50-fold improved or at least 10 to about 100-fold improved than the reference CasX protein. In some embodiments, an improved characteristic of the CasX variant is at least about 10 to about 1000-fold improved relative to the reference CasX protein.
• In some embodiments, the one or more improved characteristics of the CasX variant protein is at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90. at least about 100, at least about 250, at least about 500, or at least about 1000, at least about 5,000, at least about 10,000, or at least about 100,000-fold improved relative to a reference CasX protein. In some embodiments, an improved characteristics of the CasX variant protein is at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1,5, at least about 1.6, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 2.1, at least about 2.2, at least about 2.3, at least about 2.4, at least about 2.5, at least about 2.6, at least about 2.7, at least about 2.8, at least about 2.9, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5, at least about 5.5, at least about 6, at least about 6,5, at least about 7.0, at least about 7.5, at least about 8, at least about 8.5, at least about 9, at least about 9.5, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90 at least about 100, at least about 500, at least about 1,000, at least about 10,000, or at least about 100,000-fold improved relative to a reference CasX protein. In other cases, the one or more improved characteristics of the CasX variant is about 1.1 to 100,00-fold, about 1.1 to 10,00-fold, about 1.1 to 1,000-fold, about 1.1 to 500-fold, about 1.1 to 100-fold, about 1.1 to 50-fold, about 1.1 to 20-fold, about 10 to 100,00-fold, about 10 to 10,00-fold, about 10 to 1,000-fold, about 10 to 500-fold, about 10 to 100-fold, about 10 to 50-fold, about 10 to 20-fold, about 2 to 70-fold, about 2 to 50-fold, about 2 to 30-fold, about 2 to 20-fold, about 2 to 10-fold, about 5 to 50-fold, about 5 to 30-fold, about 5 to 10-fold, about 100 to 100,00-fold, about 100 to 10,00-fold, about 100 to 1,000-fold, about 100 to 500-fold, about 500 to 100,00-fold, about 500 to 10,00-fold, about 500 to 1,000-fold, about 500 to 750-fold. bout 1,000 to 100,00-fold, about 10,000 to 100,00-fold, about 20 to 500-fold, about 20 to 250-fold, about 20 to 200-fold, about 20 to 100-fold, about 20 to 50-fold, about 50 to 10,000-fold, about 50 to 1,000-fold, about 50 to 500-fold, about 50 to 200-fold, or about 50 to 100-fold, improved relative to the reference CasX of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3. In other cases, the one or more improved characteristics of the CasX variant is about 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, 15-fold, 16-fold, 17-fold, 18-fold, 19-fold, 20-fold, 25-fold, 30-fold, 40-fold, 45-fold, 50-fold, 55-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 110-fold, 120-fold, 130-fold, 140-fold, 150-fold, 160-fold, 170-fold, 180-fold, 190-fold, 200-fold, 210-fold, 220-fold, 230-fold, 240-fold, 250-fold, 260-fold, 270-fold, 280-fold, 290-fold, 300-fold, 310-fold, 320-fold, 330-fold, 340-fold, 350-fold, 360-fold, 370-fold, 380-fold, 390-fold, 400-fold, 425-fold, 450-fold, 475-fold, or 500-fold or more improved relative to the reference CasX of SEQ ID NO: 1. SEQ ID NO: 2 or SEQ ID NO: 3. Exemplary characteristics that can be improved in CasX variant proteins relative to the same characteristics in reference CasX proteins include, but are not limited to, improved folding of the variant, improved binding affinity to the gNA, improved binding affinity to the target DNA, improved ability to utilize a greater spectrum of PAM sequences in the editing and/or binding of target DNA, unproved unwinding of the target DNA, increased editing activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, improved protein stability, improved CasX:gNA RNA complex stability, improved protein solubility, improved CasX:gNA RNP complex solubility, improved protein yield, improved protein expression, and improved fusion characteristics. In some embodiments, the variant comprises at least one improved characteristic. In other embodiments, the variant comprises at least two improved characteristics. In further embodiments, the variant comprises at least three improved characteristics. In some embodiments, the variant comprises at least four improved characteristics. In still further embodiments, the variant comprises at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, or more improved characteristics. These improved characteristics are described in more detail below.
• j. Protein Stability
• In some embodiments, the disclosure provides a CasX variant protein with improved stability relative to a reference CasX protein. In some embodiments, improved stability of the CasX variant protein results in expression of a higher steady state of protein, which improves editing efficiency. In some embodiments, improved stability of the CasX variant protein results in a larger fraction of CasX protein that remains folded in a functional conformation and improves editing efficiency or improves purifiability for manufacturing purposes. As used herein, a “functional conformation” refers to a CasX protein that is in a conformation where the protein is capable of binding a gNA and target DNA. In embodiments wherein the CasX variant does not carry one or more mutations rendering it catalytically dead, the CasX variant is capable of cleaving, nicking, or otherwise modifying the target DNA. For example, a functional CasX variant can, in some embodiments, be used for gene-editing, and a functional conformation refers to an “editing-competent” conformation. In some exemplary embodiments, including those embodiments where the CasX variant protein results in a larger fraction of CasX protein that remains folded in a functional conformation, a lower concentration of CasX variant is needed for applications such as gene editing compared to a reference CasX protein, Thus, in some embodiments, the CasX variant with improved stability has improved efficiency compared to a reference CasX in one or more gene editing contexts.
• In some embodiments, the disclosure provides a CasX variant protein having improved thermostability relative to a reference CasX protein. In some embodiments, the CasX variant protein has improved thermostability of the CasX variant protein at a particular temperature range. Without wishing to be bound by any theory, some reference CasX proteins natively function in organisms with niches in groundwater and sediment; thus, some reference CasX proteins may have evolved to exhibit optimal function at lower or higher temperatures that may he desirable for certain applications. For example, one application of CasX variant proteins is gene editing of mammalian cells, which is typically carried out at about 37° C. In some embodiments, a CasX variant protein as described herein has improved thermostability compared to a reference CasX protein at a temperature of at least 16° C., at least 18° C. at least 20° C., at least 22° C., at least 24° C., at least 26° C., at least 28° C., at least 30° C., at least 32° C. at least 34° C., at least 35° C. at least 36° C., at least 37° C., at least 38° C., at least 39° C., at least 40° C., at least 41° C., at least 42° C., at least 44° C., at least 46° C., at least 48° C., at least 50° C., at least 52° C., or greater. In some embodiments, a CasX variant protein has improved themiostahility and functionality compared to a reference CasX protein that results in improved gene editing functionality, such as mammalian gene editing applications, which may include human gene editing applications.
• In some embodiments, the disclosure provides a CasX variant protein having improved stability of the CasX variant protein:gNA RNP complex relative to the reference CasX protein:gNA complex such that the RNP remains in a functional form. Stability improvements can include increased thermostability, resistance to proteolytic degradation, enhanced pharmacokinetic properties, stability across a range of pH conditions, salt conditions, and tonicity. Improved stability of the complex may, in some embodiments, lead to improved. editing efficiency.
• In some embodiments, the disclosure provides a CasX variant protein having improved thermostability of the CasX variant protein:gNA complex relative to the reference CasX protein:gNA complex. In some embodiments, a CasX variant protein has improved thermostability relative to a reference CasX protein. In some embodiments, the CasX variant protein:gNA RNP complex has improved thermostability relative to a complex comprising a reference CasX protein at temperatures of at least 16° C., at least 18° C., at least 20° C., at least 22° C., at least 24° C., at least 26° C., at least 28° C., at least 30° C., at least 32° C., at least 34° C., at least 35° C., at least 36° C., at least 37° C., at least 38° C., at least 39° C., at least 40° C., at least 41° C. at least 42° C., at least 44° C., at least 46° C. at least 48° C., at least 50° C., at least 52° C., or greater. In some embodiments, a CasX variant protein has improved thermostability of the CasX variant protein:gNA RNP complex compared to a reference CasX protein:gNA complex, which results in improved function for gene editing applications, such as mammalian gene editing applications, which may include human gene editing applications.
• In some embodiments, the improved stability and/or thermostability of the CasX variant protein comprises faster folding kinetics of the CasX variant protein relative to a reference CasX protein, slower unfolding kinetics of the CasX variant protein relative to a. reference CasX protein, a larger free energy release upon folding of the CasX variant protein relative to a reference CasX protein, a higher temperature at which 50% of the CasX variant protein is unfolded (Tm) relative to a reference CasX protein, or any combination thereof. These characteristics may be improved by a wide range of values; for example, at least 1.1, at least 1.5, at least 10, at least 50, at least 100, at least 500, at least 1,000, at least 5,000, or at least a 10,000-fold improved, as compared to a reference CasX protein. In some embodiments, improved thermostability of the CasX variant protein comprises a higher Tm of the CasX variant protein relative to a reference CasX protein. In some embodiments, the Tm of the CasX variant protein is between about 20° C. to about 30° C., between about 30° C. to about 40° C., between about 40° C. to about 50° C., between about 50° C. to about 60° C., between about 60° C. to about 70° C., between about 70° C. to about 80° C., between about 80° C. to about 90° C. or between about 90° C. to about 100° C., Thermal stability is determined by measuring the “melting temperature” (Tm), which is defined as the temperature at which half of the molecules are denatured. Methods of measuring characteristics of protein stability such as Tin and the free energy of unfolding are known to persons of ordinary skill in the art, and can be measured using standard biochemical techniques in vitro. For example, Tm may be measured using Differential Scanning calorimetry, a thermo-analytical technique in which the difference in the amount of heat required to increase the temperature of a sample and a reference is measured as a function of temperature (Chen et al (2003) Pharm Res 20:1952-60; Ghirlando et. al (1999) Immunol Lett 68:47-52). Alternatively, or in addition, CasX variant protein Tm may be measured using commercially available methods such as the ThermoFisher Protein Thermal Shift system. Alternatively, or in addition, circular dichroism may be used to measure the kinetics of folding and unfolding, as well as the Tm (Murray et al, (2002) J. Chromatogr Sci 40:343-9), Circular dichroism (CD) relies on the unequal absorption of left-handed and right-handed circularly polarized light by asymmetric molecules such as proteins. Certain structures of proteins, for example alpha-helices and beta-sheets, have characteristic CD spectra. Accordingly, in some embodiments, CD may be used to determine the secondary structure of a CasX variant protein.
• In some embodiments, improved stability and/or themiostability of the CasX variant protein comprises improved folding kinetics of the CasX variant protein relative to a reference CasX protein. In some embodiments, folding kinetics of the CasX variant protein are improved relative to a reference CasX protein by at least about 5, at least about 10, at least about 50, at least about 100, at least about 500, at least about 1,000, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, or at least about a 10,000-fold improvement. In some embodiments, folding kinetics of the CasX variant protein are improved relative to a reference CasX protein by at least about I kJ/mol, at least about 5 k/mol, at least about 10 kJ/mol, at least about 20 kJ/mol, at least about 30 kJ/mol, at least about 40 kJ/mol, at least about 50 kJ/mol, at least about 60 kJ/mol, at least about 70 kJ/mol, at least about 80 kJ/mol, at least about 90 kJ/mol, at least about 100 kJ/mol, at least about 150 at least about 200 at least about 250 kJ/moi, at least about 300 kJ/mol, at least about 350 kJ/mol, at least about 400 kJ/mol, at least about 450 kJ/mol, or at least about 500 kJ/mol.
• Exemplary amino acid changes that can increase the stability of a CasX variant protein relative to a reference CasX protein may include, but are not limited to, amino acid changes that increase the number of hydrogen bonds within the CasX variant protein, increase the number of disulfide bridges within the CasX variant protein, increase the number of salt bridges within the CasX variant protein, strengthen interactions between parts of the CasX variant protein, increase the buried hydrophobic surface area of the CasX variant protein, or any combinations thereof
• k. Protein Yield
• In some embodiments, the disclosure provides a CasX variant protein having improved yield during expression and purification relative to a reference CasX protein. In some embodiments, the yield of CasX variant proteins purified from bacterial or eukaryotic host cells is improved relative to a reference CasX protein. In some embodiments, the bacterial host cells are Escherichia coli cells. In some embodiments, the eukaryotic cells are yeast, plant (e.g. tobacco), insect (e.g. Spodoptera frugiperda sf9 cells), mouse, rat, hamster, guinea pig, non-human primate, or human cells. In some embodiments, the eukarvotic host cells are mammalian cells, including, but not limited to HEK293 cells, HEK293T cells, HEK293-F cells, Lenti-X 293T cells, MK cells, HepG2 cells, Saos-2 cells, HuH7 cells, A549 cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells, hybridoma cells, VERO cells, NIH3T3 cells, COS, W138 cells, MRCS cells, HeLa, HTI080 cells, or CHO cells.
• In some embodiments, improved yield of the CasX variant protein is achieved through codon optimization. Cells use 64 different codons, 61 of which encode the 20 standard amino acids, while another 3 function as stop codons. In some cases, a single amino acid is encoded by more than one codon. Different organisms exhibit bias towards use of different codons for the same naturally occurring amino acid. Therefore, the choice of codons in a protein, and matching codon choice to the organism in which the protein will be expressed, can, in some cases, significantly affect protein translation and therefore protein expression levels. In some embodiments, the CasX variant protein is encoded by a nucleic acid that has been codon optimized. In some embodiments, the nucleic acid encoding the CasX variant protein has been codon optimized for expression in a bacterial cell, a yeast cell, an insect cell, a plant cell, or a mammalian cell. In some embodiments, the mammal cell is a mouse, a rat, a hamster, a guinea pig, a monkey, or a human. In some embodiments, the CasX variant protein is encoded by a nucleic acid that has been codon optimized for expression in a human cell. In some embodiments, the CasX variant protein is encoded by a nucleic acid from which nucleotide sequences that reduce translation rates in prokaryotes and eukaryotes have been removed. For example, runs of greater than three thymine residues in a row can reduce translation rates in certain organisms or internal polyadenylation signals can reduce translation.
• In some embodiments, improvements in solubility and stability, as described herein, result in improved yield of the CasX variant protein relative to a reference CasX protein.
• Improved protein yield during expression and purification can be evaluated by methods known in the art. For example, the amount of CasX variant protein can be determined by running the protein on an SDS-page gel, and comparing the CasX variant protein to a control whose amount or concentration is known in advance to determine an absolute level of protein. Alternatively, or in addition, a purified CasX variant protein can be run on an SDS-page gel next to a reference CasX protein undergoing the same purification process to determine relative improvements in CasX variant protein yield. Alternatively, or in addition, levels of protein can be measured using immunohistochemical methods such as Western blot or ELBA with an antibody to CasX, or by HPLC. For proteins in solution, concentration can be determined by measuring of the protein's intrinsic UV absorbance, or by methods which use protein-dependent color changes such as the Lowry assay, the Smith copper/bicinchoninic assay or the Bradford dye assay. Such methods can be used to calculate the total protein (such as, for example, total soluble protein) yield obtained by expression under certain conditions. This can be compared, for example, to the protein yield of a reference CasX protein under similar expression conditions.
• I. Protein Solubility
• In some embodiments, a CasX variant protein has improved solubility relative to a reference CasX protein. In some embodiments, a CasX variant protein has improved solubility of the CasX:gNA ribonucleoprotein complex variant relative to a ribonucleoprotein complex comprising a reference CasX protein.
• In some embodiments, an improvement in protein solubility leads to higher yield of protein from protein purification techniques such as purification from E. coli. Improved solubility of CasX variant proteins may, in sonic embodiments, enable more efficient activity in cells, as a more soluble protein may be less likely to aggregate in cells. Protein aggregates can in certain embodiments be toxic or burdensome on cells, and, without wishing to be bound by any theory, increased solubility of a CasX variant protein may ameliorate this result of protein aggregation. Further, improved solubility of CasX variant proteins may allow for enhanced formulations permitting the delivery of a higher effective dose of functional protein, for example in a desired gene editing application. In some embodiments, improved solubility of a CasX variant protein relative to a reference CasX protein results in improved yield of the CasX variant protein during purification of at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, at least about 100, at least about 250, at least about 500, or at least about 1000-fold greater yield. In some embodiments, improved solubility of a CasX variant protein relative to a reference CasX protein improves activity of the CasX variant protein in cells by at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1.5, at least about 16, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 2.1, at least about 2.2, at least about 2.3, at least about 2.4, at least about 2.5. at least about 2.6, at least about 2.7, at least about 2.8, at least about 2.9, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5, at least about 5.5, at least about 6, at least about 6.5, at least about 7.0, at least about 7.5, at least about 8, at least about 8.5, at least about 9, at least about 9.5, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15-fold, or at least about 20-fold greater activity.
• Methods of measuring CasX protein solubility, and improvements thereof in CasX variant proteins, will be readily apparent to the person of ordinary skill in the art. For example, CasX variant protein solubility can in some embodiments be measured by taking densitometry readings on a gel of the soluble fraction of lysed E.coli. Alternatively, or addition, improvements in CasX variant protein solubility can be measured by measuring the maintenance of soluble protein product through the course of a full protein purification, including the methods of the Examples. For example, soluble protein product can be measured at one or more steps of gel affinity purification, tag cleavage, cation exchange purification, running the protein on a size exclusion chromatography (SEC) column. In some embodiments, the densitometry of every band of protein on a gel is read after each step in the purification process. CasX variant proteins with improved solubility may, in some embodiments, maintain a higher concentration at one or more steps in the protein purification process when compared to the reference CasX protein, while an insoluble protein variant may be lost at one or more steps due to buffer exchanges, filtration steps, interactions with a purification column, and the like.
• In some embodiments, improving the solubility of CasX variant proteins results in a higher yield in terms of mg/L of protein during protein purification when compared to a reference CasX protein.
• In some embodiments, improving the solubility of CasX variant proteins enables a greater amount of editing events compared to a less soluble protein when assessed in editing assays such as the EGFP disruption assays described herein.
• m. Affinity for the gNA
• In some embodiments, a CasX variant protein has improved affinity for the gNA relative to a reference CasX protein, leading to the formation of the ribonucleoprotein complex. Increased affinity of the CasX variant protein for the gNA may, for example, result in a lower K_d for the generation of a RNP complex, which can, in some cases, result in a more stable ribonucleoprotein complex formation. In some embodiments, the K_d of a CasX variant protein for a gNA is increased relative to a reference CasX protein by a factor of at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1.5, at least about 1.6, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, or at least about 100. In some embodiments, the CasX variant has about 1.1 to about 10-fold increased binding affinity to the gNA compared to the reference CasX protein of SEQ ID NO: 2.
• In some embodiments, increased affinity of the CasX variant protein for the gNA results in increased stability of the ribonucleoprotein complex when delivered to mammalian cells, including in vivo delivery to a subject. This increased stability can affect the function and utility of the complex in the cells of a subject, as well as result in improved pharmacokinetic properties in blood, when delivered to a subject. In some embodiments, increased affinity of the CasX variant protein, and the resulting increased stability of the ribonucleoprotein complex, allows for a lower dose of the CasX variant protein to be delivered to the subject or cells while still having the desired activity; for example in vivo or in vitro gene editing. The increased ability to form RNP and keep them in stable form can be assessed using assays such as the in vitro cleavage assays described herein. In some embodiments, the CasX variants of the disclosure are able to achieve a K_cleave when complexed as an RNP that is at last 2-fold, at least 5-fold, or at least 10-fold higher compared to RNP of reference CasX.
• In some embodiments, a higher affinity (tighter binding) of a CasX variant protein to a gNA allows for a greater amount of editing events when both the CasX variant protein and the gNA remain in an RNP complex. Increased editing events can be assessed using editing assays such as the EGFP disruption and in vitro cleavage assays described herein.
• Without wishing to be bound by theory, in some embodiments amino acid changes in the helical I domain can increase the binding affinity of the CasX variant protein with the gNA targeting sequence, while changes in the helical II domain can increase the binding affinity of the CasX variant protein with the gNA scaffold stem loop, and changes in the oligonucleotide binding domain (OBD) increase the binding affinity of the CasX variant protein with the gNA triplex.
• Methods of measuring CasX protein binding affinity for a gNA include in vitro methods using purified CasX protein and gNA. The binding affinity for reference CasX and variant proteins can be measured by fluorescence polarization if the gNA or CasX protein is tagged with a fluorophore. Alternatively, or in addition, binding affinity can he measured by biolayer interferometry, electrophoretic mobility shift assays (EMSAs), or filter binding. Additional standard techniques to quantify absolute affinities of RNA binding proteins such as the reference CasX and variant proteins of the disclosure for specific gNAs such as reference gNAs and variants thereof include, but are not limited to, isothermal calorimetry (ITC), and surface plasmon resonance (SPR), as well as the methods of the Examples.
• n. Affinity for Target Nucleic Acid
• In some embodiments, a CasX variant protein has improved binding affinity for a target nucleic acid relative to the affinity of a reference CasX protein for a target nucleic acid. CasX variants with higher affinity for their target nucleic acid may, in some embodiments, cleave the target nucleic acid sequence more rapidly than a reference CasX protein that does not have increased affinity for the target nucleic acid.
• In some embodiments, the improved affinity for the target nucleic acid comprises improved affinity for the target sequence or protospacer sequence of the target nucleic acid, improved affinity for the PAM sequence, an improved ability to search DNA for the target sequence, or any combinations thereof. Without wishing to be bound by theory, it is thought that CRISPR/Cas system proteins such as CasX may find their target sequences by one-dimension diffusion along a DNA molecule. The process is thought to include (1) binding of the ribonucleoprotein to the DNA molecule followed by (2) stalling at the target sequence, either of which may he, in some embodiments, affected by improved affinity of CasX proteins for a target nucleic acid sequence, thereby improving function of the CasX variant protein compared to a reference CasX protein.
• In some embodiments, a CasX variant protein with improved target nucleic acid affinity has increased overall affinity for DNA. In some embodiments, a CasX variant protein with improved target nucleic acid affinity has increased affinity for or the ability to utilize specific PAM sequences other than the canonical TTC PAM recognized by the reference CasX protein of SEQ ID NO: 2, including PAM sequences selected from the group consisting of TTC, ATC, GTC, and CTC, thereby increasing the amount of target DNA that can be edited compared to wild-type CasX nucleases. Without wishing to be bound by theory, it is possible that these protein variants may interact more strongly with DNA overall and may have an increased ability to access and edit sequences within the target DNA due to the ability to utilize additional PAM sequences beyond those of wild-type reference CasX, thereby allowing for a more efficient search process of the CasX protein for the target sequence. A higher overall affinity for DNA also, in some embodiments, can increase the frequency at which a CasX protein can effectively start and finish a binding and unwinding step, thereby facilitating target strand invasion and R-loop formation, and ultimately the cleavage of a target nucleic acid sequence.
• Without wishing to be bound by theory, it is possible that amino acid changes in the NTSBD that increase the efficiency of unwinding, or capture, of a non-target DNA strand in the unwound state, can increase the affinity of CasX variant proteins for target DNA. Alternatively, or in addition, amino acid changes in the NTSBD that increase the ability of the NTSBD to stabilize DNA during unwinding can increase the affinity of CasX variant proteins for target DNA. Alternatively, or in addition, amino acid changes in the OBD may increase the affinity of CasX variant protein binding to the protospacer adjacent motif (PAM), thereby increasing affinity of the CasX variant protein for target nucleic acid. Alternatively, or in addition, amino acid changes in the Helical I and/or II, RuvC and TSL domains that increase the affinity of the CasX variant protein for the target nucleic acid strand can increase the affinity of the CasX variant protein for target nucleic acid.
• In some embodiments, binding affinity of a CasX variant protein of the disclosure for a. target nucleic acid molecule is increased relative to a reference CasX protein by a factor of at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1.5, at least about 1.6, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 3, at least about 4, at least about 5. at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, or at least about 100. In some embodiments, the CasX variant protein has about 1,1 to about 100-fold increased binding affinity to the target nucleic acid compared to the reference protein of SEQ ID NO: I, SEQ ID NO: 2, or SEQ ID NO: 3.
• In some embodiments, a CasX variant protein has improved binding affinity for the non-target strand of the target nucleic acid. As used herein, the term “non-target strand” refers to the strand of the DNA target nucleic acid sequence that does not form Watson and Crick base pairs with the targeting sequence in the gNA, and is complementary to the target DNA strand. In some embodiments, the CasX variant protein has about 1.1 to about 100-fold increased binding affinity to the non-target stand of the target nucleic acid compared to the reference protein of SEQ ID NO: 1. SEQ ID NO: 2, or SEQ ID NO: 3.
• Methods of measuring CasX protein (such as reference or variant) affinity for a target and/or non-target nucleic acid molecule may include electrophoretic mobility shift assays (EMSAs), filter binding, isothermal calorimetry (ITC), and surface plasmon resonance (SPR), fluorescence polarization and biolayer interferometry (BLI). Further methods of measuring CasX protein affinity for a target include in vitro biochemical assays that measure DNA cleavage events over time.
• o. Improved Specificity for a Target Site
• In some embodiments, a CasX variant protein has improved specificity for a target nucleic acid sequence relative to a reference CasX protein. As used herein, “specificity,” sometimes referred to as “target specificity,” refers to the degree to which a CRISPR/Cas system ribonucleoprotein complex cleaves off-target sequences that are similar, but not identical to the target nucleic acid sequence; e.g., a CasX variant RNP with a higher degree of specificity would exhibit reduced off-target cleavage of sequences relative to a reference CasX protein. The specificity, and the reduction of potentially deleterious off-target effects, of CRISPR/Cas system proteins can be vitally important in order to achieve an acceptable therapeutic index for use in mammalian subjects.
• In some embodiments, a CasX variant protein has improved specificity for a target site within the target sequence that is complementary to the targeting sequence of the gNA. Without wishing to be bound by theory, it is possible that amino acid changes in the helical I and II domains that increase the specificity of the CasX variant protein for the target nucleic acid strand can increase the specificity of the CasX variant protein for the target nucleic acid overall. In some embodiments, amino acid changes that increase specificity of CasX variant proteins for target nucleic acid may also result in decreased affinity of CasX variant proteins for DNA.
• Methods of testing CasX protein (such as variant or reference) target specificity may include guide and Circularization for In vitro Reporting of Cleavage Effects by Sequencing (CIRCLE-seq), or similar methods. In brief, in CIRCLE-seq techniques, genomic DNA is sheared and circularized by ligation of stein-loop adapters, which are nicked in the stein-loop regions to expose 4 nucleotide palindromic overhangs. This is followed by intramolecular ligation and degradation of remaining linear DNA. Circular DNA molecules containing a CasX cleavage site are subsequently linearized with CasX, and adapter adapters are ligated to the exposed ends followed by high-throughput sequencing to generate paired end reads that contain information about the off-target site. Additional assays that can be used to detect off-target events, and therefore CasX protein specificity include assays used to detect and quantify hidels (insertions and deletions) formed at those selected off-target sites such as mismatch-detection nuclease assays and next generation sequencing (NGS). Exemplary mismatch-detection assays include nuclease assays, in which genomic DNA from cells treated with CasX and sgNA is PCR amplified, denatured and rehybridized to form hetero-duplex DNA, containing one wild type strand and one strand with an indel. Mismatches are recognized and cleaved by mismatch detection nucleases, such as Surveyor nuclease or T7 endonuclease I.
• p. Protospacer and PAM Sequences
• Herein, the protospacer is defined as the DNA sequence complementary to the targeting sequence of the guide RNA and the DNA complementary to that sequence, referred to as the target strand and non-target strand, respectively. As used herein, the PAM is a nucleotide sequence proximal to the protospacer that, in conjunction with the targeting sequence of the gNA, helps the orientation and positioning of the CasX for the potential cleavage of the protospacer strand(s).
• PAM sequences may be degenerate, and specific RNP constructs may have different preferred and tolerated PAM sequences that support different efficiencies of cleavage. Following convention, unless stated otherwise, the disclosure refers to both the PAM and the protospacer sequence and their directionality according to the orientation of the non-target strand. This does not imply that the PAM sequence of the non-target strand, rather than the target strand, is determinative of cleavage or mechanistically involved in target recognition. For example, when reference is to a TTC PAM, it may in fact be the complementary GAA sequence that is required for target cleavage, or it may be some combination of nucleotides from both strands. In the case of the CasX proteins disclosed herein, the PAM is located 5′ of the protospacer with a single nucleotide separating the PAM from the first nucleotide of the protospacer. Thus, in the case of reference CasX, a TTC PAM should be understood to mean a sequence following the formula 5′- . . . NNTTCN(protospacer)NNNNNN . . . 3′ (SEQ ID NO: 3296) where ‘N’ is any DNA nucleotide and ‘(protospacer)’ is a DNA sequence having identity with the targeting sequence of the guide RNA. In the case of a CasX variant with expanded PAM recognition, a TTC, CTC, GTC, or ATC PAM should be understood to mean a sequence following the formulae: 5′- . . . NNTTCN(protospacer)NNNNNN . . . 3′ (SEQ ID NO: 3296); 5′- . . . NNCTCN(protospacer)NNNNNN . . . 3′ (SEQ ID NO: 3297); 5′- . . . NNGTCN(protospacer)NNNNNN . . . 3′ (SEQ ID NO: 3298); or 5′- . . . NNATCN(protospacer)NNNNNN . . . (SEQ ID NO: 3299). Alternatively, a TC PAM should be understood to mean a sequence following the formula 5′- . . . NNNTCN(protospacer)NNNNNN . . . 3′ (SEQ ID NO: 3300).
• In some embodiments, a CasX variant has improved editing of a PAM sequence exhibits greater editing efficiency and/or binding of a target sequence in the target DNA when any one of the PAM sequences TTC, ATC, GTC, or CTC is located 1 nucleotide 5′ to the non-target strand of the protospacer having identity with the targeting sequence of the gNA in a cellular assay system compared to the editing efficiency and/or binding of an RNP comprising a reference CasX protein in a comparable assay system. In some embodiments, the PAM sequence is TTC. In some embodiments, the PAM sequence is ATC. In some embodiments, the PAM sequence is CTC. In some embodiments, the PAM sequence is GTC.
• q. Unwinding of DNA
• In some embodiments, a CasX variant protein has improved ability to unwind DNA relative to a reference CasX protein. Poor dsDNA unwinding has been shown previously to impair or prevent the ability of CRISPR/Cas system proteins AnaCas9 or Cas14s to cleave DNA. Therefore, without wishing to be bound by any theory, it is likely that increased DNA cleavage activity by some CasX variant proteins of the disclosure is due, at least in part, to an increased ability to find and unwind the dsDNA at a target site. Methods of measuring the ability of CasX proteins (such as variant or reference) to unwind DNA include, but are not limited to, in vitro assays that observe increased on rates of dsDNA targets in fluorescence polarization or biolayer interferometry,
• Without wishing to he bound by theory, it is thought that amino acid changes in the NTSB domain may produce CasX variant proteins with increased DNA unwinding characteristics. Alternatively, or in addition, amino acid changes in the OBD or the helical domain regions that interact with the PAM may also produce CasX variant proteins with increased DNA unwinding characteristics.
• r. Catalytic Activity
• The ribonucleoprotein complex of the CasX:gNA systems disclosed herein comprise a reference CasX protein or CasX variant complexed with a gNA that binds to a target nucleic acid and, in some cases, cleaves the target nucleic acid. In some embodiments, a CasX variant protein has improved catalytic activity relative to a reference CasX protein. Without wishing to be bound by theory, it is thought that in some cases cleavage of the target strand can be a limiting factor for Cas12-like molecules in creating a dsDNA break. In some embodiments, CasX variant proteins improve bending of the target strand of DNA and cleavage of this strand, resulting in an improvement in the overall efficiency of dsDNA cleavage by the CasX ribonucleoprotein complex.
• In some embodiments, a CasX variant protein has increased nuclease activity compared to a reference CasX protein. Variants with increased nuclease activity can be generated, for example, through amino acid changes in the RuvC nuclease domain. In some embodiments, amino acid substitutions in amino acid residues 708-804 of the RuvC domain can result in increased editing efficiency, as seen in FIG. 10. In some embodiments, the CasX variant comprises a nuclease domain having nicka.se activity. In the foregoing embodiment, the CasX nickase of a gene editing pair generates a single-stranded break within 10-18 nucleotides 3′ of a PAM site in the non-target strand. In other embodiments, the CasX variant comprises a nuclease domain having double-stranded cleavage activity. In the foregoing, the CasX of the gene editing pair generates a double-stranded break within 18-26 nucleotides 5′ of a PAM site on the target strand and 10-18 nucleotides 3′ on the non-target strand. Nuclease activity can be assayed by a variety of methods, including those of the Examples. In some embodiments, a CasX variant has a K_cleave constant that is at least 2-fold, or at least 3-fold, or at least 4-fold, or at least 5-fold, or at least 6-fold, or at least 7-fold, or at least 8-fold, or at least 9-fold, or at least 10-fold greater compared to a reference or wild-type CasX.
• In some embodiments, a CasX variant protein has increased target strand loading for double strand cleavage. Variants with increased target strand loading activity can be generated, for example, through amino acid changes in the TLS domain. Without wishing to be bound by theory, amino acid changes in the TSL domain may result in CasX variant proteins with improved catalytic activity. Alternatively, or in addition, amino acid changes around the binding channel for the RNA:DNA duplex may also improve catalytic activity of the CasX variant protein.
• In some embodiments, a CasX variant protein has increased collateral cleavage activity compared to a reference CasX protein. As used herein, “collateral cleavage activity” refers to additional, non-targeted cleavage of nucleic acids following recognition and cleavage of a target nucleic acid. In some embodiments, a CasX variant protein has decreased collateral cleavage activity compared to a reference CasX protein.
• In some embodiments, for example those embodiments encompassing applications where cleavage of the target nucleic acid is not a desired outcome, improving the catalytic activity of a CasX variant protein comprises altering, reducing, or abolishing the catalytic activity of the CasX variant protein. In some embodiments, a ribonucleoprotein complex comprising a dCasX variant protein binds to a target nucleic acid and does not cleave the target nucleic acid.
• In some embodiments, the CasX ribonucleoprotein complex comprising a CasX variant protein binds a target DNA but generates a single stranded nick in the target DNA. In some embodiments, particularly those embodiments wherein the CasX protein is a nickase, a CasX variant protein has decreased target strand loading for single strand nicking. Variants with decreased target strand loading may be generated, for example, through amino acid changes in the TSL domain.
• Exemplary methods for characterizing the catalytic activity of CasX proteins may include, but are not limited to, in vitro cleavage assays, including those of the Examples, below. In some embodiments, electrophoresis of DNA products on agarose gels can interrogate the kinetics of strand cleavage.
• s. Affinity for Target RNA
• In some embodiments, a ribonucleoprotein complex comprising a reference CasX protein or variant thereof binds to a target RNA and cleaves the target nucleic acid. In sonic embodiments, variants of a reference CasX protein increase the specificity of the CasX variant protein for a target RNA, and increase the activity of the CasX variant protein with respect to a target RNA when compared to the reference CasX protein, For example. CasX variant proteins can display increased binding affinity for target RNAs, or increased cleavage of target RNAs, when compared to reference CasX proteins. In some embodiments, a ribonucleoprotein complex comprising a CasX variant protein binds to a target RNA and/or cleaves the target RNA. In some embodiments, a CasX variant has at least about two-fold to about 10-fold increased binding affinity to the target nucleic acid compared to the reference protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ iD NO: 3.
• t. CasX Fusion Proteins
• In some embodiments, the disclosure provides CasX proteins comprising a heterologous protein fused to the CasX. In some cases, the CasX is a reference CasX protein. In other cases, the CasX is a CasX variant of any of the embodiments described herein.
• In some embodiments, the CasX variant protein is fused to one or more proteins or domains thereof that have a different activity of interest, resulting in a fusion protein. For example, in some embodiments, the CasX variant protein is fused to a protein (or domain thereof) that inhibits transcription, modifies a target nucleic acid, or modifies a polypeptide associated with a nucleic acid (e.g., histone modification).
• In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 fused to one or more proteins or domains thereof with an activity of interest. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 fused to one or more proteins or domains thereof with an activity of interest. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 3498-3501, 3505-3520, and 3540-3549 fused to one or more proteins or domains thereof with an activity of interest.
• In some embodiments, a heterologous polypeptide (or heterologous amino acid such as a cysteine residue or a non-natural amino acid) can be inserted at one or more positions within a CasX protein to generate a CasX fusion protein. In other embodiments, a cysteine residue can be inserted at one or more positions within a CasX protein followed by conjugation of a heterologous polypeptide described below. In some alternative embodiments, a heterologous polypeptide or heterologous amino acid can be added at the N- or C-terminus of the reference or CasX variant protein. In other embodiments, a heterologous polypeptide or heterologous amino acid can be inserted internally within the sequence of the CasX protein.
• In some embodiments, the reference CasX or variant fusion protein retains RNA-guided sequence specific target nucleic acid binding and cleavage activity. In some cases, the reference CasX or variant fusion protein has (retains) 50% or more of the activity (e.g., cleavage and/or binding activity) of the corresponding reference CasX or variant protein that does not have the insertion of the heterologous protein. In some cases, the reference CasX or variant fusion protein retains at least about 60%, or at least about 70%, at least about 80%, or at least about 90%, or at least about 92%, or at least about 95%, or at least about 98%, or about 100% of the activity (e.g., cleavage and/or binding activity) of the corresponding CasX protein that does not have the insertion of the heterologous protein.
• In some cases, the reference CasX or CasX variant fusion protein retains (has) target nucleic acid binding activity relative to the activity of the CasX protein without the inserted heterologous amino acid or heterologous polypeptide. In some cases, the reference CasX or CasX variant fusion protein retains at least about 60%, or at least about 70%, at least about 80%, or at least about 90%, or at least about 92%, or at least about 95%, or at least about 98%, or about 100% of the binding activity of the corresponding CasX protein that does not have the insertion of the heterologous protein.
• In some cases, the reference CasX or CasX variant fusion protein retains (has) target nucleic acid binding and/or cleavage activity relative to the activity of the parent CasX protein without the inserted heterologous amino acid or heterologous polypeptide. For example, in some cases, the reference CasX or CasX variant fusion protein has (retains) 50% or more of the binding and/or cleavage activity of the corresponding parent CasX protein (the CasX protein that does not have the insertion). For example, in some cases, the reference CasX or CasX variant fusion protein has (retains) 60% or more (70% or more, 80% or more, 90% or more, 92% or more, 95% or more, 98% or more, or 100%) of the binding and/or cleavage activity of the corresponding CasX parent protein (the CasX protein that does not have the insertion). Methods of measuring cleaving and/or binding activity of a CasX protein and/or a CasX fusion protein will be known to one of ordinary skill in the art, and any convenient method can be used.
• A variety of heterologous polypeptides are suitable for inclusion in a reference CasX or CasX variant fusion protein of the disclosure. In some cases, the fusion partner can modulate transcription (e.g., inhibit transcription, increase transcription) of a target DNA. For example, in sonic cases the fusion partner is a protein (or a domain from a protein) that inhibits transcription (e.g., a transcriptional repressor, a protein that functions via recruitment of transcription inhibitor proteins, modification of target DNA such as methylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histon.es, and the like). In some cases the fusion partner is a protein (or a domain from a protein) that increases transcription (e.g., a transcription activator, a protein that acts via recruitment of transcription activator proteins, modification of target DNA such as demethylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like).
• In some cases, a fusion partner has enzymatic activity that modifies a target nucleic acid; nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity or glycosylase activity.
• In some cases, a fusion partner has enzymatic activity that modifies a polypeptide a histone) associated with a target nucleic acid; e.g., methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a polypeptide with methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, tnyristoylation activity or demyristoylation activity. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a polypeptide with methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity. In some embodiments, a CasX variant comprises any one of SEQ NOS: 3498-3501, 3505-3520, and 3540-3549 and a polypeptide with methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity.
• Examples of proteins (or fragments thereof) that can he used as a suitable fusion partner to a reference CasX or CasX variant to increase transcription include but are not limited to: transcriptional activators such as VP16, VP64, VP4S, VP160, p65 subdomain (e.g., from NFkB), and activation domain of EDLL and/or transcription activator-like (TAL) activation domain (e.g., for activity in plants); histone lysine methyltransferases such as SET domain containing IA, histone lysine methyltransferase (SET2A), SET domain containing 1B, histone lysine methyltransferase (SET1B), lysine methyltransferase 2A (MLL1) to 5, ASCL1 (ASH1) achacte-scute family bHLH transcription factor 1 (ASH1), SET and MYND domain containing 2provided (SMYD2), nuclear receptor binding SET domain protein 1 (NSD1), and the like; histone lysine demethylases such as lysine demethylase 3A (JHDM2a)/Lysine-specific demethylase 3B (JHDM2b), lysine demethylase 6A (UTX), lysine demethylase 6B (JMJD3), and the like; histone acetyltransferases such as lysine acetyltransferase 2A (GCN5), lysine acetyltransferase 2B (PCAF), CREB binding protein (CBP), E1A binding protein p50 (p300), TATA-box binding protein associated factor 1 (TATO, lysine acetyltransferase 5 (T1P60/PLIP), lysine acetyltransferase 6A (MOZ/MYST3), lysine acetyltransferase 6B (MORF/MYST4), SRC proto-oncogene, non-receptor tyrosine kinase (SRC I), nuclear receptor coactivator 3 (ACTR), MYB binding protein 1a (P160), clock circadian regulator (CLOCK), and the like; and DNA demethylases such as Ten-Eleven Translocation (TET) dioxygenase 1 (TET1CD), tet methylcytosine dioxygenase 1 (TET1), demeter (DME), demeter-like 1 (DML1), demeter-like 2 (DML2), protein ROS1 (ROS1), and the like.
• Examples of proteins (or fragments thereof) that can be used as a suitable fusion partner with a reference CasX or CasX variant to decrease transcription include but are not limited to: transcriptional repressors such as the Kruppel associated box (KRAB or SKD); KOX1 repression domain; the Mad mSlN3 interaction domain (SID); the ERF repressor domain (ERD), the SRDX repression domain (e.g., for repression in plants), and the like; histone lysine methyltransferases such as PR/SET domain containing protein (Pr-SET)7/8, lysine methyltransferase 5B (SUV4-20H1), PR/SET domain 2 (RIZ1), and the like; histone lysine demethylases such as lysine demethylase 4A (JMJD2A/JHDM3A), lysine demethylase 4B (JMJD2B), lysine demethylase 4C (JMJD2C/GASC1), lysine demethylase 4D (JMJD2D), lysine demethylase 5A (JARID1A/RBP2), lysine demethylase 5B (JARID1B/PLU-1), lysine demethylase 5C (JARID 1C/SMCX), lysine demethylase 5D (JARID1D/SMCY), and the like; histone lysine deacetylases such as histone deacetylase 1 (HDAC1), HDAC2, HDAC3, HDAC8, HDAC4, HDAC5, HDAC7, HDAC9, sirtuin 1 (SIRT1), S1RT2, HDAC 11, and the like; DNA methylases such as Hhal DNA m5c-methyltransferase (M.HhaI), DNA methyltransferase (DNMT1), DNA methyltransferase 3a (DNMT3a), DNA methyltransferase 3b (DNMT3b), methyltransferase 1 (MET1), S-adenosyl-L-methionine-dependent methyltransferases superfamily protein (DRM3) (plants), DNA cytosine methyltransferase MET2a (ZMET2), chromomethylase 1 (CMT1), chromomethylase 2 (CMT2) (plants), and the like; and periphery recruitment elements such as Lamin A, Lamin B, and the like.
• In some cases, the fusion partner to a reference CasX or CasX variant has enzymatic activity that modifies the target nucleic acid (e,g., ssRNA, dsRNA, ssDNA, dsDNA). Examples of enzymatic activity that can be provided by the fusion partner include but are not limited to: nuclease activity such as that provided by a restriction enzyme (e.g., Fokl nuclease), methyltransferase activity such as that provided by a methyltransferase (e.g., Hhal DNA m5c-methyltransferase (M.Hhal), DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3a (DNMT3a), DNA methyltransferase 3b (DNMT3b), METI, DRM3 (plants), ZMET2, CMT1, CMT2 (plants), and the like), demethylase activity such as that provided by a demethylase (e.g., Ten-Eleven Translocation (TET) dioxygenase 1 (TET 1 CD), TET1, DME, DML1, DML2, ROS1, and the like), DNA repair activity. DNA damage activity, deamination activity such as that provided by a deaminase (e.g., a cytosine deaminase enzyme, e.g., an APOBEC protein such as rat apolipoprotein B inRNA editing enzyme, catalytic polypeptide 1 {APOBEC1}), dismutase activity, alkylation activity, depurinalion activity, oxidation activity, pyrimidine dimer forming activity, integrase activity such as that provided by an integrase and/or resolvase (e.g., Gin invertase such as the hyperactive mutant of the Gin invertase, GinH106Y; human immunodeficiency virus type I integrase (IN), Tn3 resolvase and the like), transposase activity, recombinase activity such as that provided by a recombinase (e.g., catalytic domain of Gin recombinase), polymerase activity, ligase activity, hehcase activity, photolyase activity, and glycosylase activity).
• In some cases, a reference CasX or CasX variant protein of the present disclosure is fused to a polypeptide selected from: a domain for increasing transcription (e.g., a VP16 domain, a VP64 domain), a domain for decreasing transcription (e.g., a KRAB domain, e.g., from the Kox1 protein), a core catalytic domain of a histone acetyltransferase (e.g., histone acetyltransferase p300), a protein/domain that provides a detectable signal (e.g., a fluorescent protein such as GFP), a nuclease domain (e.g., a Fokl nuclease), and a base editor (discussed further below).
• In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 fused to a polypeptide selected from the group consisting of a domain for decreasing transcription, a domain with enzymatic activity, a core catalytic domain of a histone acetyltransferase, a protein/domain that provides a detectable signal, a nuclease domain, and a base editor. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 fused to a polypeptide selected from the group consisting of a domain for decreasing transcription, a domain with enzymatic activity, a core catalytic domain of a histone acetyltransferase, a protein/domain that provides a detectable signal, a nuclease domain, and a base editor. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 3498-3501, 3505-3520, and 3540-3549 fused to a polypeptide selected from the group consisting of a domain for decreasing transcription, a domain with enzymatic activity, a core catalytic domain of a histone acetyltransferase, a protein/domain that provides a detectable signal, a nuclease domain, and a base editor.
• In some cases, a reference CasX protein or CasX variant of the present disclosure is fused to a base editor. Base editors include those that can alter a guanine, adenine, cytosine, thymine, or uracil base on a nucleoside or nucleotide. Base editors include, but are not limited to an adenosine deaminase, cytosine deaminase (e.g., APOBEC1), and guanine oxidase. Accordingly, any of the reference CasX or CasX variants provided herein may comprise (i.e., are fused to) a base editor; for example a reference CasX or CasX variant of the disclosure may be fused to an adenosine deaminase, a cytosine deaminase, or a guanine oxidase. In exemplary embodiments, a CasX variant of the disclosure comprising any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 is fused to an adenosine deaminase, cytosine deaminase, or a guanine oxidase.
• In some cases, the fusion partner to a reference CasX or CasX variant has enzymatic activity that modifies a protein associated with the target nucleic acid (e.g., ssRNA, dsRNA, ssDNA, dsDNA) (e.g., a histone, an RNA binding protein, a DNA binding protein, and the like). Examples of enzymatic activity (that modifies a protein associated with a target nucleic acid) that can be provided by the fusion partner with a reference CasX or CasX variant include but are not limited to: methyltransferase activity such as that provided by a histone methyltransferase (HMT) (e.g., suppressor of variegation 3-9 homolog 1 (SUV39H1, also known as KMT1A), dichromatic histone lysine methyltransferase 2 (G9A, also known as KMT1C and EHMT2), SUV39H2, ESET/SETDB 1, and the like, SET1A, SET1B, MLL1 to 5, ASH1, SMYD2, NSD1, DOT1 like histone lysine methyltransferase (DOT1L), Pr-SET7/8, lysine methyltransferase 5B (SUV4-20H1), enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2), PR/SET domain 2 (RIZ1), demethylase activity such as that provided by a histone demethylase (e.g., Lysine Demethylase 1A (KDM1A also known as LSD1), JHDM2a/b, JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, JARID1A/RBP2, JARID1B/PLU-1, JARID1C/SMCX, JARID1D/SMCY, UTX, JMJD3, and the like), acetyltransferase activity such as that provided by a histone acetylase transferase (e.g., catalytic core/fragment of the human acetyltransferase p300, GCN5, PCAF, CBP, TAF1, TIP60/PLIP, MOZ/MYST3, MORF/MYST4, HB01/MYST2, HMOF/MYST1, SRC1, ACTR, P160, CLOCK, and the like), deacetylase activity such as that provided by a histone deacetylase (e.g., HDAC1, HDAC2, HDAC3, HDAC8, HDAC4, HDAC5, HDAC7, HDAC9, SIRT1, SIRT2, HDAC11, and the like), kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity, and demyristoylation activity.
• Additional examples of suitable fusion partners to a reference CasX or CasX variant are (i) a dihydrofolate reductase (DHFR) destabilization domain (e.g., to generate a chemically controllable subject RNA-guided polypeptide), and (ii) a chloroplast transit peptide.
• Suitable chloroplast transit peptides include, but are not limited to sequences having at least 80%, at least 90%, or at least 95% identity to or are identical to:

• (SEQ ID NO: 338)

  MASMISSSAVTTVSRASRGQSAAMAPFGGLKSMTGFPVRKVNTDITSIT

  SNGGRVKCMQVWPPIGKKKFETLSYLPPLTRDSRA;

  (SEQ ID NO: 339)

  MASMISSSAVTTVSRASRGQSAAMAPFGGLKSMTGFPVRKVNTDITSIT

  SNGGRVKS;

  (SEQ ID NO: 340)

  MASSMLSSATMVASPAQATMVAPFNGLKSSAAFPATRKANNDITSITSN

  GGRVNCMQVWPPIEKKKFETISYLPDLTDSGGRVNC;

  (SEQ ID NO: 341)

  MAQVSRICNGVQNPSLISNLSKSSQRKSPLSVSLKTQQHPRAYPISSSW

  GLKKSGMTLIGSELRPLKVMSSVSTAC;

  (SEQ ID NO: 342)

  MAQVSRICNGVWNPSLISNLSKSSQRKSPLSVSLKTQQHPRAYPISSSW

  GLKKSGMTLIGSELRPLKVMSSVSTAC;

  (SEQ ID NO: 343)

  MAQINNMAQGIQTLNPNSNFHKPQVPKSSSFLVFGSKKLKNSANSMLVL

  KKDSIFMQLFCSFRISASVATAC;

  (SEQ ID NO: 344)

  MAALVTSQLATSGTVLSVTDRFRRPGFQGLRPRNPADAALGMRTVGASA

  APKQSRKPHRFDRRCLSMVV;

  (SEQ ID NO: 345)

  MAALTTSQLATSATGFGIADRSAPSSLLRHGFQGLKPRSPAGGDATSLS

  VTTSARATPKQQRSVQRGSRRFPSVVVC;

  (SEQ ID NO: 346)

  MASSVLSSAAVATRSNVAQANMVAPFTGLKSAASFPVSRKQNLDITSIA

  SNGGRVQC;

  (SEQ ID NO: 347)

  MESLAATSVFAPSRVAVPAARALVRAGTVVPTRRTSSTSGTSGVKCSAA

  VTPQASPVISRSAAAA;

  and

  (SEQ ID NO: 348)

  MGAAATSMQSLKFSNRLVPPSRRLSPVPNNVTCNNLPKSAAPVRTVKCC

  ASSWNSTINGAAATTNGASAASS.

• In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a chloroplast transit peptide. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a chloroplast transit peptide. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 3498-3501, 3505-3520, and 3540-3549 and a chloroplast transit peptide.
• In some cases, a reference CasX or CasX variant protein of the present disclosure can include an endosomal escape peptide. In some cases, an endosomal escape polypeptide comprises the amino acid sequence GLFXALLXLLXSLWXLLLXA (SEQ ID NO: 349), wherein each X is independently selected from lysine, histidine, and arginine. In some cases, an endosomal escape polypeptide comprises the amino acid sequence GLFHALLHLLHSLWHLLLHA (SEQ ID NO: 350), o H (SEQ ID NO: 351). In some embodiments, a CasX variant comprises a sequence of any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and an endosomal escape polypeptide. In some embodiments, a CasX variant comprises a sequence of any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and an endosomal escape polypeptide. In some embodiments, a CasX variant comprises a sequence of any one of SEQ NOS: 3498-3501, 3505-3520, and 3540-3549 and an endosomal escape polypeptide.
• Non-limiting examples of suitable fusion partners for a reference CasX or CasX variant for use when targeting ssRNA target nucleic acids include (but arc not limited to): splicing factors e.g., RS domains); protein translation components (e.g, translation initiation, elongation, and/or release factors; e.g., eukaryotic translation initiation factor 4 gamma {eIF4G}); RNA methylases; RNA editing enzymes (e.g., RNA deaminases, e.g., adenosine deaminase acting on RNA (ADAR), including A to I and/or C to U editing enzymes), helicases; RNA-binding proteins; and the like. It is understood that a heterologous polypeptide can include the entire protein or in some cases can include a fragment of the protein (e.g., a functional domain). In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a protein or domain selected from the group consisting of a splicing factor, a protein translation component, an RNA methylase, an RNA editing enzyme, a helicase, and an RNA binding protein. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a protein or domain selected from the group consisting of a splicing factor, a protein translation component, an RNA methylase, an RNA editing enzyme, a helicase, and an RNA binding protein. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 3498-3501, 3505-3520, and 3540-3549 and a protein or domain selected from the group consisting of a splicing factor, a protein translation component, an RNA methylase, an RNA editing enzyme, a helicase, and an RNA binding protein.
• A fusion partner for a reference CasX or CasX variant can be any domain capable of interacting with ssRNA (which, for the purposes of this disclosure, includes intramolecular and/or intermolecular secondary structures, e.g., double-stranded RNA duplexes such as hairpins, stein-loops, etc.), whether transiently or irreversibly, directly or indirectly, including but not limited to an effector domain selected from the group comprising; endonucleases (for example RNase III, the CRR22 DYW domain, Dicer, and PIN (PilT N-terminus) domains from proteins such as SMGS and SMG6); proteins and protein domains responsible for stimulating RNA cleavage (for example cleavage and polyadenylation specific factor {CPSF}, cleavage stimulation factor {CstF}, CFIm and CFIIm); exonucleases (for example chromatin-binding exonuclease XRN1 (XRN-1) or Exonuclease T); deadenylases (for example DNA 5′-adenosine monophosphate hydrolase {HNT3}); proteins and protein domains responsible for nonsense mediated RNA decay (for example UPF1 RNA helicase and ATPase {UPF1}, UPF2, UPF3, UPF3h, RNP SI, RNA binding motif protein 8A {Y14}, DEK proto-oncogene {DEK}, RNA-processing protein REF2 {REF2}, and Serine-arginine repetitive matrix 1 {SRm160}); proteins and protein domains responsible for stabilizing RNA (for example poly(A) binding protein cytoplasmic 1 {PABP}); proteins and protein domains responsible for repressing translation (for example argonaute RISC catalytic component 2 {Ago2} and Ago4); proteins and protein domains responsible for stimulating translation (for example Staufen); proteins and protein domains responsible for (e.g., capable of) modulating translation (e.g., translation factors such as initiation factors, elongation factors, release factors, etc., e.g., eIF4G); proteins and protein domains responsible for polyadenylation of RNA (for example poly(A) polymerase (PAP1), PAP-associated domain-containing protein;Poly(A) RNA polymerase gld-2 {GLD-2}, and Star-PAP); proteins and protein domains responsible for polyuridinylation of RNA (for example Terminal uridylyltransferase {CID1} and terminal uridylate transferase); proteins and protein domains responsible for RNA localization (for example from insulin like growth factor 2 mRNA binding protein 1 {IMP1}, Z-DNA binding protein 1 {ZBP1}, She:2p, She3p, and. Bicaudal-D); proteins and protein domains responsible for nuclear retention of RNA (for example Rrp6); proteins and protein domains responsible for nuclear export of RNA (for example nuclear RNA export factor 1 {TAP}, nuclear RNA export factor 1 {NX1}, THC) Complex {THO}, TREX, REF, and Aly/REF export factor {Aly}); proteins and protein domains responsible for repression of RNA splicing (for example polypyrimidine tract binding protein 1 {PTB}, KH RNA binding domain containing, signal transduction associated 1 Sam68}, and heterogeneous nuclear ribonucleoprotein A1 {hnRNP A1}); proteins and protein domains responsible for stimulation of RNA splicing (for example serine/arginine-rich (SR) domains); proteins and protein domains responsible for reducing the efficiency of transcription (for example FUS RNA binding protein {FUS (TLS)}), and proteins and protein domains responsible for stimulating transcription (for example cyclin dependent kinase 7 {CDK7} and HIV Tat). Alternatively, the effector domain may be selected from the group comprising endonucleases; proteins and protein domains capable of stimulating RNA cleavage; exonucleases; deadenylases; proteins and protein domains having nonsense mediated RNA decay activity; proteins and protein domains capable of stabilizing RNA; proteins and protein domains capable of repressing translation; proteins and protein domains capable of stimulating translation; proteins and protein domains capable of modulating translation (e.g., translation factors such as initiation factors, elongation factors, release factors, etc., e.g., eIF 4G); proteins and protein domains capable of polyadenylation of RNA; proteins and protein domains capable of polyuridinylation of RNA; proteins and protein domains having RNA localization activity; proteins and protein domains capable of nuclear retention of RNA; proteins and protein domains having RNA nuclear export activity; proteins and protein domains capable of repression of RNA splicing; proteins and protein domains capable of stimulation of RNA splicing; proteins and protein domains capable of reducing the efficiency of transcription; and proteins and protein domains capable of stimulating transcription. Another suitable heterologous polypeptide is a RIF RNA-binding domain, which is described in more detail in WO2012068627, which is hereby incorporated by reference in its entirety.
• Some suitable RNA splicing factors that can be used (in whole or as fragments thereof) as a fusion partner with a reference CasX or CasX variant have modular organization, with separate sequence-specific RNA binding modules and splicing effector domains. For example, members of the serine/arginine-rich (SR) protein family contain N-terminal RNA recognition motifs (RRMs) that bind to exonic splicing enhancers (ESEs) in pre-mRNAs and C-terminal RS domains that promote exon inclusion. As another example, the hnRNP protein hnRNP A1 binds to exonic splicing silencers (ESSs) through its RRM domains and inhibits exon inclusion through a C-terminal glycine-rich domain. Some splicing factors can regulate alternative use of splice site (ss) by binding to regulatory sequences between the two alternative sites. For example, ASF/SF2 can recognize ESEs and promote the use of intron proximal sites, whereas hnRNP A12 can bind to ESSs and shift splicing towards the use of intron distal sites. One application for such factors is to generate ESFs that modulate alternative splicing of endogenous genes, particularly disease associated genes. For example, BCL2 like 1 (Bcl-x) pre-mRNA produces two splicing isoforms with two alternative 5′ splice sites to encode proteins of opposite functions. The long splicing isoform Bcl-xL is a potent apoptosis inhibitor expressed in long-lived post mitotic cells and is up-regulated in many cancer cells, protecting cells against apoptotic signals. The short isofonn Bcl-xS is a pro-apoptotic isofonn and expressed at high levels in cells with a high turnover rate (e.g., developing lymphocytes). The ratio of the two Bcl-x splicing isoforms is regulated by multiple cc -elements that are located in either the core exon region or the exon extension region (i.e., between the two alternative 5′ splice sites). For more examples, see WO2010075303, which is hereby incorporated by reference in its entirety. Further suitable fusion partners include, but are not limited to proteins (or fragments thereof) that are boundary elements (e.g., CTCF), proteins and fragments thereof that provide periphery recruitment (e,g., Lamin A, Lamin B, etc.), and protein docking elements (e,g., FKBP/FRB, Pill/Abyl, etc.).
• In some cases, a heterologous polypeptide (a fusion partner) for use with a reference CasX or CasX variant provides for subcellular localization, i.e., the heterologous polypeptide contains a subcellular localization sequence (e.g., a nuclear localization signal (NLS) for targeting to the nucleus, a sequence to keep the fusion protein out of the nucleus, e.g., a nuclear export sequence (NES), a sequence to keep the fusion protein retained in the cytoplasm, a mitochondrial localization signal for targeting to the mitochondria, a chloroplast localization signal for targeting to a chloroplast, an ER retention signal, and the like). In some embodiments, a subject RNA-guided polypeptide or a conditionally active RNA-guided polypeptide and/or subject CasX fusion protein does not include a NLS so that the protein is not targeted to the nucleus, which can be advantageous; e.g., when the target nucleic acid is an RNA that is present in the cytosol. In some embodiments, a fusion partner can provide a tag (i.e., the heterologous polypeptide is a detectable label) for ease of tracking and/or purification (e.g., a fluorescent protein, e.g., green fluorescent protein (GFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), cyan fluorescent protein (CFF), mCherry, tdTomato, and the like; a histidine tag, e.g., a 6XHis tag; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like). In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a subcellular localization sequence or a tag. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a subcellular localization sequence or a tag. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 3498-3501, 3505-3520, and 3540-3549 and a subcellular localization sequence or a tag.
• In some cases, a reference or CasX variant protein includes (is fused to) a nuclear localization signal (NLS). In some cases, a reference or CasX variant protein is fused to 2 or more, 3 or more, 4 or more, or 5 or more 6 or more, 7 or more, 8 or more NLSs. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NISs) are positioned at or near (e.g., within 50 amino acids of) the N-temiinus and/or the C-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the C-terminus. In some cases, one or more NLSs (3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C-terminus. In some cases, an NLS is positioned at the N-terminus and an NLS is positioned at the C-terminus. In some cases, a reference or CasX variant protein includes (is fused to) between 1 and 10 NLSs (e.g,, 1-9, 1-8, 1-7, 1-6, 1-5, 2-10, 2-9, 2-8, 2-7, 2-6, or 2-5 NLSs). In some cases, a reference or CasX variant protein includes (is fused to) between 2 and 5 NLSs (e.g., 2-4, or 2-3 NLSs).
• Non-limiting examples of NLSs suitable for use with a reference CasX or CasX variant include sequences having at least about 80%, at least about 90%, or at least about 95% identity or are identical to sequences derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence FKKKRKV (SEQ ID NO: 352); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ D NO: 353); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO: 354) or RQRRNELKRSP (SEQ ID NO: 355); the hRNPA1 M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 356); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 357) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO: 358) and PPKKARED (SEQ ID NO: 359) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO: 360) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO: 361) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO: 362) and PKQKKRK (SEQ ID NO: 363) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 364) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO: 365) of the mouse Mx1 protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 366) of the human poly(ADP-ribose) polymerase; the sequence RKCLQAGMNLEARKTKK (SEQ ID NO: 367) of the steroid hormone receptors (human) glucocorticoid; the sequence PRPRKIPR (SEQ ID NO: 368) of Boma disease virus P protein (BDV-P1); the sequence PPRKKRTVV (SEQ ID NO: 369) of hepatitis C virus nonstructural protein (HCV-NS5A); the sequence NLSKKKKRKREK (SEQ ID NO: 370) of LEF1; the sequence RRPSRPFRKP (SEQ ID NO: 371) of ORF57 simirae; the sequence KRPRSPSS (SEQ ID NO: 372) of EBV LANA; the sequence KRGINDRNFWRGENERKTR (SEQ ID NO: 373) of Influenza A protein; the sequence PRPPKMARYDN (SEQ II) NO: 374) of human RNA helicase A (RHA); the sequence KRSFSKAF (SEQ ID NO: 375) of nucleolar RNA helicase II; the sequence KLKIKRPVK (SEQ ID NO: 376) of TUS-protein; the sequence PKKKRKVPPPPAAKRVKLD (SEQ ID NO: 377) associated with importin-alpha; the sequence PKTRRRPRRSQRKRPPT (SEQ ID NO: 378) from the Rex protein in HTLV-1; the sequence SRRRKANPTKLSENAKKIAKEVEN (SEQ ID NO: 379) from the EGL-13 protein of Caenorhabditis elegans; and the sequences KTRRRPRRSQRKRPPT (SEQ ID NO: 380). RRKKRRPRRKKRR (SEQ ID NO: 381), PKKKSRKPKKKSRK (SEQ ID NO: :382), HKKKHPDASVNFSEFSK (SEQ ID NO: 383), QRPGPYDRPQRPGPYDRP (SEQ ID NO: 384). LSPSLSPLLSPSLSPL (SEQ ID NO: 385), IRGIKGGKGLGKGGAKRHRK (SEQ ID NO: 386), PKRGRGRPKRGRGR (SEQ ID NO: 387). PKKKRKVPPPPAAKRVKLD (SEQ ID NO: 388) and PKKKRKVPPPPKKKRKV (SEQ NO: 389). In general, NLS (or multiple NLSs) are of sufficient strength to drive accumulation of a reference or CasX variant fusion protein in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to a reference or CasX variant fusion protein such that location within a cell may be visualized. Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immunohistochemistry. Western blot, or enzyme activity assay. Accumulation in the nucleus may also be determined indirectly.
• In some embodiments, a CasX variant comprising an N terminal NLS comprises a sequence of any one of SEQ ID NOS: 3508-3540-3549. In some embodiments, a CasX variant comprising an N terminal NLS comprises a sequence with one or more additional modifications to of any one of SEQ ID NOS: 3508-3540-3549.
• In some cases, a reference or CasX variant fusion protein includes a “Protein Transduction Domain” or PTD (also known as a CPP—cell penetrating peptide), which refers to a protein, polynucleotide, carbohydrate, or organic or inorganic compound that facilitates traversing a lipid bilayer, micelle, cell membrane, organelle membrane, or vesicle membrane. A PTD attached to another molecule, which can range from a small polar molecule to a large macromolecule and/or a nanoparticle, facilitates the molecule traversing a membrane, for example going from an extracellular space to an intracellular space, or from the cytosol to within an organelle. In some embodiments, a PTD is covalently linked to the amino terminus of a reference or CasX variant fusion protein. In some embodiments, a PTD is covalently linked to the carboxyl terminus of a reference or CasX variant fusion protein. In some cases, the PTD is inserted internally in the sequence of a reference or CasX variant fusion protein at a suitable insertion site. In some cases, a reference or CasX variant fusion protein includes (is conjugated to, is fused to) one or more PTDs (e.g., two or more, three or more, four or more PTDs). In some cases, a PTD includes one or more nuclear localization signals (NLS). Examples of PTDs include but are not limited to peptide transduction domain of HIV TAT comprising YGRKKRRQRRR (SEQ ID NO: 390), RKKRRQRR (SEQ ID NO: 391); YARAAARQARA (SEQ ID NO: 392); THRLPRRRRRR (SEQ ID NO: 393); and GGRRARRRRRR (SEQ ID NO: 394); a polyarginine sequence comprising a number of arginines sufficient to direct entry into a cell (e.g., 3, 4, 5, 6, 7, 8. 9, 10, or 10-50 arginines); a VP22 domain (Zender et al. (2002) Cancer Gene Ther. 9(6):489-96), an Drosophila Antennapedia protein transduction domain (Noguchi et al. (2003) Diabetes 52(7): 1732-1737); a truncated human calcitonin. peptide (Trehin et al. (2004) Pharm. Research 21:1248-1256); polylysine (Wender et al. (2000) Proc. Natl. Acad. Sci. USA 97: 13003-13008); RRQRRTSKLMKR (SEQ ID NO: 395); Transportan GWTLNSAGYLLGKINLKALAALAKKIL (SEQ ID NO: 396); KALAWEAKLAKALAKALAKHLAKALAKALKCEA (SEQ ID NO: 397); and RQIKIWFQNRRMKWKK (SEQ ID NO: 398). In some embodiments, the PTD is an activatable CPP (ACPP) (Aguilera et al. (2009) Integr Biol (Camb) June; 1(5-6): 371-381). ACPPs comprise a polycationic CPP (e.g., Arg9 or “R9”) connected via a cleavable linker to a matching polyanion (e.g., Glu9 or “E9”), which reduces the net charge to nearly zero and thereby inhibits adhesion and uptake into cells. Upon cleavage of the linker, the polyanion is released, locally unmasking the polyarginine and its inherent adhesiveness, thus “activating” the ACPP to traverse the membrane. In some embodiments, a CasX variant comprises any one of SEQ m NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a PTD. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a PTD. In some embodiments, a CasX variant comprises any one of SEQ ID NOS: 3498-3501, 3505-3520, and 3540-3549 and a PTD.
• In some embodiments, a reference or CasX variant fusion protein can include a CasX protein that is linked to an internally inserted heterologous amino acid or heterologous polypeptide (a heterologous amino acid sequence) via a linker polypeptide (e.g., one or more linker polypeptides). In some embodiments, a reference or CasX variant fusion protein can be linked at the C-terminal and/or N-terminal end to a heterologous polypeptide (fusion partner) via a linker polypeptide (e.g., one or more linker polypeptides) The linker polypeptide may have any of a variety of amino acid sequences. Proteins can be joined by a spacer peptide, generally of a flexible nature, although other chemical linkages are not excluded. Suitable linkers include polypeptides of between 4 amino acids and 40 amino acids in length, or between 4 amino acids and 25 amino acids in length. These linkers are generally produced by using synthetic, linker-encoding oligonucleotides to couple the proteins. Peptide linkers with a degree of flexibility can be used. The linking peptides may have virtually any amino acid sequence, bearing in mind that the preferred linkers will have a sequence that results in a generally flexible peptide. The use of small amino acids, such as glycine and alanine, are of use in creating a flexible peptide. The creation of such sequences is routine to those of skill in the art. A variety of different linkers are commercially available and are considered suitable for use. Example linker polypeptides include glycine polymers (G)n, glycine-serine polymer (including, for example, (GS)n, GSGGSn (SEQ ID NO: 399), GGSGGSn (SEQ ID NO: 400), and GGGSn (SEQ ID NO: 401), where n is an integer of at least one), glycine-alanine polymers, alanine-serine polymers, glycine-proline polymers, proline polymers and proline-alanine polymers. Example linkers can comprise amino acid sequences including, but not limited to, GGSG (SEQ ID NO: 402), GGSGG (SEQ ID NO: 403), GSSSG (SEQ ID NO: 404), GSGGG (SEQ ID NO: 405), GGGSG (SEQ ID NO: 406), GSSSG (SEQ ID NO: 407), GPGP (SEQ ID NO: 408), GGP, PPP, PPAPPA (SEQ ID NO: 409), PPPGPPP (SEQ ID NO: 410) and the like. The ordinarily skilled artisan will recognize that design of a peptide conjugated to any elements described above can include linkers that arc all or partially flexible, such that the linker can include a flexible linker as well as one or more portions that confer less flexible structure.
• V. gNA and CasX Protein Gene Editing Pairs
• In other aspects, provided herein are compositions of a gene editing pair comprising a CasX protein and a guide NA, referred to herein as a gene editing pair. In certain embodiments, the gene editing pair comprises a CasX variant protein as described herein (e.g., any one of the sequences set forth in Tables 3, 8. 9, 10 and 12) or a reference CasX protein as described herein (e.g., SEQ ID NOS:1-3), while, the guide NA is a reference gRNA (SEQ ID NOS: 4-16) or a gNA variant as described herein (e.g., SEQ ID NOS: 2101-2280), or sequence variants having at least 60%, or at least 70%, at least about 80%, or at least about 90%, or at least about 95% sequence identity thereto, wherein the gNA comprises a targeting sequence complementary to the target DNA. In those embodiments in which one component is a variant, the pair is referred to as a variant gene editing pair. In other embodiments, a gene editing pair comprises the CasX protein, a first gNA (either a reference gRNA {SEQ ID NOS: 4-16} or a gNA variant as described herein {e.g., SEQ ID NOS: 2101-2280}) with a targeting sequence, and a second gNA variant or a second reference guide nucleic acid, wherein the second gNA variant or the second reference guide nucleic acid has a targeting sequence complementary to a different or overlapping portion of the target DNA compared to the targeting sequence of the first gNA.
• In some embodiments, the variant gene editing pair has one or more improved characteristics compared to a reference gene editing pair, wherein the reference gene editing pair comprises a CasX protein of SEQ ID NOS: 1-3, a different gNA, or both. For example, in some embodiments, the variant gene editing pair comprises a CasX variant protein, and the variant gene editing pair has one or more improved characteristics compared to a reference gene editing pair comprising a reference CasX protein. In other embodiments, the variant gene editing pair comprises a gNA variant, and the variant gene editing pair has one or more improved characteristics compared to a reference gene editing pair comprising a reference gRNA. In other embodiments, the variant gene editing pair comprises a gNA variant and a CasX variant protein, and the variant gene editing pair has one or more improved characteristics compared to a reference gene editing pair comprising a reference CasX protein and a reference gRNA.
• In some embodiments of the variant gene editing pairs provided herein, the CasX is a variant protein as described herein (e.g., the sequences set forth in Tables 3, 8, 9, 10 and 12 or sequence variants having at least 60%, or at least 70%, at least about 80%, or at least about 90%, or at least about 95%, or at least about 99% sequence identity to the listed sequences) while the gNA is a reference gRNA of SEQ ID NO: 5 or SEQ ID NO: 4. In some embodiments of the variant gene editing pairs provided herein, the CasX comprises a reference CasX protein of SEQ ID NO: 1. SEQ ID NO: 2, or SEQ ID NO: 3 while the gNA variant is a sequence of SEQ ID NOS:2101-2280, or sequence variants having at least 60%, or at least 70%, at least about 80%, or at least about 90%, or at least about 95% sequence identity to the listed sequences.
• In some embodiments, the variant gene editing pair has one or more improved characteristics compared to a reference gene editing pair comprising a reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. In some embodiments, the variant gene editing pair has one or more improved characteristics compared to a reference gene editing pair comprising a reference gRNA of SEQ ID NO: 5 or SEQ ID NO: 4. In some embodiments, the variant gene editing pair has one or more improved characteristics compared to a reference gene editing pair comprising a reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ NO: 3 and a reference gRNA of SEQ ID NO: S or SEQ ID NO: 4.
• Exemplary improved characteristics, as described herein, may in some embodiments, and include improved CasX:gNA RNP complex stability, improved binding affinity between the CasX and gNA, improved kinetics of RNP complex formation, higher percentage of cleavage-competent RNP, improved RNP binding affinity to the target DNA, improved unwinding of the target DNA, increased editing activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, or improved resistance to nuclease activity. In the foregoing embodiments, the improvement is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 50-fold, at least about 100-fold, at least about 500-fold, at least about 1000-fold, at least about 5000-fold, at least about 10,000-fold, or at least about 100,000-fold compared to the characteristic of a reference CasX protein and reference gNA pair. In other cases, the one or more of the improved characteristics may be improved about 1.1 to 100,00-fold, about 1.1 to 10,00-fold, about 1.1 to 1,000-fold, about 1.1 to 500-fold, about 1.1 to 100-fold, about 1.1 to 50-fold, about 1.1 to 20-fold, about 10 to 100,00-fold, about 10 to 10,00-fold, about 10 to 1,000-fold, about 10 to 500-fold, about 10 to 100-fold, about 10 to 50-fold, about 10 to 20-fold, about 2 to 70-fold, about 2 to 50-fold, about 2 to 30-fold, about 2 to 20-fold, about 2 to 10-fold, about 5 to 50-fold, about 5 to 30-fold, about 5 to 10-fold, about 100 to 100,00-fold, about 100 to 10,00-fold, about 100 to 1,000-fold, about 100 to 500-fold, about 500 to 100.00-fold, about 500 to 10,00-fold, about 500 to 1,000-fold, about 500 to 750-fold, about 1,000 to 100,00-fold, about 10,000 to 100,00-fold, about 20 to 500-fold, about 20 to 250-fold, about 20 to 200-fold, about 20 to 100-fold, about 20 to 50-fold, about 50 to 10,000-fold, about 50 to 1,000-fold, about 50 to 500-fold, about 50 to 200-fold, or about 50 to 100-fold, improved relative to a reference gene editing pair. In other cases, the one or more of the improved characteristics may be improved about 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, 15-fold, 16-fold, 17-fold, 18-fold, 19-fold, 20-fold, 25-fold, 30-fold, 40-fold, 45-fold, 50-fold, 55-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 110-fold, 120-fold, 130-fold, 140-fold, 150-fold, 160-fold, 170-fold, 180-fold, 190-fold, 200-fold, 210-fold, 220-fold, 230-fold, 240-fold, 250-fold, 260-fold, 270-fold, 280-fold, 290-fold, 300-fold, 310-fold, 320-fold, 330-fold, 340-fold, 350-fold, 360-fold, 370-fold, 380-fold, 390-fold, 400-fold, 425-fold, 450-fold, 475-fold, or 500-fold or more improved relative to a reference gene editing pair.
• In some embodiments, the variant gene editing pair comprises a gNA variant comprising a sequence of any one of SEQ ID NOs: 2101-2280 and a reference CasX protein comprising an amino acid sequence of SEQ ID NO: 1, In some embodiments, the variant gene editing pair comprises a gNA variant comprising a sequence of any one of SEQ ID NOS: 2101-2280 and a CasX variant protein comprising a variant of the reference CasX protein of SEQ NO: 2. In some embodiments, the variant gene editing pair comprises a reference gRNA comprising a sequence of SEQ ID NO: 5 or SEQ ID NO: 4 and a CasX variant protein comprising a variant of the reference CasX protein of SEQ ID NO: 2. In some embodiments, the CasX variant protein comprises a Y789T substitution of SEQ ID NO: 2; a deletion of P at position 793 of SEQ ID NO: 2, a Y789D substitution of SEQ ID NO: 2, a T72S substitution of SEQ ID NO: 2, a I546V substitution of SEQ ID NO: 2, a E552A substitution of SEQ ID NO: 2, a A636D substitution of SEQ ID NO: 2, a F536S substitution of SEQ ID NO: 2, a A708K substitution of SEQ II) NO: 2, a Y797L substitution of SEQ NO: 2, a L792G substitution of SEQ ID NO: 2, a A739V substitution of SEQ ID NO: 2, a G791M substitution of SEQ ID NO: 2, an insertion of A at position 661 of SEQ ID NO: 2, a A788W substitution of SEQ ID NO: 2, a K390R substitution of SEQ ID NO: 2, a A751S substitution of SEQ ID NO: 2, a E385A substitution of SEQ ID NO: 2, a combination of S794R and Y797L substitutions of SEQ ID NO: 2, an insertion of P at 696 of SEQ ID NO: 2, a combination of K416E and A708K substitutions of SEQ ID NO: 2, an insertion of M at position 773 of SEQ ID NO: 2, a G695H substitution of SEQ ID NO: 2, an insertion of AS at position 793 of SEQ ID NO: 2, an insertion of AS at position 795 of SEQ ID NO: 2, a C477R substitution of SEQ ID NO: 2, a C477K substitution of SEQ ID NO: 2, a C479A substitution of SEQ ID NO: 2, a C479L substitution of SEQ ID NO: 2, a combination of an A708K substitution and a deletion of P at position 793 of SEQ ID NO: 2, a I55F substitution of SEQ ID NO: 2, a K210R substitution of SEQ ID NO: 2, a C233S substitution of SEQ ID NO: 2, a D231N substitution of SEQ ID NO: 2, a Q338E substitution of SEQ ID NO: 2, a Q338R substitution of SEQ ID NO: 2, a L379R substitution of SEQ ID NO: 2, a K390R substitution of SEQ ID NO: 2, a 148.Q substitution of SEQ ID NO: 2, a F495S substitution of SEQ ID NO: 2, a D600N substitution of SEQ ID NO: 2, a T886K substitution of SEQ ID NO: 2, a combination of a deletion of P at position 793I and a P793AS substitution of SEQ ID NO: 2, a A739V substitution of SEQ ID NO: 2, a K460N substitution of SEQ ID NO: 2, a I199F substitution of SEQ ID NO: 2, a. G492P substitution of SEQ ID NO: 2, a T153I substitution of SEQ ID NO: 2, a R591I substitution of SEQ ID NO: 2, an insertion of AS at position 795 of SEQ ID NO: 2, an insertion of AS at position 796 of SEQ ID NO: 2, an insertion of L at position 889 of SEQ ID NO: 2, a E121D substitution of SEQ ID NO: 2, a S270W substitution of SEQ ID NO: 2, a E712Q substitution of SEQ ID NO: 2, a K942Q substitution of SEQ ID NO: 2, a E552K substitution of SEQ ID NO: 2, a K25Q substitution of SEQ ID NO: 2, a N47D substitution of SEQ ID NO: 2, a combination Q367K and I4425S substitutions of SEQ NO: 2, an insertion of T at position 696 of SEQ ID NO: 2, a L685I substitution of SEQ ID NO: 2, a N880D substitution of SEQ ID NO: 2, a combination of a A708K substitution, a deletion of P at position 793 and a A739V substitution of SEQ ID NO: 2, a Q102R substitution of SEQ ID NO: 2, a M734K substitution of SEQ ID NO: 2, a A724S substitution of SEQ II) NO: 2, a. T704K substitution of SEQ ID NO: 2, a P224K substitution of SEQ ID NO: 2, a combination of Q338R and A339E substitutions of SEQ ID NO: 2, a combination of Q338R and A339K substitutions of SEQ ID NO: 2, a K25R substitution of SEQ ID NO: 2, a M29E substitution of SEQ ID NO: 2, a H152D substitution of SEQ ID NO: 2, a S219R substitution of SEQ ID NO: 2,a E475K substitution of SEQ ID NO: 2, a combination of S507G and G508R substitutions of SEQ ID NO: 2, a g226R substitution of SEQ ID NO: 2, a A377K substitution of SEQ ID NO: 2, a E480K substitution of SEQ ID NO: 2., a K416E substitution of SEQ ID NO: 2, a H164R substitution of SEQ ID NO: 2, a K767R substitution of SEQ ID NO: 2, a I7F substitution of SEQ ID NO: 2, a in29R substitution of SEQ ID NO: 2, a H435R substitution of SEQ ID NO: 2, a E385Q substitution of SEQ ID NO: 2, a E385K substitution of SEQ ID NO: 2, a I279F substitution of SEQ ID NO: 2, a D489S substitution of SEQ ID NO: 2, a D732N substitution of SEQ ID NO: 2, a A739T substitution of SEQ ID NO: 2, a W885R substitution of SEQ ID NO: 2, a E53K substitution of SEQ ID NO: 2, a A238T substitution of SEQ ID NO: 2, a P283Q substitution of SEQ ID NO: 2, a E292K substitution of SEQ NO: 2, a Q628E substitution of SEQ ID NO: 2, a combination of F556I+D646A+G695D+A751S+A820P substitutions of SEQ ID NO: 2, a R388Q substitution of SEQ ID NO: 2, a combination of L491I and M77IN substitutions of SEQ ID NO: 2, a G791M substitution of SEQ ID NO: 2, a L792K substitution of SEQ ID NO: 2, a L792E substitution of SEQ ID NO: 2, a M779N substitution of SEQ ID NO: 2, a G27D substitution of SEQ ID NO: 2, a combination of L379R and A708K substitutions and a deletion of P at position 793 of SEQ ID NO: 2, a combination of C477K and A708K substitutions and a deletion of P at position 793 of SEQ ID NO: 2, a combination of L379R, C477K and A708K substitutions and a deletion of P at position 793 of SEQ ID NO: 2, a combination of 1.379R, A708K and A739V substitutions and a deletion of P at position 793 of SEQ ID NO: 2, a combination of C477K, A708K and A739V substitutions and a deletion of P at position. 793 of SEQ ID NO: 2, a combination of L379R, C477K, A708K and A739V substitutions and a deletion of P a.t position 793 of SEQ ID NO: 2, a K955R, substitution of SEQ ID NO: 2, a S867R substitution of SEQ ID NO: 2, a R693I substitution of SEQ ID NO: 2, a F189Y substitution of SEQ ID NO: 2, a V635M substitution of SEQ ID NO: 2, a F399L substitution of SEQ ID NO: 2, a E498K substitution of SEQ ID NO: 2, a E386R substitution of SEQ ID NO: 2, a V254G substitution of SEQ ID NO: 2, a P793S substitution of SEQ ID NO: 2, a K188E substitution of SEQ ID NO: 2, QT945KI substitution of SEQ ID NO: 2, a T620P substitution of SEQ NO: 2, a T946P substitution of SEQ ID NO: 2, a TT949PP substitution of SEQ ID NO: 2, a N952T substitution of SEQ ID NO: 2 or a K682E substitution of SEQ ID NO: 2.
• In some embodiments, the variant gene editing pair comprises a CasX gRNA of SEQ ID NO: 5 and a CasX variant protein comprising a combination of L379R and A708K substitutions and a deletion of P at position 793 of SEQ ID NO: 2. In some embodiments, the variant gene editing pair comprises a reference CasX protein SEQ ID NO: 2 and sgNA scaffold variant of SEQ ID NO: 5.
• In some embodiments of the sgNA: protein variant pairs of the disclosure, the CasX variant protein is selected from the group consisting of: a CasX variant protein comprising a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of T620P of SEQ ID NO: 2; a CasX variant protein comprising a substitution of M77 IA of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of D732N of SEQ ID NO: 2; a CasX variant protein comprising a substitution of W782Q of SEQ ID NO: 2; a CasX variant protein comprising a substitution of M771Q of SEQ ID NO: 2; a CasX variant protein comprises a substitution of R458I and a substitution of A739V of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of M77IN of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of A708K, a deletion of P at position 793 and a substitution of A739T of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of D489S of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of D732N of SEQ ID NO: 2; a CasX variant protein comprising a substitution of V711K of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of Y797L of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of A708K and a deletion of P at position 793 of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of C477K, a substitution of A708K, a deletion of P at position 793 and a substitution of M771N of SEQ ID NO: 2; a CasX variant protein comprising a substitution of A708K, a substitution of P at position 793 and a substitution of E386S of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379R, a substitution of C477K, a substitution of A708K and a deletion of Pat position 793 of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L792D of SEQ ID NO: 2; a CasX variant protein comprising a substitution of G79IF of SEQ ID NO: a CasX variant protein comprising a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L379, a substitution of A708K, a deletion of P at position 793 and a substitution of A739V of SEQ ID NO: 2; a CasX variant protein comprising a substitution of C477K, a substitution of A708K and a substitution of P at position 793 of SEQ ID NO: 2; a CasX variant protein comprising a substitution of L249I and a substitution of M77IN of SEQ ID NO: 2; a CasX variant protein comprising a substitution of V747K of SEQ ID NO: 2; and a CasX variant protein comprises a substitution of L379R, substitution of C477, a substitution of A708K, a deletion of P at position 793 and a substitution of M779N of SEQ ID NO: 2; and the sequence encoding the sgNA variant is selected from the group consisting of SEQ ID NO: 2104, SEQ ID NO: 2163, SEQ ID NO: 2107. SEQ ID NO: 2164, SEQ ID NO: 2165, SEQ ID NO: 2166, SEQ ID NO: 2103, SEQ ID NO: 2167, SEQ NO: 2105, SEQ ID NO: 2108, SEQ ID NO: 2112, SEQ ID NO: 2160, SEQ ID NO: 2170, SEQ ID NO: 2114, SEQ ID NO: 2171, SEQ ID NO: 2112, SEQ ID NO: 2173. SEQ ID NO: 2102, SEQ ID NO: 2174, SEQ ID NO: 2175, SEQ ID NO: 2109, SEQ ID NO: 2176, SEQ ID NO: 2238, or SEQ ID NO: 2239.
• In some embodiments, the gene editing pair comprises a CasX selected from any one of CasX of sequence SEQ ID NO: 270, SEQ ID NO: 292, SEQ ID NO: 311, SEQ ID NO: 333, or SEQ ID NO: 336, and a gNA selected from any one of SEQ ID NOS: 2104, 2106, or 2238.
• In some embodiments, the gene editing pair comprises a CasX variant selected from any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 3498-3501, 3505-3520, and 3540-3549.
• In some embodiments, the gene editing pair comprises a CasX variant selected from any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a gNA selected from the group consisting of any one of SEQ ID NOS: 412-3295. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415, and a gNA selected from the group consisting of any one of SEQ ID NOS: 412-3295. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 3498-3501, 3505-3520, and 3540-3549, and a gNA selected from the group consisting of any one of SEQ ID NOS: 412-3295.
• In some embodiments, the gene editing pair comprises a CasX variant selected from any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415 and a gNA selected from the group consisting of any one of SEQ ID NOS: 2101-2280. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415, and a gNA selected from the group consisting of any one of SEQ ID NOS: 2101-2280. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 3498-3501, 3505-3520, and 3540-3549, and a gNA selected from the group consisting of any one of SEQ ID NOS: 2101-2280,
• In some embodiments, the gene editing pair comprises a CasX variant selected from any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520. 3540-3549 and 4412-4415 and a gNA selected from the group consisting of any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, and 2259-2280. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415, and a gNA selected from the group consisting of any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, and 2259-2280.. In some embodiments, the gene editing pair comprises a CasX variant selected from any one of 3498-3501, 3505-3520, and 3540-3549, and a gNA selected from the group consisting of any one of SEQ ID NOS: 2236, 2237, 2238, 2241. 2244, 2248, 2249, and 2259-2280.
• In still further embodiments, the present disclosure provides a gene editing pair comprising a CasX protein and a gNA, wherein the gNA is a guide RNA variant as described herein. In some embodiments of the gene editing pairs of the disclosure, the Cas protein is a CasX variant as described herein. In some embodiments, the CasX protein is a reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and the gNA is a guide RNA variant as described herein. Exemplary improved characteristics of the gene editing pair embodiments, as described herein, may in some embodiments include improved protein:gNA complex stability, improved ribonuclear protein complex (RNP) formation, higher percentage of cleavage-competent RNP, improved binding affinity between the CasX protein and gNA, improved binding affinity to the target DNA, improved unwinding of the target DNA, increased activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, or improved resistance to nuclease activity. In the foregoing embodiments, the improvement is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 50-fold, at least about 100-fold, at least about 500-fold, at least about 1000-fold, at least about 5000-fold, at least about 10,000-fold, or at least about 100,000-fold compared to the characteristic of a reference CasX protein and reference gNA pair.
• In some embodiments, wherein the gene editing pair comprises both a CasX variant protein and a gNA variant as described herein, the one or more characteristics of the gene editing pair is improved beyond what can be achieved by varying the CasX protein or the gNA alone. In some embodiments, the CasX variant protein and the gNA variant act additively to improve one or more characteristics of the gene editing pair. In some embodiments, the CasX variant protein and the gNA variant act synergistically- to improve one or more characteristics of the gene editing pair. In the foregoing embodiments, the improvement is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 50-fold, at least about 100-fold, at least about 500-fold, at least about 1000-fold, at least about 5000-fold, at least about 10,000-fold, or at least about 100,000-fold compared to the characteristic of a reference CasX protein and reference gNA pair.
VI. Methods of Making CasX Variant Protein and gNA Variants
• The CasX variant proteins and gNA variants as described herein may be constructed through a variety of methods. Such methods may include, for example, Deep Mutational Evolution (DME), described below and in the Examples.
• a. Deep Mutational Evolution (DME)
• In some embodiments, DME is used to identify CasX protein and sgNA scaffold variants with improved function. The DME method, in some embodiments, comprises building and testing a comprehensive set of mutations to a starting biomolecule to produce a library of biomolecule variants; for example, a library of CasX variant proteins or sgNA scaffold variants. DME can encompass making all possible substitutions, as well as all possible small insertions, and all possible deletions of amino acids (in the case of proteins) or nucleotides (in the case of RNA or DNA) to the starting biomolecule. A schematic illustrating DME methods is shown in FIG. 1. In some embodiments, DME comprises a subset of all such possible substitutions, insertions, and deletions. In certain embodiments of DME, one or more libraries of variants are constructed, evaluated for functional changes, and this information used to construct one or more additional libraries. Such iterative construction and evaluation of variants may lead, for example, to identification of mutational themes that lead to certain functional outcomes, such as regions of the protein or RNA that when mutated in a certain way lead to one or more improved functions. Layering of such identified mutations may then further improve function, for example through additive or synergistic interactions. DME comprises library design, library construction, and library screening. In some embodiments, multiple rounds of design, construction, and screening are undertaken.
• b. Library Design
• DME methods produce variants of biomolecules, which are polymers of many monomers. In some embodiments, the biomolecule comprises a protein or a ribonucleic acid (RNA) molecule, wherein the monomer units are amino acids or ribonucleotides, respectively. The fundamental units of biomolecule mutation comprise either: (1) exchanging one monomer for another monomer of different identity (substitutions); (2) inserting one or more additional monomer in the biomolecule (insertions); or (3) removing one or more monomer from the biomolecule (deletions). DME libraries comprising substitutions, insertions, and deletions, alone or in combination, to any one or more monomers within any biomolecule described herein, are considered within the scope of the invention.
• In some embodiments, DME is used to build and test the comprehensive set of mutations to a biomolecule, encompassing all possible substitutions, as well as small insertions and deletions of amino acids (in the case of proteins) or nucleotides (in the case of RNA). The construction and functional readout of these mutations can be achieved with a variety of established molecular biology methods. In some embodiments, the library comprises a subset of all possible modifications to monomers. For example, in some embodiments, a library collectively represents a single modification of one monomer, for at least 10% of the total monomer locations in a biomolecule, wherein each single modification is selected from the group consisting of substitution, single insertion, and single deletion. In some embodiments, the library collectively represents the single modification of one monomer, for at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or up to 100% of the total monomer locations in a starting biomolecule. In certain embodiments, for a certain percentage of the total monomer locations in a starting biomolecule, the library collectively represents each possible single modification of a one monomer, such as all possible substitutions with the 19 other naturally occurring amino acids (for a protein) or 3 other naturally occurring ribonucleotides (for RNA), insertion of each of the 20 naturally occurring amino acids (for a protein) or 4 naturally occurring ribonucleotides (for RNA), or deletion of the monomer. In still further embodiments, insertion at each location is independently greater than one monomer, for example insertion of two or more, three or more, or four or more monomers, or insertion of between one to four, between two to four, or between one to three monomers. In some embodiments, deletion at location is independently greater than one monomer, for example deletion of two or more, three or more, or four or more monomers, or deletion of between one to four, between two to four, or between one to three monomers. Examples of such libraries of CasX variants and gNA variants are described in Examples 24 and 25, respectively.
• In some embodiments, the biomolecule is a protein and the individual monomers are amino acids. In those embodiments where the biomolecule is a protein, the number of possible DME mutations at each monomer (amino acid) position in the protein comprise 19 amino acid substitutions, 20 amino acid insertions and 1 amino acid deletion, leading to a total of 40 possible mutations per amino acid in the protein.
• In some embodiments, a DME library of CasX variant proteins comprising insertions is 1 amino acid insertion library, a 2 amino acid insertion library, a 3 amino acid insertion library, a 4 amino acid insertion library, a 5 amino acid insertion library, a 6 amino acid insertion library, a 7 amino acid insertion library, an 8 amino acid insertion library, a 9 amino acid insertion library or a 10 amino acid insertion library. In some embodiments, a DME library of CasX variant proteins comprising insertions comprises between 1 and 4 amino acid insertions.
• In some embodiments, the biomolecule is RNA. In those embodiments where the biomolecule is RNA, the number of possible DME mutations at each monomer (ribonucleotide) position in the RNA comprises 3 nucleotide substitutions, 4 nucleotide insertions, and 1 nucleotide deletion, leading to a total of 8 possible mutations per nucleotide.
• In some embodiments, DME library design comprises enumerating all possible mutations for each of one or more target monomers in a biomolecule. As used herein, a “target monomer” refers to a monomer in a biomolecule polymer that is targeted for DME with the substitutions, insertions and deletions described herein. For example, a target monomer can be an amino acid at a specified position in a protein, or a nucleotide at a specified position in an RNA. A biomolecule can have at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100 or more target monomers that are systematically mutated to produce a DME library of biomolecule variants. In some embodiments, every monomer in a biomolecule is a target monomer. For example, in DME of a protein where there are two target amino acids, DME library design comprises enumerating the 40 possible DME mutations at each of the two target amino acids. In a further example, in DME of an RNA where there are four target nucleotides, DME library design comprises enumerating the 8 possible DME mutations at each of the four target nucleotides. In some embodiments, each target monomer of a biomolecule is independently randomly selected or selected by intentional design. Thus, in some embodiments, a DME library comprises random variants, or variants that were designed, or variants comprising random mutations and designed mutations within a single biomolecule, or any combinations thereof.
• In some embodiments of DME methods, DME mutations are incorporated into double-stranded DNA encoding the biomolecule. This DNA can be maintained and replicated in a standard cloning vector, for example a bacterial plasmid, referred to herein as the target plasmid. An exemplary target plasmid contains a DNA sequence encoding the starting biomolecule that will be subjected to DME, a bacterial origin of replication, and a suitable antibiotic resistance expression cassette. in some embodiments, the antibiotic resistance cassette confers resistance to kanamycin, ampicillin, spectinomycin, bleomycin, streptomycin, erythromycin, tetracycline or chloramphenicol. In some embodiments, the antibiotic resistance cassette confers resistance to kanamycin.
• A library comprising said variants can be constructed in a variety of ways. In certain embodiments, plasmid recombineering is used to construct a library. Such methods can use DNA oligonucleotides encoding one or more mutations to incorporate said mutations into a plasmid encoding the reference biomolecule. For biomolecule variants with a plurality of mutations, in some embodiments more than one oligonucleotide is used. In some embodiments, the DNA oligonucleotides encoding one or more mutations wherein the mutation region is flanked by between 10 and 100 nucleotides of homology to the target plasmid, both 5′ and 3′ to the mutation. Such oligonucleotides can in some embodiments be commercially synthesized and used in PCR amplification. An exemplary template for an oligonucleotide encoding a mutation is provided below:
• 5′-(N)_10-100-Mutation-(N′)_10-1000-3′
• In this exemplary oligonucleotide design, the Ns represent a sequence identical to the target plasmid, referred to herein as the homology arms. When a particular monomer in the biomolecule is targeted for mutation, these homology arms directly flank the DNA encoding the monomer in the target plasmid. In some exemplary embodiments where the biomolecule undergoing DME is a protein, 40 different oligonucleotides, using the same set of homology arms, are used to encode the enumerated 40 different amino acid mutations for each amino acid residue in the protein that is targeted for DME. When the mutation is of a single amino acid, the region encoding the desired mutation or mutations comprises three nucleotides encoding an amino acid (for substitutions or single insertions), or zero nucleotides (for deletions). In some embodiments, the oligonucleotide encodes insertion of greater than one amino acid. For example, wherein the oligonucleotide encodes the insertion of X amino acids, the region encoding the desired mutation comprises 3*X nucleotides encoding the X amino acids. In some embodiments, the mutation region encodes more than one mutation, for example mutations to two or more monomers of a biomolecule that are in close proximity (e.g., next to each other, or within 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more monomers of each other).
• Nucleotide sequences code for particular amino acid monomers in a substitution or insertion mutation in an oligo as described herein will be known to the person of ordinary skill in the art. For example, TIT or TTC triplets can be used to encode phenylalanine TTA, TTG, CTT, CTC, CTA or CTG can be used to encode leucine; ATT, ATC or ATA can be used to encode isoleucine; ATG can be used to encode methionine; GTT, GTC, GTA or GIG c can be used to encode valine; TCT, TCC, TCA, TCG, AGT or AGC can be used to encode serine; CCT, CCC, CCA or CCG can be used to encode proline: ACT, ACC, ACA or ACG can be used to encode threonine; GCT, GCC, GCA or GCG can be used to encode alanine; TAT or TAC can be used to encode tyrosine; CAT or CAC can be used to encode histidine; CAA or CAG can be used to encode glutamine, AAT or AAC can be used to encode asparagine; AAA or AAG can be used to encode lysine; CAT or GAC can he used to encode aspartic acid: GAA or GAG can be used to encode glutamic acid; TGT or TGC c can be used to encode cysteine; TGG can be used to encode tryptophan; CGT, CGC, CGA, CGG, AGA or AGG can be used to encode arginine; and GGT, GGC, GGA or GGG can be used to encode glycine. In addition, ATG is used for initiation of the peptide synthesis as well as for methionine and TAA, TAG and TGA can be used to encode for the termination of the peptide synthesis.
• In some exemplary embodiments where the biomolecule undergoing DME is an RNA, 8 different oligonucleotides, using the same set of homology arms, encode the above enumerated 8 different single nucleotide mutations for each nucleotide in the RNA that is targeted for DME. When the mutation is of a single ribonucleotide, the region of the oligo encoding the mutations can consist of the following nucleotide sequences: one nucleotide specifying a nucleotide (for substitutions or insertions), or zero nucleotides (for deletions). In some embodiments, the oligonucleotides are synthesized as single stranded DNA oligonucleotides. In some embodiments, all oligonucleotides targeting a particular amino acid or nucleotide of a biomolecule subjected to DME are pooled. In some embodiments, all oligonucleotides targeting a biomolecule subjected to DME are pooled. There is no limit to the type or number of mutations that can be created simultaneously in a DME library.
• c. DME Library Construction
• in some embodiments, plasmid recombineering is utilized to construct one or more DME libraries. Plasmid recombineering is described in Higgins, Sean A., Sorel V. Y. Ouonkap, and David F. Savage (2017) “Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering” ACS Synthetic Biology, the contents of which are incorporated herein by reference in their entirety.
• An exemplary library construction protocol shown below:
• Day 1: A bla, bio-, lambda-Red 1, mutS-, cmR E. coli strain for example, EcNR2, Addgene ID: 26931) is streaked out on a LB agar plate containing standard concentrations of the antibiotics Chloramphenicol and Ampicillin. Colonies are grown overnight at 30° C.
• Day 2: A single colony of EcNR2 is picked into 5 mL of LB liquid media containing standard concentrations of the antibiotics Chloramphenicol and Ampicillin. The culture is grown overnight with shaking at 30° C.
• Day 3: Electrocompetent cells are made using any method known in the art. An non-limiting, exemplary protocol for making electrocompetent cells comprises:
• (1) Dilute 50 uL of the overnight culture into 50 mL of LB liquid media containing standard concentrations of the antibiotics Chloramphenicol and Ampicillin. Grow this 50 mL culture with shaking at 30° C.
• (2) Once the 50 mL culture has grown to an OD600=0.5, transfer to shaking growth at 42° C. in a liquid water bath. Care should be taken to limit this growth at 42° C. to 15 minutes.
• (3) After heated growth, transfer the culture to an ice water bath and swirl for at least one minute to cool the culture.
• (4) Pellet the culture by spinning at 4,000×g for 10 minutes. Decant the supernatant.
• (5) Carefully wash and re-suspend the pellet by adding ice cold water up to 50 mL. Repeat spin step 4.
• (6) Resuspend the pellet in 1 mL of ice cold water. The cells are now competent for a standard electroporation step.
• The electrocompetent E. coil are then transformed with the DME oligonucleotides:
• (1) Pooled DME oligonucleotides are diluted in water to a final concentration of 20 μM. If more than one mutation is to be generated simultaneously, the corresponding oligonucleotides should be combined and mixed thoroughly.
• (2) Pure target plasmid, for example, from a miniprep, is diluted in water to a final concentration of 10 ng per
• (3) Mix on ice:
• • 2.5 μL DME oligonucleotide mixture
  • 1 μL target plasmid
  • 46.5 μL electrocoinpetent EcNR2 cells
• (4) Transfer the mixture to a sterile 0.1 cm electroporation cuvette on ice and perform an electroporation. For example, the parameters of 1800 kV, 200 Ω, 25 μF can be used.
• (5) Recover the electroporated cells by adding 1 mL of standard warm SOC media. Grow the culture for one hour with shaking at 30′ C.
• (6) After the recovery, add 4 mL of additional standard LB media to the culture. Add Kanamycin antibiotic at standard concentrations in order to select for the electroporated target plasmid. The culture is then grown=overnight with shaking at 30° C.
• Day 4. Methods of isolating the target plasmid from overnight cultures will be readily apparent to one of ordinary skill in the art, For example, target plasmid can be isolated using commercial MiniPrep kits such as the MiniPrep kit from Qiagen. The plasmid library obtained comprises mutated target plasmids. In some embodiments, the plasmid library comprises between 10% and 30% mutated target plasmids. Additional mutations can be progressively added by repeatedly passing the library through rounds of electroporation and outgrowth, with no practical limit on the number of rounds that may be performed. Thus, for example, in some embodiments the library comprises plasmids encoding greater than one mutation per plasmid. For example, in some embodiments the library comprises plasmids independently comprising one, two, three, four, five, six, seven eight, nine, or greater mutations per plasmid. in some embodiments, plasmids that do not comprise any mutations are also present (e.g., plasmids which did not incorporate a DME oligonucleotide).
• In other embodiments, methods other than plasmid recombineering are used to construct one or more DME libraries, or a combination of plasmid recombineering and other methods are used to construct one or more DME libraries. For example. DME libraries may, in some embodiments, be constructed using one of the other mutational methods described herein. Such libraries may then be taken through the library screening as described herein, and further iterations be carried out if desired.
• d. Library Screening
• Any appropriate method for screening or selecting a DME library is envisaged as following within the scope of the inventions. High throughput methods may be used to evaluate large libraries with thousands of individual mutations. In some embodiments, the throughput of the library screening or selection assay has a throughput that is in the millions of individual cells. In some embodiments, assays utilizing living cells are preferred, because phenotype and genotype are physically linked in living cells by nature of being contained within the same lipid bilayer. Living cells can also be used to directly amplify sub-populations of the overall library. In other embodiments, smaller assays are used in DME methods, for example to screen a focused library developed through multiple rounds of mutation and evaluation. Exemplary methods of screening libaries are described in Examples 24 and 25.
• An exemplary, but non-limiting DME screening assay comprises Fluorescence-Activated Cell Sorting (FACS). In some embodiments, FACS may be used to assay millions of unique cells in a DME. library. An exemplary FACS screening protocol comprises the following steps:
• (1) PCR amplifying the purified plasmid library from the library construction phase. Flanking PCR primers can be designed that add appropriate restriction enzyme sites flanking the DNA encoding the biomolecule. Standard oligonucleotides can be used as PCR primers, and can be synthesized commercially. Commercially available PCR reagents can be used for the PCR amplification, and protocols should be performed according to the manufacturer's instructions. Methods of designing PCR primers, choice of appropriate restriction enzyme sites, selection of PCR reagents and PCR amplification protocols will be readily apparent to the person of ordinary skill in the art.
• (2) The resulting PCR product is digested with the designed flanking restriction enzymes. Restriction enzymes may be commercially available, and methods of restriction enzyme digestion will be readily apparent to the person of ordinary skill in the art.
• (3) The PCR product is ligated into a new DNA vector. Appropriate DNA vectors may include vectors that allow for the expression of the DME library in a cell. Exemplary vectors include, but are not limited to, retroviral vectors, lentiviral vectors, adenoviral vectors, adeno-associated viral (AAV) vectors and plasmids. This new DNA vector can be part of a protocol such as lentiviral integration in mammalian tissue culture, or a simple expression method such as plasmid transformation in bacteria. Any vectors that allow for the expression of the biomolecule, and the DME library of variants thereof, in any suitable cell type, are considered within the scope of the disclosure, Cell types may include bacterial cells, yeast cells, and mammalian cells. Exemplary bacterial cell types may include E. coli. Exemplary yeast cell types may include Saccharomyces cerevisiae. Exemplary mammalian cell types may include mouse, hamster, and human cell lines, such as HEK293 cells, HEK293T cell, HEK293-F cells, Lenti-X 293T cells, BHK cells. HepG2 cells, Saos-2 cells, HuH7 cells, A549 cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells, hybridoma cells. VERO tolls NIH3T3 cells, COS, W138 cells, MRCS cells, HeLa, HT1080 cells, or CHO cells. Choice of vector and cell type will be readily apparent to the person of ordinary skill in the art. DNA ligase enzymes can be purchased commercially, and protocols for their use will also be readily apparent to one of ordinary skill in the art.
• (4) Once the DME library has been cloned into a vector suitable for in vivo expression, the DME library is screened. If the biomolecule has a function which alters fluorescent protein production in a living cell, the biomolecule's biochemical function will be correlated with the fluorescence intensity of the cell overall. By observing a population of millions of cells on a flow cytometer, a DME library can be seen to produce a broad distribution of fluorescence intensities, Individual sub-populations from this overall broad distribution can be extracted by FACS. For example, if the function of the biomolecule is to repress expression of a fluorescent protein, the least bright cells will he those expressing biomolecules whose function has been improved by DME. Alternatively, if the function of the biomolecule is to increase expression of a fluorescent protein, the brightest cells will be those expressing biomolecules whose function has been improved by DME. Cells can be isolated based on fluorescence intensity by FACS and grown separately from the overall population. An exemplary FACS screening assay is shown in FIG. 2.
• (5) After FACS sorting cells expressing a DME library of biomolecule variants, cultures comprising the original DME library andlor only highly functional biomolecule variants, as determined by FACS sorting, can be amplified separately. If the cells that were FACS sorted comprise cells that express the DME library of biomolecule variants from a plasmid (for example, E. coli cells transformed with a plasmid expression vector), these plasmids can be isolated, for example through miniprep. Conversely if the DME library of biomolecule variants has been integrated into the genomes of the FACs sorted cells, this DNA region can be PCR amplified and, optionally, subcloned into a suitable vector for further characterization using methods known in the alt. Thus, the end product of library screening is a DNA library representing the initial, or ‘naive’, DME library, as well as one or more DNA libraries containing sub-populations of the naive DME library, which comprise highly functional mutant variants of the biomolecule identified by the screening processes described herein.
• In some embodiments, DME libraries that have been screened or selected for highly functional variants are further characterized. In some embodiments, further characterizing the DME library comprises analyzing DME variants individually through sequencing, such as Sanger sequencing, to identify the specific mutation or mutations that gave rise to the highly functional variant. Individual mutant variants of the biomolecule can be isolated through standard molecular biology techniques for later analysis of function. In some embodiments, further characterizing the DME library comprises high throughput sequencing of both the naive library and the one or more libraries of highly functional variants. This approach may, in some embodiments, allow for the rapid identification of mutations that are over-represented in the one or more libraries of highly functional variants compared to the naive DME library. Without wishing to be bound by any theory, mutations that are over-represented in the one or more libraries of highly functional variants arc likely to be responsible for the activity of the highly functional variants. In some embodiments, further characterizing the DME library comprises both sequencing of individual variants and high throughput sequencing of both the naive library and the one or more libraries of highly functional variants.
• High throughput sequencing can produce high throughput data indicating the functional effect of the library members. In embodiments wherein one or more libraries represents every possible mutation of every monomer location, such high throughput sequencing can evaluate the functional effect of every possible DME mutation. Such sequencing can also be used to evaluate one or more highly functional sub-populations of a given library, which in some embodiments may lead to identification of mutations that result in improved function. An exemplary protocol for high throughput sequencing of a library with a highly functional sub-population is as follows:
• (1) High throughput sequencing of the Naive DME library. N. High throughput sequence the highly functional sub-population library, F. Any high throughput sequencing platform that can generate a suitable abundance of reads can be used. Exemplary sequencing platforms include, but are not limited to Illumina, Ion Torrent, 454 and PacBio sequencing platforms.
• (2) Select a particular mutation to evaluate, i. Calculate the total fractional abundance of i in N, i(N). Calculate the total fractional abundance of i in F, i(F).
• (3) Calculate the following: [(i(F) 1)/(i(N)+1)]. This value, the ‘enrichment ratio’, is correlated with the function of the particular mutant variant i of the biomolecule.
• (4) Calculate the enrichment ratio for each of the mutations observed in deep sequencing of the DME libraries.
• (5) The set of enrichment ratios for the entire library can be converted to a log scale such that a value of zero represents no enrichment (i.e. an enrichment ratio of one), values greater than zero represent enrichment, and values less than zero represent depletion. Alternatively, the log scale can be set such that 1.5 represents enrichment, and −0.6 represents depletion, as in FIG. 3A, FIG. 3B, FIG. 4A, FIG. 4C. These resealed values can be referred to as the relative ‘fitness’ of any particular mutation. These fitness values quantitatively indicate the effect a particular mutation has on the biochemical function of the biomolecule.
• (6) The set of calculated DME fitness values can be mapped to visually represent the fitness landscape of all possible mutations to a biomolecule. The fitness values can also be rank ordered to determine the most beneficial mutations contained within the DME library.
• e. Iterating DME
• In some embodiments, a highly functional variant produced by DME has more than one mutation. For example, combinations of different mutations can in some embodiments produce optimized biomolecules whose function is further improved by the combination of mutations. In some embodiments, the effect of combining mutations on function of the biomolecule is linear. As used herein, a combination of mutations that is linear refers to a combination whose effect on function is equal to the sum of the effects of each individual mutation when assayed in isolation. In some embodiments, the effect of combining mutations on function of the biomolecule is synergistic. As used herein, a combination of mutations that is synergistic refers to a combination whose effect on function is greater than the sum of the effects of each individual mutation when assayed in isolation. Other mutations may exhibit additional unexpected nonlinear additive effects, or even negative effects. This phenomenon is known as epistasis.
• Epistasis can be unpredictable, and is a significant source of variation when combining mutations. Epistatic effects can be addressed through additional high throughput experimental methods in DME library construction and assay. In some embodiments, the entire DME protocol can be iterated, returning to the library construction step and selecting only mutations identified as having desired effects (such as increased functionality) from an initial DME library screen. Thus, in some embodiments, DME library construction and screening is iterated, with one or more cycles focusing the library on a subset of mutations having desired effects. In such embodiments, layering of selected mutations may lead to improved variants. In some alternative embodiments. DME can be repeated with the full set of mutations, but targeting a novel, pre-mutated version of the biomolecule. For example, one or more highly functional variants identified in a first round of DME library construction, assay, and characterization can he used as the target plasmid for further rounds of DME using a broad, unfocused set of further mutations (such as every possible mutation, or a subset thereof), and the process repeated. Any number, type of iterations or combinations of iterations of DME are envisaged as within the scope of the disclosure.
• f. Deep Mutational Scanning
• In some embodiments, Deep Mutational Scanning (DMS) is used to identify CasX variant proteins with improved function. Deep mutational scanning assesses protein plasticity as it relates to function. In DMS methods, every amino acid of a protein is changed to every other amino acid and absolute protein function assayed. For example, every amino acid in a CasX protein can be changed to every other amino acid, and the mutated CasX proteins assayed for their ability to bind to or cleave DNA. Exemplary assays such as the CRISPRi assay or bacterial-based cleavage assays that can be used to characterize collections of DMS CasX variant proteins are described in Oakes et al. (2016) “Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch” Nat Biotechnol 34(6):646-5I and. Liu et al. (2019) “Cask enzymes comprise a distinct family of RNA-guided genome editors” Nature doi.org/10.1038/s41586-019-0908; the contents of which are incorporated herein by reference.
• In some embodiments, DMS is used to identify CasX proteins with improved DNA binding activity. In some embodiments, DNA binding activity is assayed using a CRISPRi assay. In a non-limiting, exemplary embodiment of a CRISPRi assay, cells expressing a fluorescent protein such as green fluorescent protein (GFP) or red fluorescent protein (REP) are assayed using FACS to identify Cask variants capable of repressing expression of the fluorescent protein in a sgNA dependent fashion. In this example, a catalytically dead CasX (dCasX) is used to generate the collection of DMS mutants being assayed. The wild-type CasX protein binds to its cognate sgNA and forms a protein-RNA complex. The complex binds to specific DNA targets by Watson-Crick base pairing between the sgNA and the DNA target, in this case a DNA sequence encoding the fluorescent protein. In the case of wild-type CasX, the DNA will be cleaved due to the nuclease activity of the CasX protein. However, without wishing to be hound by theory, it is likely that dCasX is still able to form a complex with the sgNA and bind to specific DNA target. When targeting of dCasX occurs to the protein-coding region, it blocks RNA polymerase II and transcript initiation and/or elongation, leading to a reduction in fluorescent protein expression that can be detected by FACs.
• In some embodiments, DMS is used to identify CasX proteins with improved DNA cleavage activity. Methods of assaying the DNA cleavage efficiency of CasX variant proteins will be apparent to one of ordinary skill in the art. For example, CasX proteins complexed with an sgNA with a spacer complementary to a particular target DNA sequence can be used to cleave the DNA target sequence in vitro or in vivo in a suitable cell type, and the frequency of insertions and deletions at the site of cleavage are assayed. Without wishing to be bound by theory, cleavage or nicking by CasX generates double-strand breaks in DNA, whose subsequent repair by the non-homologous end joining pathway (NHE.1) gives rise to small insertions or deletions (indels) at the site of the double-strand breaks. The frequency of indels at the site of CasX cleavage can be measured using high throughput or Sanger sequencing of the target sequence. Alternatively, or in addition, frequency of indel generation by CasX cleavage of a target sequence can be measured using mismatch assays such as T7 Endonuclease I (T7I) or Surveyor mismatch assays.
• In some embodiments, following DMS, a map of the genotypes of DMS mutants linked with their resulting phenotype (for example, a heat map) is generated and used to characterize fundamental principles of the protein. All possible mutations are characterized as leading to functional or nonfunctional protein products to establish that protein's functional landscape.
• g. Error Prone PCR
• In some embodiments, Error Prone PCR is used to generate CasX protein or sgNA scaffold variants with improved function. Polymerases that replicate DNA have different levels of fidelity. One way of introducing random mutations to a gene is through an error prone polymerase that will incorporate incorrect nucleotides at a range of frequencies. This frequency can be modulated depending on the desired outcome. In some embodiments, a polymerase and conditions for polymerase activity are selected that result in a frequency of nucleotide changes that produces an average of n 1-4 amino acid changes in a protein sequence. An exemplary error prone polymerase comprises Agilent's Gen:MorphII kit. The GeneMorphil kit can be used to amplify a DNA sequence encoding a wild type CasX protein (for example, a protein of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3), according to the manufacturer's protocol, thereby subjecting the protein to unbiased random mutagenesis and generating a diverse population of CasX variant proteins. This diverse population of CasX variant proteins can then be assayed using the same assays described above for DMS to observe how changes in genotype relate to changes in phenotype.
• h. Cassette Mutagenesis
• In some embodiments, cassette mutagenesis is used to generate CasX variant protein or sgNA scaffold variants with improved function. Cassette mutagenesis takes advantage of unique restriction enzyme sites that are replaced by degenerative nucleotides to create small regions of high diversity in select areas of a gene of interest such as a CasX protein or sgNA scaffold. In an exemplary cassette mutagenesis protocol, restriction enzymes are used to cleave near the sequence targeted for mutagenesis on DNA molecule encoding a CasX protein or sgNA scaffold contained in a suitable vector. This step removes the sequence targeted for mutagenesis and everything between the restriction sites. Then, synthetic double stranded DNA molecules containing the desired mutation and ends that are complimentary to the restriction digest ends are ligated in place of the sequence that has been removed by restriction digest, and suitable cells, such as E. coli are transformed with the ligated vector. In some embodiments, cassette mutagenesis can be used to generate one or more specific mutations in a CasX protein or sgNA scaffold. In some embodiments, cassette mutagenesis can be used to generate a library of CasX variant proteins or sgNA scaffold variants that can be screened or selected for improved function using the methods described herein. For example, in using cassette mutagenesis to generate CasX variants, parts of the Non-Target Strand Binding (NTSB) domain can be replaced with a sequence of degenerate nucleotides. Sequences of degenerate nucleotides can he highly localized to regions of the CasX protein, for example regions of the NTSB that are of interest because of their highly mobile elements or their direct contacts with DNA. Libraries of CasX variant proteins generated via cassette mutagenesis can then be screened using the assays described herein for DME, DMS and error prone PCR and variants can be selected for improved function.
• i. Random Mutagenesis
• In some embodiments, random mutagenesis is used to generate CasX variant proteins or sgNA scaffold variants with improved function. Random mutagenesis is an unbiased way of changing DNA. Exemplary methods of random mutagenesis will be known to the person of ordinary skill in the art and include exposure to chemicals. UV light, X-rays or use of unstable cell lines. Different mutagenic agents produce different types of mutations, and the ordinarily skilled artisan will be able to select the appropriate agent to generate the desired type of mutations. For example. ethylmethanesulfonate (EMS) and N-ethyl-N-nitrosourea (ENU) can be used to generate single base pair changes, while X-rays often result in deletions and gross chromosomal rearrangements. UV light exposure produces (inners between adjacent pyrimidines in DNA, which can result in point mutations, deletions and rearrangements. Error prone cell lines can also be used to introduce mutations, for example on a plasmid comprising a CasX protein or sgNA scaffold of the disclosure. A population of DNA molecules encoding a CasX protein (for example, a protein of SEQ ID NO: 1, SEQ II) NO: 2. or SEQ NO: 3) or an sgNA scaffold can be exposed to a mutagen to generate collection of CasX variant proteins or sgNA scaffold variants, and these collections can be assayed for improved function using any of the assays described herein.
• j. Staggered Extension Process (StEP)
• In some embodiments, a staggered extension process (StEP) is used to generate CasX variant proteins or sgNA scaffold variants with improved function. Staggered extension process is a specialized PCR protocol that allows for the breeding of multiple variants of a protein during a PCR reaction, StEP utilizes a polymerase with low processivity, (for example Taq or Vent polymerase) to create short primers off of two or more different template strands with a significant level of sequence similarity. The short primers are then extended for short time intervals allowing for shuffling of the template strands. This method can also be used as a means to stack DME variants, Exemplary StEP protocols are described by Zhao, H. et al. (1998) “Molecular evolution by staggered extension process (StEP) in vitro recombination” Nature Biotechnology 16: 258-261, the contents of which are incorporated herein by reference in their entirety. StEP can be used to generate collections of CasX variant proteins or sgNA scaffold. variants, and these collections can be assayed for improved function using any of the assays described herein.
• k. Gene Shuffling
• In some embodiments, gene shuffling is used to generate CasX variant proteins or sgNA scaffold variants with improved function. In some embodiments, gene shuffling is used to combine (sometimes referred to herein as “stack”) variants produced through other methods described herein, such as plasmid recombineering. In an exemplary gene shuffling protocol, a DNase, for example DNase I, is used to shear a set of parent genes into pieces of 50-100 base pair (bp) in length. In some embodiments, these parent genes comprise CasX variant proteins with improved function created and isolated using the methods described herein. In some embodiments, these parent genes comprise sgNA scaffold variants with improved function created and isolated using the methods described herein. Dnase fragmentation is then followed by a polymerase chain reaction (PCR) without primers. DNA fragments with sufficient overlapping homologous sequence will anneal to each other and are then extended by DNA polymerase. If different fragments comprising different mutations anneal, the result is a new variant combining those two mutations. in some embodiments, PCR without primers is followed by PCR extension, and purification of shuffled DNA molecules that have reached the size of the parental genes (e.g., a sequence encoding a CasX protein or sgNA scaffold). These genes can then be amplified with another PCR, for example by adding PCR primers complementary to the 5′ and 3′ ends of gene undergoing shuffling. In some embodiments, the primers may have additional sequences added to their 5′ ends, such as sequences for restriction enzyme recognition sites needed for ligation into a cloning vector.
• I. Domain Swapping
• In some embodiments, domain swapping is used to generate CasX variant proteins or sgNA scaffold variants with improved function. To generate CasX variant proteins, engineered domain swapping can be used to mix and match parts with other proteins and CRISPR molecules. For example, CRISPR proteins have conserved RuvC domains, so the CasX RuvC domain could be swapped for that of other CRISPR proteins, and the resulting protein assayed for improved DNA cleavage using the assays described herein. For sgNAs, the scaffold stem, extended stein or loops can be exchanged with structures found in other RNAs, for example the scaffold stem and extended stem of the sgNA can be exchanged with thermostable stem loops from other RNAs, and the resulting variant assayed for unproved function using the assays described herein. In some embodiments, domain swapping can be used to insert new domains into the CasX protein or sgNA. In some exemplary embodiments where domain swapping is applied to a protein, the inserted domain comprises an entire second protein.
• VII. Vectors
• In some embodiments, provided herein are vectors comprising polynucleotides encoding the CasX variant proteins and sgNA or dgNA variants and, optionally, donor template polynucleotides, described herein. In some cases, the vectors are utilized for the expression and recovery of the CasX, gNA (and, optionally, the donor template) components of the gene editing pair. In other cases, the vectors are utilized for the delivery of the encoding polynucleotides to target cells for the editing of the target nucleic acid, as described more fully, below.
• In some embodiments, provided herein are polynucleotides encoding the sgNA or dgNA variants described herein. In some embodiments, said polynucleotides are DNA. In other embodiments, said polynucleotides are RNA. In some embodiments, provided herein are vectors comprising the polynucleotides sequences encoding the sgNA or dgNA variants described herein. In some embodiments, the vectors comprising the polynucleotides include bacterial plasmids, viral vectors, and the like. In some embodiments, a CasX variant protein and a sgNA variant are encoded on the same vector. In some embodiments, a CasX variant protein and a sgNA variant are encoded on different vectors.
• In some embodiments, the disclosure provides a vector comprising a nucleotide sequence encoding the components of the CasX:gNA system. For example, in some embodiments provided herein is a recombinant expression vector comprising a) a nucleotide sequence encoding a CasX variant protein; and b) a nucleotide sequence encoding a gNA variant described herein. In some cases, the nucleotide sequence encoding the CasX variant protein and/or the nucleotide sequence encoding the gNA variant are operably linked to a promoter that is operable in a cell type of choice (e.g., a prokaryotic cell, a eukaryotic cell, a plant cell, an animal cell, a mammalian cell, a primate cell, a rodent cell, a human cell). Suitable promoters for inclusion in the vectors are described herein, below.
• In some embodiments, the nucleotide sequence encoding the CasX variant protein is codon optimized. This type of optimization can entail a mutation of a CasX-encoding nucleotide sequence to mimic the codon preferences of the intended host organism or cell while encoding the same protein. Thus, the codons can be changed, but the encoded protein remains unchanged. For example, if the intended target cell was a human cell, a human codon-optimized CasX variant-encoding nucleotide sequence could be used. As another non-limiting example, if the intended host cell were a mouse cell, then a mouse codon-optimized CasX variant-encoding nucleotide sequence could be generated. As another non-limiting example, if the intended host cell were a plant cell, then a plant codon-optimized CasX variant protein-encoding nucleotide sequence could be generated. As another non-limiting example, if the intended host cell were a bacterial cell, then a bacterial codon-optimized CasX variant protein-encoding nucleotide sequence could be generated.
• In some embodiments, provided herein are one or more recombinant expression vectors such as (i) a nucleotide sequence of a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target sequence of a target nucleic acid (e.g., a target genome); (ii) a nucleotide sequence that encodes a gNA or a gNA variant as described herein, that may be provided in a single-guide or dual-guide form, (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell); and (iii) a nucleotide sequence encoding a CasX protein or a CasX variant protein (e.g., operably linked to a promoter that is operable in a target cell such as a eukaryotic cell). In some embodiments, the sequences encoding the gNA and CasX proteins are in different recombinant expression vectors, and in other embodiments the gNA and CasX proteins are in the same recombinant expression vector. In some embodiments, the sequences encoding the gNA, the CasX protein, and the donor template(s are in different recombinant expression vectors, and in other embodiments one or more are in the same recombinant expression vector. In some embodiments, either the sgNA in the recombinant expression vector, the CasX protein encoded by the recombinant expression vector, or both, are variants of a reference CasX protein or gNAs as described herein. In the case of the nucleotide sequence encoding the gNA, the recombinant expression vector can be transcribed in vitro, for example using T7 promoter regulatory sequences and T7 polymerase in order to produce the gRNA, which can then be recovered by conventional methods; e.g, purification via gel electrophoresis. Once synthesized, the gRNA may be utilized in the gene editing pair to directly contact a target DNA or may be introduced into a cell by any of the well-known techniques for introducing nucleic acids into cells (e.g., microinjection, electroporation, transfection, etc.).
• Depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. may be used in the expression vector.
• In some embodiments, a nucleotide sequence encoding a reference or variant CasX and/or gNA is operably linked to a control element; e.g., a transcriptional control element, such as a promoter. In some embodiments, a nucleotide sequence encoding a reference CasX variant protein is operably linked to a control element; e.g., a transcriptional control clement, such as a promoter. In some cases, the promoter is a constitutively active promoter. In some cases, the promoter is a regulatable promoter. In some cases, the promoter is an inducible promoter. In some cases, the promoter is a tissue-specific promoter. In some cases, the promoter is a cell type-specific promoter. In some cases, the transcriptional control element (e.g., the promoter) is functional in a targeted cell type or targeted cell population. For example, in some cases, the transcriptional control element can be functional in eukaryotic cells, e.g., hematopoictic stem cells (e.g., mobilized peripheral blood (mPB) CD34(+) cell, bone marrow (BM) CD34(+) cell, etc.). By transcriptional activation, it is intended that transcription will be increased above basal levels in the target cell by 10 fold, by 100 fold, more usually by 1000 fold.
• Non-limiting examples of eukaryotic promoters (promoters functional in a eukaryotic cell) include EF1alpha, EF1alpha. core promoter, those from cytomegalovirus (CMV) immediate early, herpes simplex virus (HSV) thymidine kinase, early and late SV40, long terminal repeats (LTRs) from retrovirus, and mouse metallothionein-I. Further non-limiting examples of eukaraytic promoters include the CMV promoter full-length promoter, the minimal CMV promoter, the chicken β-actin promoter, the hPGK promoter, the HSV TK promoter, the Mini-TK promoter, the human synapsin I promoter which confers neuron-specific expression, the Mecp2 promoter for selective expression in neurons, the minimal IL-2 promoter, the Rous sarcoma virus enhancer/promoter (single), the spleen focus-forming virus long terminal repeat (LTR) promoter, the SV40 promoter, the SV40 enhancer and early promoter, the TBG promoter: promoter from the human thyroxine-binding globulin gene (Liver specific), the PGK promoter, the human ubiquitin C promoter, the UCOE promoter (Promoter of HNRPA2B1-CBX3), the Histone H2 promoter, the Histone H3 promoter, the U1a1 small nuclear RNA promoter (226 nt), the U 1b2 small nuclear RNA promoter (246 nt) 26, the TTR minimal enhancer/promoter, the b-kinesin promoter, the human eIF4A1 promoter, the ROSA26 promoter and the Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) promoter.
• Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. The expression vector may also contain a ribosome binding site for translation initiation and a transcription terminator. The expression vector may also include appropriate sequences for amplifying expression. The expression vector may also include nucleotide sequences encoding protein tags (e.g., 6'His tag, hetnagglutinin tag, fluorescent protein, etc.) that can be fused to the CasX protein, thus resulting in a chimeric CasX polypeptide.
• In some embodiments, a nucleotide sequence encoding a gNA variant and/or a CasX variant protein is operably linked to a promoter that is an inducible promoter (i.e., a promoter whose state, active/“ON” or inactive/“OFF”, is controlled by an external stimulus, e.g., the presence of a particular temperature, compound, or protein) or a promoter that is a constitutively active promoter (i.e., a. promoter that is constitutively in an a.ctive/“ON” state). In other embodiments, a nucleotide sequence encoding a gNA variant and/or a CasX variant protein is operably linked to a spatially restricted promoter (i.e., transcriptional control element, enhancer, tissue specific promoter, cell type specific promoter, etc.), and it may be a temporally restricted promoter (i.e., the promoter is in the “ON” state or “OFF” state during specific stages of embryonic development or during specific stages of a biological process, hair follicle cycle in mice).
• In certain embodiments, suitable promoters can be derived from viruses and can therefore he referred to as viral promoters, or they can be derived from any organism, including prokaryotic or eukaryotic organisms. Suitable promoters can be used to drive expression by any RNA polymerase (e.g., pol I, pol H, pol III). Exemplary promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rows sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6), an enhanced U6 promoter, a human HI promoter (HI), a POL1 promoter, a 7SK promoter, tRNA promoters and the like.
• In some embodiments, a nucleotide sequence encoding a gNA is operably linked to (under the control of) a promoter operable in a eukaryotic cell (e.g., a U6 promoter, an enhanced U6 promoter, an HI promoter, and the like). As would be understood by one of ordinary skill in the art, when expressing an RNA (e.g., a sRNA) from a nucleic acid (e.g., an expression vector) using a U6 promoter (e.g in a eukaryotic cell), or another PolIII promoter, the RNA may need to he mutated if there are several Ts in a row (coding for Us in the RNA). This is because a string of Ts (e.g., 5 Ts) in DNA can act as a terminator for polymerase III (Pol III). Thus, in order to ensure transcription of a gRNA (e.g., the activator portion and/or targeter portion, in dual guide or single guide format) in a eukaryotic cell, it may sometimes he necessary to modify the sequence encoding the gRNA to eliminate runs of Ts. In some cases, a nucleotide sequence encoding a CasX protein a wild type CasX protein, a nickase CasX protein, a dCasX protein, a chimeric CasX protein and the like)) is operably linked to a promoter operable in a eukaryotic cell (e.g., a CMV promoter, an EF1alpha promoter, an estrogen receptor-regulated promoter, and the like).
• In certain embodiments, inducible promoters suitable for use may include any inducible promoter described herein or known to one of ordinary skill in the art. Examples of inducible promoters include, without limitation. T7 RNA polymerase promoter, T3 RNA polymerase promoter, isopropyl-beta-D-thiogalactopyranoside (IPTG)-regulated promoter, lactose induced promoter, chemically/biochemically-regulated and physically-regulated promoters such as alcohol-regulated promoters, tetracycline-regulated promoters (e.g., anhydrotetracycline (aTc)-responsive promoters and other tetracycline -responsive promoter systems, which include a tetracycline repressor protein (tetR), a tetracycline operator sequence (tea)) and a tetracycline transactivator fusion protein (ITA), steroid-regulated promoters (e.g., promoters based on the rat glucocorticoid receptor, human estrogen receptor, moth ecdysone receptors, and promoters from the steroid/retinoid/thyroid receptor superfamily), metal-regulated promoters (e.g., promoters derived from metallothionein (proteins that bind and sequester metal ions) genes from yeast, mouse and human), pathogenesis-regulated promoters (e.g., induced by salicylic acid, ethylene or benzothiadiazole (BTH) temperature/heat-inducible promoters (e.g., heat shock promoters), and light-regulated promoters (e.g., light responsive promoters from plant cells).
• In some cases, the promoter is a spatially restricted promoter (i.e., cell type specific promoter, tissue specific promoter, etc.) such that in a multi-cellular organism, the promoter is active (i.e., “ON”) in a subset of specific cells. Spatially restricted promoters may also be referred to as enhancers, transcriptional control elements, control sequences, etc. Any convenient spatially restricted promoter may be used as long as the promoter is functional in the targeted host cell eukaryotic cell; prokaryotic cell).
• In some cases, the promoter is a reversible promoter. Suitable reversible promoters, including reversible inducible promoters are known in the art. Such reversible promoters may be isolated and derived from many organisms, e.g., eukaryotes and prokaryotes. Modification of reversible promoters derived from a first organism for use in a second organism, e.g., a first prokaryote and a second a eukaryote, a first eukaryote and a second a prokaryote, etc., is well known in the art. Such reversible promoters, and systems based on such reversible promoters but also comprising additional control proteins, include, but are not limited to, alcohol regulated promoters (e.g., alcohol dehydrogenase I (alcA) gene promoter, promoters responsive to alcohol transactivator proteins (AlcR), etc.), tetracycline regulated promoters, (e.g., promoter systems including let Activators. TetON, TetOFF, etc.), steroid regulated promoters (e.g., rat glucocorticoid receptor promoter systems, human estrogen receptor promoter systems, retinoid promoter systems, thyroid promoter systems, ecdysone promoter systems, mifepristone promoter systems, etc.), metal regulated promoters (e.g., metallothionein promoter systems, etc.), pathogenesis-related regulated promoters (e.g., salicylic acid regulated promoters, ethylene regulated promoters, benzothiadiazole regulated promoters, etc.), temperature regulated promoters (e.g., heat shock inducible promoters (e.g., HSP-70, HSP-90, soybean heat shock promoter, etc.), light regulated promoters, synthetic inducible promoters, and the like.
• Recombinant expression vectors of the disclosure can also comprise elements that facilitate robust expression of reference or CasX variant proteins and/or reference or variant gNAs of the disclosure. For example, recombinant expression vectors can include one or more of a polyadenylation signal (PolyA), an intronic sequence or a post-transcriptional regulatory element such as a woodchuck hepatitis post-transcriptional regulatory element (WPRE), Exemplary polyA sequences include hGH poly(A) signal (short), HSV TK poly(A) signal, synthetic polyadenylation signals, SV40 poly(A) signal, β-globin poly(A) signal and the like. In addition, vectors used for providing a nucleic acid encoding a gNA and/or a CasX protein to a cell may include nucleic acid sequences that encode for selectable markers in the target cells, so as to identify cells that have taken up the gNA and/or CasX protein. A person of ordinary skill in the art will be able to select suitable elements to include in the recombinant expression vectors described herein.
• A recombinant expression vector sequence can be packaged into a virus or virus-like particle (also referred to herein as a “particle” or “virion”) for subsequent infection and transfommtion of a cell, ex vivo, in vitro or in vivo. Such particles or virions will typically include proteins that encapsidate or package the vector genome. In some embodiments, a recombinant expression vector of the present disclosure is a recombinant adeno-associated virus (AAV) vector. In some embodiments, a recombinant expression vector of the present disclosure is a recombinant lentivirus vector. In some embodiments, a recombinant expression vector of the present disclosure is a recombinant retroviral vector.
• Adeno-associated virus (AAV) is a small (20 nm). nonpathogenic virus that is useful in treating human diseases in situations that employ a viral vector for delivery to a cell such as a eukaryotic cell, either in vivo or ex vivo for cells to be prepared for administering to a subject. A construct is generated, for example a construct encoding any of the CasX proteins and/or gNA embodiments as described herein, and is flanked with AAV inverted terminal repeat (ITR) sequences, thereby enabling packaging of the AAV vector into an AAV viral particle.
• An “AAV” vector may refer to the naturally occurring wild-type virus itself or derivatives thereof. The term covers all subtypes, serotypes and pseudotypes, and both naturally occurring and recombinant forms, except where required otherwise. As used herein, the term “serotype” refers to an AAV which is identified by and distinguished from other AAVs based on capsid protein reactivity with defined antisera, e.g., there are many known serotypes of primate AAVs. In some embodiments, the AAV vector is selected from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV 10, AAV-Rh74 (Rhesus macaque-derived AAV), and AAVRh10, and modified capsids of these serotypes. For example, serotype AAV-2 is used to refer to an AAV which contains capsid proteins encoded from the cap gene of AAV-2 and a genome containing 5′ and 3′ ITR sequences from the same AAV-2 serotype. Pseudotyped AAV refers to an AAV that contains capsid proteins from one serotype and a viral genome including 5′-3′ ITRs of a second serotype. Pseudotyped rAAV would be expected to have cell surface binding properties of the capsid serotype and genetic properties consistent with the IT, serotype. Pseudotyped recombinant AAV (rAAV) are produced using standard techniques described in the art. As used herein, for example, rAAV1 may be used to refer an AAV having both capsid proteins and 5′-3′ ITRs from the same serotype or it may refer to an AAV having capsid proteins from serotype 1 and 5′-3′ ITRs from a different AAV serotype, e.g., AAV serotype 2. For each example illustrated herein the description of the vector design and production describes the serotype of the capsid and 5′-3′ ITR sequences.
• An “AAV virus” or “AAV viral particle” refers to a viral particle composed of at least one AAV capsid protein (preferably by all of the capsid proteins of a wild-type AAV) and an encapsidated polynucleotide. If the particle additionally comprises a heterologous polynucleotide (i.e., a polynucleotide other than a wild-type AAV genome to be delivered to a mammalian cell), it is typically referred to as “rAAV”. An exemplay heterologous polynucleotide is a polynucleotide comprising a Cast protein and/or sgRNA and, optionally, a donor template of any of the embodiments described herein.
• By “adeno-associated virus inverted terminal repeats” or “AAV ITRs” is meant the art recognized regions found at each end of the AAV genome which function together in cis as origins of DNA replication and as packaging signals for the virus. AAV ITRs, together with the AAV rep coding region, provide for the efficient excision and rescue from, and integration of a nucleotide sequence interposed between two flanking ITRs into a mammalian cell genome. The nucleotide sequences of AAV ITR regions are known. See, for example Kotin, R. M. (1994) Human Gene Therapy 5:793-801; Berns, K. I. “Parvoviridae and their Replication” in Fundamental Virology, 2^nd Edition, (B. N. Fields and D. M. Knipe, eds.). As used herein, an AAV ITR need not have the wild-type nucleotide sequence depicted, but may be altered, e.g,, by the insertion, deletion or substitution of nucleotides. Additionally, the AAV ITR may be derived from any of several AAV serotypes, including without limitation, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV-Rh74, and AAVRh10, and modified capsids of these serotypes. Furthermore, 5′ and 3′ ITRs which flank a selected nucleotide sequence in an AAV vector need not necessarily be identical or derived from the same AAV serotype or isolate, so long as they function as intended, i.e., to allow for excision and rescue of the sequence of interest from a host cell genome or vector, and to allow integration of the heterologous sequence into the recipient cell genome when AAV Rep gene products are present in the cell. Use of AAV serotypes for integration of heterologous sequences into a host cell is known in the art (see, e.g., WO2018195555A1 and US20180258424A1, incorporated by reference herein.).
• By “AAV rep coding region” is meant the region of the AAV gamine which encodes the replication proteins Rep 78, Rep 68, Rep 52 and Rep 40. These Rep expression products have been shown to possess many functions, including recognition, binding and nicking of the AAV origin of DNA replication, DNA helicase activity and modulation of transcription from AAV (or other heterologous) promoters. The Rep expression products are collectively required for replicating the AAV genome. By “AAV cap coding region” is meant the region of the AAV genome which encodes the capsid proteins VP1, VP2, and VP3, or functional homologues thereof. These Cap expression products supply the packaging functions which are collectively required for packaging the viral genome.
• In some embodiments, AAV capsids utilized for delivery of the encoding sequences for the CasX and gNA, and, optionally, the donor template nucleotides to a host cell can be derived from any of several AAV serotypes, including without limitation, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV-Rh74 (Rhesus macaque-derived AAV), arid AAVRh10, and the AAV ITRs are derived from AAV serotype 2.
• In order to produce rAAV viral particles, an AAV expression vector is introduced into a suitable host cell using known techniques, such as by transfection. Packaging cells are typically used to form virus particles; such cells include HEK293 cells (and other cells known in the art), which package adenovirus. A number of transfection techniques are generally known in the art; see, e.g., Sambrook et al. (1989) Molecular Cloning, a laboratory manual, Cold Spring Harbor Laboratories, New York. Particularly suitable transfection methods include calcium phosphate co-precipitation, direct microinjection into cultured cells, electroporation, liposome mediated gene transfer, lipid-mediated transduction, and nucleic acid delivery using high-velocity microprojectiles.
• In some embodiments, host cells transfected with the above-described AAV expression vectors are rendered capable of providing AAV helper functions in order to replicate and encapsidate the nucleotide sequences flanked by the AAV ITRs to produce rAAV viral particles. AAV helper functions are generally AAV-derived coding sequences which can be expressed to provide AAV gene products that, in turn, function in trans for productive AAV replication. AAV helper functions are used herein to complement necessary AAV functions that are missing from the AAV expression vectors, Thus, AAV helper functions include one, or both of the major AAV ORFs (open reading frames), encoding the rep and cap coding regions, or functional homologues thereof. Accessory functions can be introduced into and then expressed in host cells using methods known to those of skill in the art. Commonly, accessory functions are provided by infection of the host cells with an unrelated helper virus. In some embodiments, accessory functions are provided using an accessory function vector. Depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc., may be used in the expression vector.
• In other embodiments, retroviruses, for example, lentiviruses, may be suitable for use as vectors for delivery of the encoding nucleic acids of the CasX:gNA systems of the present disclosure. Commonly used retroviral vectors are “defective”, e,g. unable to produce viral proteins required for productive infection, and may be referred to a virus-like particles (VLP). Rather, replication of the vector requires growth in a packaging cell line. To generate viral particles comprising nucleic acids of interest, the retroviral nucleic acids comprising the nucleic acid are packaged into VLP capsids by a packaging cell line. Different packaging cell lines provide a different envelope protein (ecotropic, amphotropic or xenotropic) to be incorporated into the capsid, this envelope protein determining the specificity of the viral particle for the cells (ecotropic for marine and rat; amphotropic for most mammalian cell types including human, dog and mouse; and xenotropic for most mammalian cell types except murine cells). The appropriate packaging cell line may be used to ensure that the cells are targeted by the packaged viral particles. Methods of introducing subject vector expression vectors into packaging cell lines and of collecting the viral particles that are generated by the packaging lines are well known in the art.
• For non-viral delivery, vectors can also be delivered wherein the vector or vectors encoding the CasX variants and gNA are formulated in nanoparticies, wherein the nanoparticles contemplated include, but are not limited to nanospheres, liposomes, quantum dots, polyethylene glycol particles, hydrogels, and micelles. Lipid nanoparticles are generally composed of an ionizable cationic lipid and three or more additional components, such as cholesterol, DOPE, polylactic acid-co-glycolic acid, and a polyethylene glycol (PEG) containing lipid. In some embodiments, the CasX variants of the embodiments disclosed herein are formulated in a nanoparticle. In some embodiments, the nanoparticle comprises the gNA of the embodiments disclosed herein. In some embodiments, the nanoparticle comprises RNP of the CasX variant complexed with the gNA. In some embodiments, the system comprises a nanoparticle comprising nucleic acids encoding the CasX variants and the gNA and, optionally, a donor template nucleic acid. In some embodiments, the components of the CasX:gNA system are formulated in separate nanaoparticies for delivery to cells or for administration to a subject in need thereof.
• VIII. Applications
• The CasX proteins, guides, nucleic acids, and variants thereof provided herein, as well as vectors encoding such components, are useful for various applications, including therapeutics, diagnostics, and research.
• Provided herein are methods of cleaving a target DNA, comprising contacting the target DNA with a CasX protein and gNA pair. In some embodiments, the pair comprises a CasX variant protein and a gNA, wherein the CasX variant protein is a CasX variant of SEQ ID NO: 2 as described herein (e.g., a sequence of Tables 3, 8, 9, 10 and 12), and wherein the contacting results in cleavage and, optionally, editing of the tamet DNA. In other embodiments, the pair comprises a reference CasX protein and a gNA. In some embodiments, the gNA is a gNA variant of the disclosure (e.g., a sequence of SEQ ID NOS: 2101-2280), or a reference gRNA scaffold comprising SEQ ID NO: 5 or SEQ ID NO: 4, and further comprises a spacer that is complementary to the target DNA.
• In yet further aspects, the disclosure provides methods of cleaving a target DNA, comprising contacting the target DNA with a CasX protein and gNA pair of any of the embodiments described herein, wherein the contacting results in cleavage and optionally editing of the target DNA. In some embodiments, the scaffold of the gNA variant comprises a sequence of SEQ ID NO: 2101-2280, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% sequence identity thereto, and further comprises a spacer that is complementary to the target DNA. In some embodiments, the CasX protein is a CasX variant protein of any of the embodiments described herein (e.g., a sequence of Tables 3, 8, 9, 10 and 12), or a reference CasX protein SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• In some embodiments, the methods of editing a target DNA comprise contacting target DNA with a CasX protein and gNA pair as described herein and a donor polynucleotide, sometimes referred to as a donor template. In some embodiments, CasX protein and gNA pairs generate site-specific double strand breaks (DSBs) or single strand breaks (SSBs) (e.g., when the CasX variant protein is a nickase) within double-stranded DNA (dsDNA) target nucleic acids, which are repaired either by non-homologous end joining (NHEJ), homology-directed repair (HDR), homology-independent targeted integration, micro-homology mediated end joining (MMEJ), single strand annealing (SSA) or base excision repair (BER). In some cases, contacting a target DNA with a gene editing pair occurs under conditions that are permissive for NHEJ, HDR, or MMEJ. Thus, in some cases, a method as provided herein includes contacting the target DNA with a donor polynucleotide (e.g., by introducing the donor polynucleotide into a cell), wherein the donor polynucleotide, a portion of the donor polynucleotide, a copy of the donor polynucleotide, or a portion of a copy of the donor polynucleotide integrates into the target DNA. For example, an exogenous donor template which may comprise a corrective sequence (or a deletion to knock-out the defective allele) to be integrated flanked by an upstream sequence and a downstream sequence is introduced into a cell. The upstream and downstream sequences relative to the cleavage site(s) share sequence similarity with either side of the site of integration in the target DNA (i.e., homologous arms), facilitating the insertion. In other cases, an exogenous donor template which may comprise a corrective sequence is inserted between the ends generated by CasX cleavage by homology-independent targeted integration (HITI) mechanisms. The exogenous sequence inserted by HITI can be any length, for example, a relatively short sequence of between 1 and 50 nucleotides in length, or a longer sequence of about 50-1000 nucleotides in length. The lack of homology can be, for example, having no more than 20-50% sequence identity and/or lacking in specific hybridization at low stringency. In other cases, the lack of homology can further include a criterion of having no more than 5, 6, 7, 8, or 9 bp identity. In some cases, the method does not comprise contacting a cell with a donor polynucleotide, and the target DNA is modified such that nucleotides within the target DNA are deleted or inserted according to the cells own repair pathways.
• The donor template sequence may comprise certain sequence differences as compared to the genomic sequence, e.g., restriction sites, nucleotide polymorphisms, selectable markers (e.g., drug resistance genes, fluorescent proteins, enzymes etc.), etc., which may be used to assess for successful insertion of the donor nucleic acid at the cleavage site or in some cases may be used for other purposes (e.g., to signify expression at the targeted genomic locus). Alternatively, these sequence differences may include flanking recombination sequences such as FLPs, loxP sequences, or the like, that can be activated at a later time for removal of the marker sequence. In some embodiments of the method, the donor polynucleotide comprises at least about 10, at least about 50, at least about 100. or at least about 200, or at least about 300, or at least about 400, or at least about 500, or at least about 600, or at least about 700, or at least about 800, or at least about 900, or at least about 1000, or at least about 10,000, or at least 15,000 nucleotides of a wild-type gene. In other embodiments, the donor polynucleotide comprises at least about 10 to about 15,000 nucleotides, or at least about 200 to about 10,000 nucleotides, or at least about 400 to about 6000 nucleotides, or at least about 600 to about 4000 nucleotides, or at least about 1000 to about 2000 nucleotides of a wild-type gene. In some embodiments, the donor template is a single stranded DNA template or a single stranded RNA template. In other embodiments, the donor template is a double stranded DNA template.
• In some embodiments, contacting the target DNA with a CasX protein and gNA gene editing pair of the disclosure results in gene editing. In some embodiments, the editing occurs in vitro, outside of a cell, in a cell-free system. In some embodiments, the editing occurs in vitro, inside of a cell, for example in a cell culture system. In some embodiments, the editing occurs in vivo inside of a cell, for example in a cell in an organism. In some embodiments, the cell is a eukaryotic cell. Exemplary eukaryotic cells may include cells selected from the group consisting of a plant cell, a fungal cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a pig cell, a dog cell, a primate cell, a non-human primate cell, and a human cell. In some embodiments, the cell is a human cell. In some embodiments, the cell is an embryonic stem cell, an induced pluripotent stem cell, a germ cell, a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic stem cell, a neuron progenitor cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, a retinal cell, a cancer cell, a T-cell, a B-cell, an NK cell, a fetal cardiomyocyte, a myofibroblast, a mesenchymal stem cell, an autotransplated expanded cardiomyocyte, an adipocyte, a totipotent cell, a pluripotent cell, a blood stem cell, a myoblast, an adult stein cell, a bone marrow cell, a mesenchymal cell, a parenchymal cell, an epithelial cell, an endothelial cell, a mesothelial cell, fibroblasts, osteoblasts, chondrocytes, exogenous cell, endogenous cell, stem cell, hematopoietic stem cell, bone-marrow derived progenitor cell, myocardial cell, skeletal cell, fetal cell, undifferentiated cell, multi-potent progenitor cell, unipotent progenitor cell, a monocyte, a cardiac myoblast, a skeletal myoblast, a macrophage, a capillary endothelial cell, a xenogenic cell, an allogenic cell, or a post-natal stem cell. In alternative embodiments, the cell is a prokaryotic cell.
• Methods of editing of the disclosure can occur in vitro outside of a cell, in vitro inside of a cell or in vivo inside of a cell. The cell can be in a subject. In some embodiments, editing occurs in the subject having a mutation in an allele of a gene wherein the mutation causes a disease or disorder in the subject. In some embodiments, editing changes the mutation to a wild type allele of the gene. In some embodiments, editing knocks down or knocks out expression of an allele of a gene causing a disease or disorder in the subject. In some embodiments, editing occurs in vitro inside of the cell prior to introducing the cell into a subject. In some embodiments, the cell is autologous or allogeneic.
• Methods of introducing a nucleic acid (e.g., a nucleic acid comprising a donor polynucleotide sequence, one or more nucleic acids encoding a CasX protein and/or a gNA, or variants thereof as described herein) into a cell are known in the art, and any convenient method can be used to introduce a nucleic acid (e.g., an expression construct such as an AAV or virus like particle (VLP; e.g. a capsid derived from one or more components of a retrovirus, described supra) vector comprising the encoded CasX and gNA components, as described, supra) into a cell. Suitable methods include e.g., viral infection, transfection, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, nucleofection, electroporation, direct addition by cell penetrating CasX proteins that are fused to or recruit donor DNA, cell squeezing, calcium phosphate precipitation, direct microinjection, nanoparticle-mediated nucleic acid delivery, and the like.
• Introducing recombinant expression vectors into cells can occur in any suitable culture media and under any suitable culture conditions that promote the survival of the cells. Introducing recombinant expression vectors into a target cell can be carried out in vivo, in vitro or ex vivo.
• In some embodiments, a CasX variant protein can be provided as RNA. The RNA can be provided by direct chemical synthesis, or may be transcribed in vitro from a DNA (e.g., a DNA encoding mRNA comprising a sequence encoding the CasX variant protein). Once synthesized, the RNA may, for example, be introduced into a cell by any of the well-known techniques for introducing nucleic acids into cells (e.g., microinjection, electroporation, transfection).
• Nucleic acids may be provided to the cells using well-developed transfection techniques, and the commercially available TransMessenger® reagents from Qiagen, Stemfect™ RNA Transfection Kit from Stemgent, and TransIT®-mRNA Transfection Kit from Minis Bio LLC, Lonza nucleofection, Maxagen electroporation and the like.
• In some embodiments, vectors may be provided directly to a target host cell. For example, cells may be contacted with vectors comprising the subject nucleic acids (e.g, recombinant expression vectors having the donor template sequence and encoding the gNA variant; recombinant expression vectors encoding the CasX variant protein) such that the vectors are taken up by the cells. Methods for contacting cells with nucleic acid vectors that are plasmids include electroporation, calcium chloride transfection, microinjection, and lipofection are well known in the art. For viral vector delivery, cells can be contacted with viral particles comprising the subject viral expression vectors; e.g., the vectors are viral particles such as AAV or VLP that comprise polynucleotides that encode the CasX:gNA components or that comprise CasX:gNA RNP. For non-viral delivery, vectors or the CasX:gNA components can also be formulated for delivery in nanoparticles, wherein the nanoparticles contemplated include, but are not limited to nanospheres, liposomes, quantum dots, polyethylene glycol particles, hydrogels, and micelles.
• A nucleic acid comprising a nucleotide sequence encoding a CasX variant protein is in some cases an RNA. Thus, in some embodiments a CasX variant protein can be introduced into cells as RNA. Methods of introducing RNA into cells are known in the art and may include, for example, direct injection, transfection, or any other method used fbr the introduction of DNA. A CasX variant protein may instead be provided to cells as a polypeptide. Such a polypeptide may optionally be fused to a polypeptide domain that increases solubility of the product. The domain may be linked to the polypeptide through a defined protease cleavage site, e.g. a TEV sequence, which is cleaved by TEV protease. The linker may also include one or more flexible sequences, e.g. from 1 to 10 glycine residues. In some embodiments, the cleavage of the fusion protein is performed in a buffer that maintains solubility of the product, e.g. in the presence of from 0.5 to 2 M urea, in the presence of polypeptides and/or polynucleotides that increase solubility, and the like. Domains of interest may include endosomolytic domains, e.g. influenza HA domain; and other polypeptides that aid in production, e,g. IF2 domain, GST domain, GRPE domain, and the like. The polypeptide may be formulated for improved stability. For example, the peptides may be PEGylated, where the polyethyleneoxy group provides for enhanced lifetime in the blood stream.
• Additionally or alternatively, a reference or CasX variant protein of the present disclosure may be fused to a polypeptide permeant domain to promote uptake by the cell. A number of permeant domains are known in the art and may be used in the non-integrating polypeptides of the present disclosure, including peptides, peptidomimetics, and non-peptide carriers. For example, WO2017/106569 and US20180363009A1, incorporated by reference herein in its entirety, describe fusion of a Cas protein with one or more nuclear localization sequences (NLS) to facilitate cell uptake. In other embodiments, a permeant peptide may be derived from the third alpha helix of Drosophila melanogaster transcription factor Antennapaedia, referred to as penetratin, which comprises the amino acid sequence RQIKIWFQNRRMKWKK (SEQ ID NO: 398). As another example, the permeant peptide comprises the HIV-1 tat basic region amino acid sequence, which may include, for example, amino acids 49-57 of naturally-occurring tat protein, Other permeant domains include poly-arginine motifs, for example, the region of amino acids 34-56 of HIV-1 rev protein, nona-arginine, octa-arginine, and the like. The site at which the fusion is made may be selected in order to optimize the biological activity, secretion or binding characteristics of the polypeptide. The optimal site will be determined by routine experimentation.
• A CasX variant protein of the present disclosure may be produced in vitro or by eukaryotic cells or by prokaryotic cells transformed with encoding vectors (described above), and it may be further processed by unfolding, e.g. heat denaturation, dithiothreitol reduction, etc. and may be further refolded, using methods known in the art. In the case of production of the gNA of the present disclosure, recombinant expression vectors encoding the gNA can be transcribed in vitro, for example using T7 promoter regulatory sequences and T7 polymerase in order to produce the gRNA, which can then he recovered by conventional methods; e.g., purification via gel electrophoresis. Once synthesized, the sRNA may be utilized in the gene editing pair to directly contact a target DNA or may be introduced into a cell by any of the well-known techniques for introducing nucleic acids into cells (e.g,, microinjection, electroporation, transfection, etc.).
• In some embodiments, modifications of interest that do not alter the primary sequence of the CasX variant protein may include chemical derivatization of polypeptides, e.g., acylation, acetylation, carboxylation, amidation, etc. Also included are modifications of glycosylation, e.g. those made by modifying the glycosylation patterns of a polypeptide during its synthesis and processing or in further processing steps; e.g. by exposing the polypeptide to enzymes which affect glycosylation, such as mammalian glycosylating or deglycosylating enzymes. Also embraced are sequences that have phosphorylated amino acid residues, e.g. phosphotyrosine, phosphoserine, or phosphothreonine.
• In other embodiments, the present disclosure provides nucleic acids encoding a gNA variant or encoding a CasX variant and reference CasX proteins that have been modified using ordinary molecular biological techniques and synthetic chemistry so as to improve their resistance to proteolytic degradation, to change the target sequence specificity, to optimize solubility properties, to alter protein activity (e.g., transcription modulatory activity, enzymatic activity, etc.) or to render them more suitable. Analogs of such polypeptides include those containing residues other than naturally occurring L-amino acids, e.g. D-amino acids or non-naturally occurring synthetic amino acids, D-amino acids may be substituted for some or all of the amino acid residues.
• A CasX variant protein of the disclosure may be prepared by in vitro synthesis, using conventional methods as known in the art, Various commercial synthetic apparatuses are available, for example, automated synthesizers by Applied Biosystems, Inc., Beckman, etc. By using synthesizers, naturally occurring amino acids may be substituted with unnatural amino acids, The particular sequence and the manner of preparation will be determined by convenience, economics, purity required, and the like. If desired, various groups may be introduced into the peptide during synthesis or during expression, which allow for linking to other molecules or to a surface. Thus cysteines can be used to make thioethers, histidines for linking to a metal ion complex, carboxyl groups for forming amides or esters, amino groups for forming amides, and the like.
• A CasX variant protein of the disclosure may also be isolated and purified in accordance with conventional methods of recombinant synthesis. A lysate may be prepared of the expression host and the lysate purified using high performance liquid chromatography (HPLC), exclusion chromatography, gel electrophoresis, affinity chromatography, or other purification technique. For the most part, the compositions which are used will comprise 50% or more by weight of the desired product, more usually 75% or more by weight, preferably 95% or more by weight, and for therapeutic purposes, usually 99,5% or more by weight, in relation to contaminants related to the method of preparation of the product and its purification. Usually, the percentages will be based upon total protein. Thus, in some cases, a CasX polypeptide, or a CasX fusion polypeptide, of the present disclosure is at least 80% pure, at least 85% pure, at least 90% pure, at least 95% pure, at least 98% pure, or at least 99% pure (e.g., free of contaminants, non-CasX proteins or other macromolecules, etc.).
• In some embodiments, to induce cleavage or any desired modification to a target nucleic acid (e.g., genomic DNA), or any desired modification to a polypeptide associated with target nucleic acid in an in vitro cell, the gNA variant and/or the CasX variant protein of the present disclosure and/or the donor template sequence, whether they be introduced as nucleic acids or polypeptides, are provided to the cells for about 30 minutes to about 24 hours, e.g., hour, 1.5 hours, 2 hours, 2.5 hours, 3 hours, 3.5 hours 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 12 hours, 16 hours, 18 hours, 20 hours, or any other period from about 30 minutes to about 24 hours, which may be repeated with a frequency of about every day to about every 7 days, e.g., every 1.5 days, every 2 days, every 3 days, or any other frequency from about every day to about every 7days. The agent(s) may be provided to the subject cells one or more times, e.g. one time, twice, three times, or more than three times, and the cells allowed to incubate with the agent(s) for some amount of time following each contacting event; e.g., 16-24 hours, after which time the media is replaced with fresh media and the cells are cultured further.
• In some embodiments, the disclosure provides methods of treating a disease in a subject in need thereof comprising modifying a gene in a cell. of the subject, the modifying comprising; a) administering to the subject a CasX protein of any of the embodiments described herein and a gNA of any of the embodiments described herein wherein the targeting sequence of the gNA has a sequence that hybridizes with the target nucleic acid; b) a nucleic acid encoding the CasX protein and gNA of any of the embodiments described herein; c) a vector comprising the nucleic acids encoding the CasX and gNA; d) a VLP comprising a CasX:gNA RNP; or e) combinations thereof. In some embodiments of the method, the CasX protein and the gNA are associated together in a protein complex, for example a rihonuclear protein complex (RNP).
• In other embodiments, the methods of treating a disease in a subject in need thereof comprise administering to the subject a) a CasX protein or a polynucleotide encoding a CasX protein, b) a guide nucleic acid (gNA) comprising a targeting sequence or a polynucleotide encoding a gNA wherein the targeting sequence of the gNA has a sequence that hybridizes with the target nucleic acid, and c) a donor template comprising at least a portion or the entirety of a gene to be modified.
• In some embodiments of the method of treating a disease, wherein a vector is administered to the subject, the vector is administered at a dose of at least about 1×10⁹ vector genomes (vg), at least about 1×10¹⁰ vg, at least about 1×10¹¹ vg, at least about 1×10¹² vg, at least about 1×10¹³ vg, at least about 1×10¹⁴ vg. at least about 1×10¹⁵ vg, or at least about 1×10¹⁶ vg. The vector can be administered by a route of administration selected from the group consisting of intraparenchymal, intravenous, intra-arterial, intracerebroventricular, intracisternal, intrathecal, intracranial, intravitreal, subretinal, and intraperitoneal routes.
• A number of therapeutic strategies have been used to design the compositions for use in the methods of treatment of a subject with a disease. In some embodiments, the invention provides a method of treatment of a subject having a disease, the method comprising administering to the subject a CasX:gNA composition or a vector of any of the embodiments disclosed herein according to a treatment regimen comprising one or more consecutive doses using a therapeutically effective dose. In exemplary embodiments the CasX:gNA composition comprises a CasX variant of any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415, or a vector encoding the same. In some embodiments of the treatment regimen, the therapeutically effective dose of the composition or vector is administered as a single dose. In other embodiments of the treatment regimen, the therapeutically effective dose is administered to the subject as two or more doses over a period of at least two weeks, or at least one month, or at least two months, or at least three months, or at least four months, or at least five months, or at least six months. In some embodiments of the treatment regiment, the effective doses are administered by a route selected from the group consisting of subcutaneous, intradermal, intraneural, intranodal, intramedullary, intramuscular, intralumbar, intrathecal, subarachnoid, intraventricular, intracapsular, intravenous, intralytnphatical, intravitreal, subretinal, or intraperitoneal routes, wherein the administering method is injection, transfusion, or implantation.
• In some embodiments of the methods of treatment of a subject with a disease, the method comprises administering to the subject a CasX:gNA composition as an RNP within a VLP disclosed herein according to a treatment regimen comprising one or more consecutive doses using a therapeutically effective dose.
• In some embodiments, the administering of the therapeutically effective amount of a CasX:gNA modality, including a vector comprising a polynucleotide encoding a CasX protein and a guide nucleic acid, or the administering of a CasX-gNA composition disclosed herein, to knock down or knock out expression of a gene product to a subject with a disease leads to the prevention or amelioration of the underlying disease such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disease. In sonic embodiments, the administration of the therapeutically effective amount of the CasX-gNA modality leads to an improvement in at least one clinically-relevant parameter for a disease.
• In embodiments in which two or more different targeting complexes are provided to the cell (e.g., two gNA comprising two or more different spacers that are complementary to different sequences within the same or different target nucleic acid), the complexes may be provided simultaneously (e.g. as two polypeptides and/or nucleic acids), or delivered simultaneously. Alternatively, they may be provided consecutively, e.g. the targeting complex being provided first, followed by the second targeting complex, etc. or vice versa.
• To improve the delivery of a DNA vector into a target cell, the DNA can be protected from damage and its entry into the cell facilitated, for example, by using lipoplexes and polyplexes. Thus, in some cases, a nucleic acid of the present disclosure (e.g., a recombinant expression vector of the present disclosure) can be covered with lipids in an organized structure like a micelle, a liposome, or a lipid nanoparticle. When the organized structure is complexed with DNA it is called a lipoplex. There are three types of lipids, anionic (negatively-charged), neutral, or cationic (positively-charged). Lipoplexes that utilize cationic lipids have proven utility for gene transfer. Cationic lipids, due to their positive charge, naturally complex with the negatively charged DNA. Also as a result of their charge, they interact with the cell membrane. Endocvtosis of the lipoplex then occurs, and the DNA is released into the cytoplasm. The cationic lipids also protect against degradation of the DNA by the cell.
• Complexes of polymers with DNA are referred to as polyplexes. Most polyplexes consist of cationic polymers and their production is regulated by ionic interactions. One large difference between the methods of action of polyplexes and lipoplexes is that polyplexes cannot release their DNA load into the cytoplasm, so to this end, co-transfection with endosome -lytic agents (to lyse the endosome that is made during endocytosis) such as inactivated adenovirus must occur. However, this is not always the case; polymers such as polyethylenimine have their own method of endosome disruption as does chitosan and trimethylchitosan.
• Dendrimers, a highly branched macromolecule with a spherical shape, may be also be used to genetically modify stem cells. The surface of the dendrimer panicle may be functionalized to alter its properties. In particular, it is possible to construct a cationic dendrimer (i.e., one with a positive surface charge). When in the presence of genetic material such as a DNA plasmid charge complementarily leads to a temporary association of the nucleic acid with the cationic dendrimer. On reaching its destination, the dendrimer-nucleic acid complex can be taken up into a cell by endocytosis.
• In some cases, a nucleic acid of the disclosure (e.g., an expression vector) includes an insertion site for a guide sequence of interest. For example, a nucleic acid can include an insertion site for a guide sequence of interest, where the insertion site is immediately adjacent to a nucleotide sequence encoding the portion of a gNA variant (e.g. the scaffold region) that does not change when the guide sequence is changed to hybridize to a desired target sequence. Thus, in some cases, an expression vector includes a nucleotide sequence encoding a gNA, except that the portion encoding the spacer sequence portion of the gNA is an insertion sequence (an insertion site). An insertion site is any nucleotide sequence used for the insertion of a spacer in the desired sequence. “Insertion sites” for use with various technologies are known to those of ordinary skill in the art and any convenient insertion site can be used. An insertion site can be for any method for manipulating nucleic acid sequences. For example, in some cases the insertion site is a multiple cloning site (MCS) (e.g., a site including one or more restriction enzyme recognition sequences), a site for ligation independent cloning, a site for recombination based cloning (e.g., recombination based on att sites), a nucleotide sequence recognized by a. CRISPR/Cas (e.g. Cas9) based technology, and the like.
• IX. Cells
• In still further embodiments, provided herein are cells comprising components of any of the CasX:gNA systems described herein. In some embodiments, the cells comprise any of the gNA variant embodiments as described herein, or the reference gRNA of SEQ ID NO: 5 or SEQ ID NO: 4 and finther comprises a spacer that is complementary to the target DNA. In some embodiments, the cells further comprise a CasX variant as described herein (es, the sequences of Tables 3, 8, 9, 10 and 12 ora reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO. 3). In other embodiments, the cells comprise RNP of any of the CasX:gNA embodiments described herein. In other embodiments, the disclosure provides cells comprising vectors encoding the CasX:gNA systems of any of the embodiments described herein. In still other embodiments, the cells comprise target DNA that has been edited by the CasX:gNA embodiments described herein; either to correct a mutation (knock-in) or to knock-down or knock-out a defective gene,
• In some embodiments, the cell is a eukaryotic cell, for example a human cell. In alternative embodiments, the cell is a prokaryotic cell.
• In some embodiments, the cell is a modified cell (e.g., a genetically modified cell) comprising nucleic acid comprising a nucleotide sequence encoding a CasX variant protein of the disclosure. In some embodiments, the genetically modified cell is genetically modified with an mRNA comprising a nucleotide sequence encoding a CasX variant protein. In some embodiments, the cell is genetically modified with a recombinant expression vector comprising: a) a nucleotide sequence encoding a CasX variant protein of the present disclosure; and b) a nucleotide sequence encoding a gNA of the disclosure, and, optionally, comprises a nucleotide sequence encoding a donor template. In some cases, such cells are used to produce the individual components or RNP of CasX gNA systems for use in editing target DNA. In other cases, cells that have been genetically modified in this way may be administered to a subject for purposes such as gene therapy, e.g., to treat a disease or condition caused by a genetic mutation or defect.
• A cell that can serve as a recipient for a CasX variant protein and/or gNA of the present disclosure and/or a nucleic acid comprising a nucleotide sequence encoding a CasX variant protein and/or a gNA variant, can be any of a variety of cells, including, e.g., in vitro cells; in vivo cells; ex viva cells; primary cells; cells of an immortalized cell line; cancer cells; animal cells; plant cells; algal cells; fungal cells; etc. A cell can be a recipient of a CasX RNP of the present disclosure. A cell can be a recipient of a single component of a CasX system of the present disclosure. A cell can be a recipient of a vector encoding the CasX, gNA and, optionally, a donor template of the CasX:gNA systems of any of the embodiments described herein.
• Non-limiting examples of cells that can serve as host cells for production of the CasX:gNA systems disclosed herein include: a prokaryotic cell, eukaryotic cell, a bacterial cell, an archaeal cell, a cell of a single-cell eukaryotic organism, a protozoa cell, a cell from a plant (e.g., cells from plant crops, fruits, vegetables, grains, soy bean, corn, maize, wheat, seeds, tomatoes, rice, cassava, sugarcane, pumpkin, hay, potatoes, cotton, cannabis, tobacco, flowering plants, conifers, gymnosperms, angiosperms, ferns, clubmosses, homworts, liverworts, mosses, dicotyledons, monocotyledons, etc.), an algal cell, (e.g., Botryococcus braunii, Chlamydomonas reinhardtii, Nannochloropsis gadiana, Chlorella pyrenoidosa, Sargassum patens, C. agardh, and the like), seaweeds (e.g. kelp) a fungal cell (e.g,, a yeast cell, a cell from a mushroom), an animal cell, a cell from an invertebrate animal (e.g., fruit fly, cnidarian, echinoderm, nematode, etc.), a cell from a vertebrate animal (e.g., fish, amphibian, reptile, bird, mammal), a cell from a mammal (e.g., an ungulate (e.g., a pig, a cow, a goat, a sheep); a rodent (e.g., a rat, a mouse); a non-human primate; a human; a feline (e.g., a cat); a canine (e,g., a dog); etc.), and the like. In some cases, the cell is a cell that does not originate from a natural organism (e.g., the cell can be a synthetically made cell; also referred to as an artificial cell).
• In certain embodiments, as provided herein, a cell can be an in vitro cell (e.g., established cultured cell line including, but not limited to HEK293 cells, HEK293T HEK293-F cells, Lenti-X 293T cells, BHK cells, HepG2 cells, Saos-2 cells, HuH7 cells, A549 cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells, hybridoma cells, VERO cells, NIH3T3 cells, COS, W138 cells, MRC5 cells, HeLa, HT1080 cells, or CHO cells). A cell can be an ex viva cell (cultured cell from an individual). Such cells can be autologous with respect to a subject to be administered said cell(s). In other embodiments, the cells can be allogeneic with respect to a subject to be administered said cell(s). A cell can be an in viva cell (e.g., a cell in an individual). A cell can be an isolated cell. A cell can be a cell inside of an organism. A cell can be an organism. A cell can be a cell in a cell culture (e.g., in vitro cell culture). A cell can be one of a collection of cells. A cell can be a prokaryotic cell or derived from a prokaryotic cell, A cell can be a bacterial cell or can be derived from a bacterial cell. A cell can be an archaeal cell or derived from an archaeal cell. A cell can be a eukaryotic cell or derived from a eukaryotic cell. A cell can be a plant cell or derived from a plant cell. A cell can be an animal cell or derived from an animal cell. A cell can be an invertebrate cell or derived from an invertebrate cell. A cell can be a vertebrate cell or derived from a vertebrate cell. A cell can be a mammalian cell or derived from a mammalian cell. A cell can be a rodent cell or derived from a rodent cell. A cell can be a human cell or derived from a human cell. A cell can be a microbe cell or derived from a microbe cell. A cell can be a fungi cell or derived from a fungi cell. A cell can be an insect cell. A cell can be an arthropod cell. A cell can be a protozoan cell. A cell can be a helminth cell.
• Suitable cells may include, in some embodiments, a stem cell (e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell; a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.); a somatic cell, e.g. a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic stem cell, a neuron progenitor cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, a retinal cell, a cancer cell, a T-cell, a B-cell, a fetal cardiomyocyte, a myofibroblast, a mesenchymal stem cell, an autotransplated expanded cardiomyocyte, an adipocyte, a totipotent cell, a pluripotent cell, a blood stem cell, a myoblast, an adult stem cell, a bone marrow cell, a mesenchymal cell, a parenchymal cell, an epithelial well, an endothelial cell, a mesothelial cell, fibroblasts, osteoblasts, chondrocytes, exogenous cell, endogenous cell, stem cell, hematopoietic stem cell, bone-marrow derived progenitor cell, myocardial cell, skeletal cell, fetal cell, undifferentiated cell, multi-potent progenitor cell, unipotent progenitor cell, a monocyte, a cardiac myoblast, a skeletal myoblast, a macrophage, a capillary endothelial cell, a xenogenic cell, an allogenic cell, and a post-natal stem cell.
• In some embodiments, the cell is an immune cell. In some cases, the immune cell is a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, or a macrophage. In some cases, the immune cell is a cytotoxic T cell. In some cases, the immune cell is a helper T cell. In some cases, the immune cell is a regulatory T cell (Treg). In some cases, the cell expresses a chimeric antigen receptor.
• In some embodiments, the cell is a stein cell. Stem cells may include, for example, adult stem cells. Adult stem cells can also be referred to as somatic stem cells. In some embodiments, the stem cell is a hematopoietic stem cell (HSC), neural stem cell or a mesenchymal stein cell. In other embodiments, the stem cell is a mesenchvinal stem cell (MSC). MSCs originally derived from the embryonal mesoderm and isolated from adult bone marrow, can differentiate to form muscle, bone, cartilage, fat, marrow stroma, and tendon. Methods of isolating MSC are known in the art; and any known method can be used to obtain MSC.
• A cell in some embodiments is an arthropod cell.
• X. Kits and Articles of Manufacture
• In another aspect, provided herein are kits comprising a CasX protein and one or a plurality of gNA of any of the embodiments of the disclosure and a suitable container (for example a tube, vial or plate). In some embodiments, the kit comprises a gNA variant of the disclosure, or the reference gRNA of SEQ ID NO: 5 or SEQ ID NO: 4. Exemplary gNA variants that can be included comprise a sequence of any one of SEQ ID NO: 2101-2280.
• In some embodiments, the kit comprises a CasX variant protein of the disclosure (e.g. a sequence of Tables 3, 8, 9, 10 and 12), or the reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ TD NO: 3. In exemplary embodiments, a kit of the disclosure comprises a CasX variant of any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, the kit comprises a CasX variant of any one of SEQ NOS: 247-337, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, the kit comprises a CasX variant of any one of 3498-3501, 3505-3520, and 3540-3549.
• In some embodiments, the kit comprises a gNA or a vector encoding a gNA, wherein the gNA comprises a sequence selected from the group consisting of SEQ ID NOS: 412-3295. In some embodiments, the gNA comprises a sequence selected from the group consisting of SEQ ID NOS: 2101-2280. In some embodiments, the gNA comprises a sequence selected from the group consisting of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, and 2259-2280.
• In certain embodiments, provided herein are kits comprising a CasX protein and gNA editing pair comprising a CasX variant protein of Tables 3, 8, 9, 10 and 12 and a gNA variant as described herein (e.g., a sequence of Table 2). In exemplary embodiments, a kit of the disclosure comprises a CasX and gNA editing pair, wherein the CasX variant comprises of any one of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415. In some embodiments, the gNA of the gene editing pair comprises any one of SEQ ID NOS: 412-3295. In some embodiments, the gNA of the gene editing pair comprises any one of SEQ ID NOS: 2101-2280. in some embodiments, the gNA of the gene editing pair comprises any one of SEQ ID NOS: 2236, 2237, 2238, 2241, 2244, 2248, 2249, or 2259-2280.
• In some embodiments, the kit further comprises a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing. In some embodiments, the kit further comprises a pharmaceutically acceptable carrier, diluent or excipient.
• In some embodiments, the kit comprises appropriate control compositions for gene editing applications, and instructions for use.
• In some embodiments, the kit comprises a vector comprising a sequence encoding a CasX variant protein of the disclosure, a gNA variant of the disclosure, optionally a donor template, or a combination thereof.
• The present description sets forth numerous exemplary configurations, methods, parameters, and the like. It should be recognized, however, that such description is not intended as a limitation on the scope of the present disclosure, but is instead provided as a description of exemplary embodiments. Embodiments of the present subject matter described above may be beneficial alone or in combination, with one or more other aspects or embodiments. Without limiting the foregoing description, certain non-limiting embodiments of the disclosure are provided below. As will he apparent to those of skill in the art upon reading this disclosure, each of the individually numbered embodiments may be used or combined with any of the preceding or following individually numbered embodiments. This is intended to provide support for all such combinations of embodiments and is not limited to combinations of embodiments explicitly provided below:
Embodiment Set #1
• Embodiment 1. A variant of a reference CasX protein, wherein the CasX variant is capable of forming a complex with a guide nucleic acid, and wherein the complex binds a target nucleic acid, and wherein the CasX variant comprises at least one modification in at least one of the following domains of the reference CasX protein:
• (a) a non-target strand binding (NTSB) domain that binds to the non-target strand of DNA, wherein the NTSB domain comprises a four-stranded beta sheet;
• (b) a target strand loading (TSL) domain that places the target DNA in a cleavage site of the CasX variant, the TSL domain comprising three positively charged amino acids, wherein the three positively charged amino acids bind to the target strand of DNA,
• (c) a helical I domain that interacts with both the target DNA and a spacer region of a guide RNA, wherein the helical I domain comprises one or more alpha helices;
• (d) a helical II domain that interacts with both the target DNA and a scaffold stem of the guide RNA;
• (e) an oligonucleotide binding domain (OBD) that binds a triplex region of the guide RNA; and
• (f) a RuvC DNA cleavage domain;
• wherein the CasX variant exhibits at least one improved characteristic as compared to the reference CasX protein.
• Embodiment 2. The CasX variant of Embodiment 1, wherein the reference CasX comprises the sequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3, or at least 60% similarity thereto.
• Embodiment 3. The CasX variant of Embodiment 2. wherein the reference CasX comprises the sequence of SEQ ID NO: 1, or at least 60% similarity thereto.
• Embodiment 4. The CasX variant of Embodiment 2, wherein the reference CasX comprises the sequence of SEQ ID NO: 2, or at least 60% similarity thereto.
• Embodiment 5. The CasX variant of Embodiment 2, wherein the reference CasX comprises the sequence of SEQ ID NO: 3, or at least 60% similarity thereto.
• Embodiment 6. The CasX variant of any one of Embodiment 1 to Embodiment 5, wherein the complex binds a target DNA and cleaves the target DNA.
• Embodiment 7. The CasX variant of any one of Embodiment 1 to Embodiment 5, wherein the complex binds a target DNA but does not cleave the target DNA.
• Embodiment 8. The CasX variant of any one of Embodiment 1 to Embodiment 5, wherein the complex binds a target DNA and generates a single stranded nick in the target DNA.
• Embodiment 9. The CasX variant of any one of Embodiment 1 to Embodiment 8, wherein at least one modification comprises at least one amino acid substitution in a domain.
• Embodiment 10. The CasX variant of any one of Embodiment 1 to Embodiment 9, wherein at least one modification comprises at least one amino acid deletion in a domain.
• Embodiment 11. The CasX variant of Embodiment 10, wherein at least one modification comprises the deletion of 1 to 4 consecutive or non-consecutive amino acids in the protein.
• Embodiment 12. The CasX variant of any one of Embodiment 1 to Embodiment 10, wherein modification comprises at least one amino acid insertion in a domain.
• Embodiment 13. The CasX variant of Embodiment 12, wherein at least one modification comprises the insertion of 1 to 4 consecutive or non-consecutive amino acids in a domain.
• Embodiment 14. The CasX variant of any one of 1 to Embodiment 13, having at least 60% similarity to one of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 15. The CasX variant of Embodiment 14, wherein the variant has at least 60% similarity sequence identity to SEQ ID NO: 2.
• Embodiment 16. The CasX variant of any one of Embodiment 1 to Embodiment 15. wherein the improved characteristic is selected from the group consisting of improved folding of the variant, unproved binding affinity to the guide RNA, improved binding affinity to the target DNA, altered binding affinity to one or more PAM sequences, improved unwinding of the target DNA, increased activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, improved protein stability, improved protein:guide RNA complex stability, improved protein solubility, improved protein:guide RNA complex solubility, improved protein yield, and improved fusion characteristics.
• Embodiment 17. The CasX variant of any one of Embodiment 1 to Embodiment 16, wherein at least one of the at least one improved characteristic of the CasX variant is at least about 1.1 to about 100,000 times improved relative to the reference protein.
• Embodiment 18. The CasX variant of any one of Embodiment 1 to Embodiment 17, wherein at least one of the at least one improved characteristics of the CasX variant is at least about 10 to about 100 times improved relative to the reference protein.
• Embodiment 19. The CasX variant any one of Embodiment 1 to Embodiment 18, wherein the CasX variant has about 1.1 to about 100 times increased binding affinity to the guide RNA compared to the protein of SEQ ID NO: 2.
• Embodiment 20. The Cask variant any one of Embodiment 1 to Embodiment 19, wherein the CasX variant has about one to about two times increased binding affinity to the target DNA compared to the protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 21. The CasX variant of any one of Embodiment 1 to Embodiment 2.0, wherein the CasX protein comprises between 400 and 3000 amino acids.
• Embodiment 22. The CasX variant of any one of Embodiment 1 to Embodiment 21, comprising at least one modification in at least two domains of the reference CasX protein.
• Embodiment 23. The Cask variant of any one of Embodiment 1 to Embodiment 22, comprising two or more modifications in at least one domain of the reference CasX protein.
• Embodiment 24. The CasX variant of any one of Embodiment 1 to Embodiment 23, wherein at least one modification comprises deletion of at least a portion of one domain of the reference CasX protein.
• Embodiment 25. The CasX variant of any one of Embodiment 1 to Embodiment 24, comprising at least one modification of a region of non-contiguous residues that fomi a channel in which guide RNA:target DNA complexing occurs.
• Embodiment 26. The Cask variant of any one of Embodiment 1 to Embodiment 25, comprising at least one modification of a region of non-contiguous residues that form an interface which binds with the guide RNA.
• Embodiment 27. The CasX variant of any one of Embodiment 1 to Embodiment 26, comprising at least one modification of a region of non-contiguous residues that form a channel which binds with the non-target strand DNA.
• Embodiment 28. The CasX variant of any one of Embodiment 1 to Embodiment 27, comprising at least one modification of a region of non-contiguous residues that form an interface which binds with the PAM.
• Embodiment 29. The CasX variant of any one of Embodiment 1 to Embodiment 28, comprising at least one modification of a region of non-contiguous surface-exposed residues.
• Embodiment 30. The CasX variant of any one of Embodiment 1 to Embodiment 29, comprising at least one modification of a region of non-contiguous residues that fomi a core through hydrophobic packing in a domain of the variant
• Embodiment 3 I. The CasX variant of any one of Embodiment 1 to Embodiment 30, wherein between 2 to 15 residues of the region are charged.
• Embodiment 32. The CasX variant of any one of Embodiment 1 to Embodiment 31, wherein between 2 to 15 residues of the region are polar.
• Embodiment 33. The CasX variant of any one of Embodiment 1 to Embodiment 32, wherein between 2 to 15 residues of the region stack with DNA or RNA bases.
• Embodiment 34. A variant of a reference guide nucleic acid (NA) capable of binding a reference CasX protein, wherein:
• the reference nucleic acid comprises a tracrNA sequence and a crNA sequence, wherein:
• • the tracrNA comprises a scaffold stem loop region comprising an bubble,
  • the tracrNA and the crNA form a stem and a triplex region, and
  • the tracrNA and the crNA are fused, and form a fusion stem loop region;
• the variant comprises at least one modification to the reference guide NA, and
• the variant exhibits at least one improved characteristic compared to the reference guide RNA.
• Embodiment 35. The guide NA variant of Embodiment 34, comprising a tracrRNA stem loop comprising the sequence -EUU-N_3-20-UUU-.
• Embodiment 36. The guide NA variant of Embodiment 34 or Embodiment 35, comprising a crRNA sequence with -AAAG- in a location 5 to the spacer region.
• Embodiment 37. The guide NA variant of Embodiment 36, wherein the -AAAG- sequence is immediately 5′ to the spacer region.
• Embodiment 38. The guide NA variant of any one of Embodiment 34 to Embodiment 37, wherein the at least one improved characteristic is selected from the group consisting of improved stability, improved solubility, improved resistance to nuclease activity, increased folding rate of the NA, decreased side product formation during folding, increased productive folding, improved binding affinity to a reference CasX protein, improved binding affinity to a target DNA, improved gene editing, and improved specificity.
• Embodiment 39. The guide NA variant of any one of Embodiment 34 to Embodiment 37, wherein at least one modification comprises at least one nucleic acid substitution in a region.
• Embodiment 40. The guide NA variant of any one of Embodiment 34 to Embodiment 39, wherein at least one modification comprises at least one nucleic acid deletion in a region,
• Embodiment 41. The guide NA variant of Embodiment 40, wherein at least one modification comprises deletion of 1 to 4 nucleic acids in a region.
• Embodiment 42. The guide NA variant of any one of Embodiment 34 to Embodiment 40, wherein at least one modification comprises at least one nucleic acid insertion in a region.
• Embodiment 43. The guide NA variant of Embodiment 42, wherein at least one modification comprises insertion of 1 to 4 nucleic acids in a region.
• Embodiment 44. The guide NA variant of any one of Embodiment 34 to Embodiment 42, comprising a scaffold region at least 60% homologous to SEQ ID NO: 5.
• Embodiment 45. The guide NA variant of any one of Embodiment 34 to Embodiment 44, comprising a scaffold NA stem loop at least 60% homologous to SEQ ID NO: 6.
• Embodiment 46. The guide NA variant of any one of Embodiment 34 to Embodiment 45, comprising an extended stem loop at least 60% homologous to SEQ ID NO: 7.
• Embodiment 47. The guide NA variant of any one of Embodiment 34 to Embodiment 46, wherein the guide NA variant sequence is at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, or at least 70% homologous to SEQ ID NO: 4.
• Embodiment 48. The guide NA variant of any one of Embodiment 34 to Embodiment 47, comprising an extended stem loop region comprising fewer than 10,000 nucleotides.
• Embodiment 49. The guide NA variant of any one of Embodiment 34 to Embodiment 44, wherein the scaffold stem loop or the extended stem loop is swapped for an exogenous stem loop.
• Embodiment 50. The guide NA variant of any one of Embodiment 34 to Embodiment 49, further comprising a hairpin loop that is capable of binding a protein, RNA or DNA.
• Embodiment 51. The guide NA variant of Embodiment 50, wherein the hairpin loop is from MS2, QB, U1A, or PP7.
• Embodiment 52. The guide NA variant of any one of Embodiment 34 to Embodiment 48, further comprising one or more ribozymes.
• Embodiment 53. The guide NA variant of Embodiment 52, wherein the one or more ribozymes are independently fused to a terminus of the guide RNA variant.
• Embodiment 54. The guide NA variant of Embodiment 52 or Embodiment 53, wherein at least one of the one or more ribozymes are an hepatitis delta virus (HDV) ribozyme, hammerhead ribozyme, pistol ribozyme, hatchet ribozyme, or tobacco ringspot virus (TRSV) ribozyme.
• Embodiment 55. The guide NA variant of any one of Embodiment 34 to Embodiment 54, further comprising a protein binding motif
• Embodiment 56. The guide NA variant of any one of Embodiment 34 to Embodiment 55, further comprising a thermostable stem loop.
• Embodiment 57. The guide NA variant of Embodiment 34, comprising the sequence of any one of SEQ ID NO: 9 to SEQ ID NO: 66.
• Embodiment 58. The guide NA variant of any one of Embodiment 34 to Embodiment 57, further comprising a spacer region.
• Embodiment 59. The guide NA variant of any one of Embodiment 34 to Embodiment 58, wherein the reference guide RNA comprises SEQ ID NO: 5.
• Embodiment 60. The guide NA variant of any one of Embodiment 38 to Embodiment 59, wherein the reference CasX protein comprises SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 61. A gene editing pair comprising a CRISPR-associated protein (Cas protein) and a guide NA, wherein the Cas protein is a CasX variant of any one of Embodiment 1 to Embodiment 33.
• Embodiment 62. The gene editing pair of 61, wherein the guide NA is a guide NA variant of any one of Embodiment 34 to Embodiment 60, or the guide NA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 63. The gene editing pair of Embodiment 61 or Embodiment 62, wherein the gene editing pair has one or more improved characteristics compared to a gene editing pair comprising a CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3; and a guide RNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 64. The gene editing pair of Embodiment 63, wherein the one or more improved characteristics comprises improved protein:guide NA complex stability, improved protein:guide NA complex stability, improved binding affinity between the protein and guide NA, improved kinetics of complex formation, improved binding affinity to the target DNA, improved unwinding of the target DNA, increased activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, or improved resistance to nuclease activity.
• Embodiment 65. A gene editing pair comprising a CRISPR-associated protein (Cas protein) and a guide NA, wherein the guide NA is a guide NA variant of any one of Embodiment 34 to Embodiment 60.
• Embodiment 66. The gene editing pair of Embodiment 65, wherein the Cas protein is a CasX variant of any one of Embodiment 1 to Embodiment 22, or a CasX protein of SEQ ID NO: SEQ ID NO: 2, or SEQ ID NO. 3.
• Embodiment 67. The gene editing pair of Embodiment 65 or Embodiment 66, wherein the gene editing pair has one or more improved characteristics.
• Embodiment 68. The gene editing pair of :Embodiment 67, wherein the one or more improved characteristics comprises improved protein:guide NA complex stability, improved protein:guide NA complex stability, improved binding affinity between the protein and guide NA, improved binding affinity to the target DNA, improved unwinding of the target DNA, increased activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, or unproved resistance to nuclease activity.
• Embodiment 69. A method of editing a target DNA, comprising combining the target DNA with a gene editing pair, the gene editing pair comprising a CasX variant and a guide RNA, wherein the CasX variant is a CasX variant of any one of Embodiment 1 to Embodiment 33, and wherein the combining results in editing of the target DNA.
• Embodiment 70. The method of 69, wherein the guide NA is a guide NA variant of any one of Embodiment 34 to Embodiment 60, or the guide RNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 71. The method of Embodiment 69 or Embodiment 70, wherein editing occurs in vitro outside of a cell.
• Embodiment 72. The method of Embodiment 69 or Embodiment 70, wherein editing occurs in vitro inside of a cell.
• Embodiment 73. The method of Embodiment 69 or Embodiment 70, wherein editing occurs in vivo inside of a cell.
• Embodiment 74. The method of any one of Embodiment 71 to Embodiment 73, wherein the cell is a eukaryotic cell.
• Embodiment 75. The method of Embodiment 74, wherein the eukaryotic cell is selected from the group consisting of a plant cell, a fungal cell, a protist cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.
• Embodiment 76. The method of any one of Embodiment 71 to Embodiment 73, wherein the cell is a prokaryotic cell.
• Embodiment 77. A method of editing a target DNA, comprising combining the target DNA with a gene editing pair, the gene editing pair comprising a CRISPR-associated protein (Cas protein) and a guide NA variant, wherein the guide NA variant is a guide NA variant of any one of Embodiment 34 to Embodiment 60, and wherein the combining results in editing of the target DNA.
• Embodiment 78. The method of Embodiment 77, wherein the Cas protein is a CasX variant of any one of Embodiment 1 to Embodiment 33, or a CasX protein of SEQ NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 79. The method of Embodiment 77 or Embodiment 78, wherein editing occurs in vitro outside of a cell.
• Embodiment 80. The method of Embodiment 77 or Embodiment 78, wherein editing occurs in vitro inside of a. cell.
• Embodiment 81. The method of Embodiment 77 or Embodiment 78, wherein contacting occurs in vivo inside of a cell.
• Embodiment 82. The method of any one of Embodiment 79 to Embodiment 81, wherein the cell is a eukarvotic cell.
• Embodiment 83. The method of Embodiment 82, wherein the eukaryotic. cell is selected from the group consisting of a plant cell, a fungal cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a. parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.
• Embodiment 84. The method of any one of Embodiment 79 to Embodiment 81, wherein the cell is a prokaryotic cell.
• Embodiment 85. A cell comprising a CasX variant, wherein the CasX variant is a CasX variant of any one of Embodiment lto Embodiment33.
• Embodiment 86. The cell of Embodiment 85, further comprising a guide NA variant of any one of Embodiment 34to Embodiment 60, or the guide RNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 87. A cell comprising a guide NA variant, wherein the guide NA variant is a guide NA variant of any one of Embodiment 34to Embodiment 60.
• Embodiment 88. The cell of Embodiment 87, further comprising a CasX variant of any one of Embodiment 1 to Embodiment 33, or a CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO. 3.
• Embodiment 89. The cell of any one of 85to Embodiment 88, wherein the cell is a eukaryotic cell.
• Embodiment 90, The cell of any one of 85to Embodiment 88, wherein the cell is a prokaryotic cell.
• Embodiment 91. A polynucleotide encoding the CasX variant of any one of Embodiment 1 to Embodiment 33.
• Embodiment 92. A vector comprising the polynucleotide of Embodiment 91.
• Embodiment 93. The vector of Embodiment 92, wherein the vector is a bacterial plasmid.
• Embodiment 94. A cell comprising the polynucleotide of Embodiment 91, or the vector of Embodiment 92 or Embodiment 93.
• Embodiment 95. A composition, comprising the CasX variant of any one of Embodiment 1 to Embodiment 33.
• Embodiment 96. The composition of 95, further comprising a guide RNA variant of any one of Embodiment 34 to Embodiment 60, or the guide RNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 97. The composition of Embodiment 95 or Embodiment 96, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 98. A composition, comprising a guide RNA variant of any one of Embodiment 34 to Embodiment 60,
• Embodiment 99. The composition of Embodiment 98, further comprising the CasX variant of any one of 1 to Embodiment 33, or the CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 100. The composition of Embodiment 98 or Embodiment 99, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 101. A composition, comprising the gene editing pair of any one of Embodiment 61to Embodiment 68.
• Embodiment 102. The composition of Embodiment 101, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 103. A kit, comprising the CasX variant of any one of Embodiment lto Embodiment 33 and a container.
• Embodiment 104. The kit of Embodiment 103, further comprising a guide NA variant of any one of Embodiment 34to Embodiment 60, or the guide RNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 105. The kit of Embodiment 103 or Embodiment 104, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 106. A kit, comprising a guide NA variant of any one of Embodiment 34to Embodiment 60.
• Embodiment 107. The kit of 106, further comprising the CasX variant of any one of Embodiment I to Embodiment 33, or the CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 108. The kit of Embodiment 106 or Embodiment 107, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 109. A kit, comprising the gene editing pair of any one of Embodiment 61 to Embodiment 68.
• Embodiment 110. The kit of Embodiment 109, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 111. A CasX variant comprising any one of the sequences listed in Table 3.
• Embodiment 112. A guide RNA variant comprising any one of the sequences listed in Table 1 or Table 2.
• Embodiment 113. The CasX variant of any one of Embodiment 1 to Embodiment 33, wherein the reference CasX protein comprises a first domain from a first CasX protein and second domain from a second CasX protein.
• Embodiment 114. The CasX variant of Embodiment 113, wherein the first domain is selected from the group consisting of the NTSB, TSL helical I, helical II, OBD, and RuvC domains.
• Embodiment 115. The CasX variant of Embodiment 113, wherein the second domain is selected from the group consisting of the NTSB, TSL, helical I, helical II, OBD, and RuvC domains.
• Embodiment 116. The method of any one of Embodiment 113 to Embodiment 115, wherein the first and second domains are not the same domain.
• Embodiment 117. The CasX variant of any one of Embodiment 113 to Embodiment 116, wherein the first CasX protein comprises a sequence of SEQ ID NO: 1 and the second CasX protein comprises a sequence of SEQ ID NO: 2.
• Embodiment 118. The CasX variant of any one of Embodiment 113 to Embodiment 116, wherein the first CasX protein comprises a sequence of SEQ NO: 1 and the second. CasX protein comprises a sequence of SEQ ID NO: 3.
• Embodiment 119. The CasX variant of any one of Embodiment 113 to Embodiment 116, wherein the first CasX protein comprises a sequence of SEQ II) NO: 2 and the second CasX protein comprises a sequence of SEQ ID NO: 3.
• Embodiment 120. The CasX variant of any one of Embodiment 1 to Embodiment 33 or 113to Embodiment 119, wherein the CasX protein comprises at least one chimeric domain comprising a first part from a first CasX protein and a second part from a second CasX protein.
• Embodiment 121. The CasX variant of Embodiment 120, wherein the at least one chimeric domain is selected from the group consisting of the NTSB, TSL, helical I, helical II, OBD, and RuvC domains.
• Embodiment 122. The CasX variant of Embodiment 120 or Embodiment 121, wherein the first CasX protein comprises a sequence of SEQ 1D NO: 1 and the second CasX protein comprises a sequence of SEQ ID NO: 2.
• Embodiment 123. The CasX variant of Embodiment 120 or Embodiment 121. wherein the first CasX protein comprises a sequence of SEQ ID NO: 1 and the second CasX protein comprises a sequence of SEQ ID NO: 3.
• Embodiment 124, The CasX variant of Embodiment 120 or Embodiment 121, wherein the first CasX protein comprises a sequence of SEQ ID NO: 2 and the second CasX protein comprises a sequence of SEQ ID NO: 3.
• Embodiment 125. The CasX variant of Embodiment 120. wherein the at least one chimeric comprises a chimeric RuvC domain.
• Embodiment 126. The CasX variant of 125. wherein the chimeric RuvC domain comprises amino acids 661 to Embodiment 824 of SEQ ID NO: 1 and amino acids 922to Embodiment 978 of SEQ ID NO: 2.
• Embodiment 127. The CasX variant of 125, wherein the chimeric RuvC domain comprises amino acids 648 to 812 of SEQ ID NO: 2 and amino acids 935 to 986 of SEQ ID NO: 1.
• Embodiment 128. The guide NA variant of any one of 34 to Embodiment 60, wherein the reference guide NA comprises a first region from a first guide NA and a second region from a second guide NA.
• Embodiment 129, The guide NA variant of 128, wherein the first region is selected from the group consisting of a triplex region, a scaffold stem loop, and an extended stem loop.
• Embodiment 130. The guide NA variant of 128 or 129, wherein the second region is selected from the group consisting of a triplex region, a scaffold stem loop, and an extended stem loop.
• Embodiment 131. The guide NA variant of any one of Embodiments 128 to Embodiment 130, wherein the first and second regions are not the same region.
• Embodiment 132, The guide NA variant of any one of Embodiments 128 to Embodiment 131, wherein the first guide NA comprises a sequence of SEQ ID NO: 4 and the second guide NA comprises a sequence of SEQ ID NO: 5.
• Embodiment 133. The guide NA variant of any one of Embodiments 34-60 or Embodiments 128-132, comprising at least one chimeric region comprising a first part from a first guide NA and a second part from a second guide NA.
• Embodiment 134. The guide NA variant of Embodiment 133, wherein the at least one chimeric region is selected from the group consisting of a triplex region, a scaffold stem loop. and an extended stem loop.
• Embodiment 135. The guide NA variant of Embodiment 134. wherein the first guide NA comprises a sequence of SEQ ID NO: 4 and the second guide NA comprises a sequence of SEQ ID NO: 5.
Embodiment Set #2
• Embodiment 1. A variant of a reference CasX protein, wherein the CasX variant is capable of forming a complex with a guide nucleic acid (gNA), and wherein the complex can bind a target nucleic acid, and wherein the CasX variant comprises at least one modification in at least one domain of the reference CasX protein selected from:
• a. a non-target strand binding (NTSB) domain that binds to the non-target strand of DNA, wherein the NTSB domain comprises a four-stranded beta sheet;
• b. a target strand loading (TSL) domain that places the target DNA in a cleavage site of the CasX variant, the TSL domain comprising three positively charged amino acids, wherein the three positively charged amino acids bind to the target strand of DNA,
• c. a helical I domain that interacts with both the target DNA and a targeting sequence of a gNA, wherein the helical I domain comprises one or more alpha helices;
• d. a helical II domain that interacts with both the target DNA and a scaffold stem of the gNA;
• e. an oligonucleotide binding domain (OBD) that binds a triplex region of the gNA; or
• f. a RuvC DNA cleavage domain;
• wherein the CasX variant exhibits one or more improved characteristics as compared to the reference CasX protein.
• Embodiment 2. The CasX variant of Embodiment 1, wherein the CasX reference comprises the sequence of SEQ ID NO: 1, SEQ TD NO: 2, or SEQ ID NO: 3.
• Embodiment 3. The CasX variant of Embodiment 1 or Embodiment 2, wherein the at least one modification comprises at least one amino acid substitution in a domain of the CasX variant.
• Embodiment 4. The CasX variant of any one of the preceding Embodiments, wherein the at least one modification comprises the substitution of 1 to 10 consecutive or non-consecutive amino acid substitutions in the CasX variant.
• Embodiment 5. The CasX variant of any one of the preceding Embodiments, wherein at least one modification comprises at least one amino acid deletion in a domain of the CasX variant.
• Embodiment 6. The CasX variant of any one of the preceding Embodiments, wherein the at least one modification comprises the deletion of 1 to 10 consecutive or non-consecutive amino acids in the CasX variant.
• Embodiment 7. The CasX variant of any one of the preceding Embodiments, wherein the at least one modification comprises the substitution of 1 to 10 consecutive or non-consecutive amino acid substitutions and the deletion of 1 to 10 consecutive or non-consecutive amino acids in the CasX variant.
• Embodiment 8. The CasX variant of any one of the preceding Embodiments, wherein the at least one modification comprises at least one amino acid insertion in a domain of the CasX variant.
• Embodiment 9. The CasX variant of any one of the preceding Embodiments, wherein the at least one modification comprises the insertion of Ito 4 consecutive or non-consecutive amino acids in a domain of the CasX variant.
• Embodiment 10. The CasX variant of any one of the preceding Embodiments, wherein the CasX variant has a sequence selected from the group consisting of the sequences of Table 3, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99%, sequence identity thereto,
• Embodiment 11. The CasX variant of any one of the preceding Embodiments, wherein the CasX protein has binding affinity for a protospacer adjacent motif (PAM) sequence selected from the group consisting of ATC, GTC, and CTC.
• Embodiment 12. The CasX variant of any one of the preceding Embodiments, wherein the CasX protein further comprises one or more nuclear localization signals (NLS).
• Embodiment 13. The CasX variant of Embodiment 12, wherein the one or more NLS are selected from the group of sequences consisting of PKKKRKV (SEQ ID NO: 352), KRPAATKKAGQAKKKK (SEQ ID NO: 353), PAAKRVKLD (SEQ ID NO: 3541), RQRRNELKRSP (SEQ ID NO: 355), NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 356), RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 357), VSRKRPRP (SEQ ID NO: 358), PPKKARED (SEQ ID NO: 359), PQPKKKPL (SEQ ID NO: 360), SALIKKKKKMAP (SEQ ID NO: 361), DRLRR (SEQ ID NO: 362), PKQKKRK (SEQ ID NO: 363), RKLKKKIKKL (SEQ ID NO: 364), REKKKFLKRR (SEQ ID NO: 365), KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 366), RKCLQAGMNLEARKTKK (SEQ ID NO: 367), PRPRKIPR (SEQ ID NO: 368), PPRKKRTVV (SEQ ID NO: 369), NLSKKKKRKREK (SEQ ID NO: 370), RRPSRPFRKP (SEQ ID NO: 371). KRPRSPSS (SEQ ID NO: 372), KRGINDRNFWRGENERKTR (SEQ ID NO: 373), PRPPKMARYDN (SEQ ID NO: 374), KRSFSKAF (SEQ ID NO: 375), KLKIKRPVK (SEQ ID NO: 376), PKTRRRPRRSQRKRPPT (SEQ ID NO: 378), RRKKRRPRRKKRR (SEQ ID NO: 381), PKKKSRKPKKKSRK (SEQ ID NO: 382), HKKKHPDASVNFSEFSK (SEQ ID NO: 383), QRPGPYDRPQRPGPYDRP (SEQ ID NO: 384), LSPSLSPLLSPSLSPL (SEQ ID NO: 385), RGKGGKGLGKGGAKRIIRK (SEQ ID NO: 386). PKRGRGRPKRGRGR (SEQ ID NO: 387), and MSRRRKANPTKLSENAKKLAKEVEN (SEQ ID NO: 411).
• Embodiment 14. The CasX variant of Embodiment 12 or Embodiment 13, wherein the one or more NLS are expressed at the C-terminus of the CasX protein.
• Embodiment 15. The CasX variant of Embodiment 12 or Embodiment 13, wherein the one or more NLS are expressed at the N-terminus of the CasX protein.
• Embodiment 16. The CasX variant of Embodiment 12 or Embodiment 13. wherein the one or more NLS are expressed at the N-terminus and C-terminus of the CasX protein.
• Embodiment 17. The CasX variant of any one of the preceding Embodiments, wherein the improved characteristic is selected from the group consisting of improved folding of the variant, improved binding affinity to the gNA, improved binding affinity to the target DNA, altered binding affinity to one or more PAM sequences of the target DNA, improved unwinding of the target DNA, increased activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target DNA strand, improved protein stability, improved protein:gNA complex stability, improved protein solubility, improved protein:gNA complex solubility, improved protein yield, improved protein expression, and improved fusion characteristics.
• Embodiment 18. The CasX variant of any one of the preceding Embodiments, wherein at least one or more of the improved characteristics of the CasX variant is at least about 1.1 to about 100,000-fold improved relative to the reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 19. The CasX variant of any one of the preceding Embodiments, wherein one or more of the improved characteristics of the CasX variant is at least about 10 to about 100-fold improved relative to the reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 20. The CasX variant any one of the preceding Embodiments, wherein the CasX variant has about 1.1 to about 100-fold increased binding affinity to the gNA compared to the protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 21. The CasX variant any one of the preceding Embodiments, wherein the CasX variant has about 1.1 to about 10-fold increased binding affinity to the target DNA compared to the protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 22. The CasX variant of any one of the preceding Embodiments, wherein the CasX variant comprises between 400 and 3000 amino acids.
• Embodiment 23. The CasX variant of any one of the preceding Embodiments, comprising at least one modification in at least two domains of the CasX variant relative to the reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 24. The CasX variant of any one of the preceding Embodiments, comprising two or more modifications in at least one domain of the CasX variant relative to the reference CasX protein of SEQ ID NO: 1. SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 25. The CasX variant of any one of the preceding Embodiments, wherein at least one modification comprises deletion of at least a portion of one domain of the CasX variant relative to the reference CasX protein of SEQM NO: I, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 26. The CasX variant of any one of the preceding Embodiments, comprising at least one modification of a region of non-contiguous amino acid residues of the CasX variant that form a channel in which gNA:target DNA complexing with the CasX variant occurs.
• Embodiment 27. The CasX variant of any one of the preceding Embodiments, comprising at least one modification of a region of non-contiguous amino acid residues of the CasX variant that form an interface which binds with the gNA.
• Embodiment 28. The CasX variant of any one of the preceding Embodiments, comprising at least one modification of a region of non-contiguous amino acid residues of the CasX variant that form a channel which binds with the non-target strand DNA.
• Embodiment 29. The CasX variant of any one of the preceding Embodiments, comprising at least one modification of a region of non-contiguous amino acid residues of the CasX variant that form an interface which binds with the PAM.
• Embodiment 30. The CasX variant of any one of the preceding Embodiments, comprising at least one modification of a region of non-contiguous surface-exposed amino acid residues of the CasX variant.
• Embodiment 31. The CasX variant of any one of the preceding Embodiments, comprising at least one modification of a region of non-contiguous amino acid residues that form a core through hydrophobic packing in a domain of the CasX variant.
• Embodiment 32. The CasX variant of any one of Embodiments 25-30, wherein the modification is a deletion, an insertion, and/or a substitution of one or more amino acids of the region.
• Embodiment 33. The CasX variant of any one of Embodiments 25-32, wherein between 2 to 15 amino acid residues of the region of the CasX variant are substituted with charged amino acids.
• Embodiment 34. The CasX variant of any one of Embodiments 25-32, wherein between 2 to 15 amino acid residues of a region of the CasX variant are substituted with polar amino acids.
• Embodiment 35. The CasX variant of any one of Embodiments 25-32, wherein between 2 to 15 amino acid residues of a region of the CasX variant are substituted with amino acids that stack with DNA or RNA bases.
• Embodiment 36. The CasX variant of any one of the preceding Embodiments, wherein the CasX variant protein comprises a nuclease domain having nickase activity.
• Embodiment 37. The CasX variant of any one of Embodiments 1-35, wherein the CasX variant protein comprises a nuclease domain having double-stranded cleavage activity.
• Embodiment 38. The CasX variant of any one of Embodiments 1-35, wherein the CasX protein is a catalytically inactive CasX (dCasX) protein, and wherein the dCasX and the gNA retain the ability to bind to the target nucleic acid.
• Embodiment 39. The CasX variant of Embodiment 38, wherein the dCasX comprises a mutation at residues:
• a. D672, E769, and/or D935 corresponding to the CasX protein of SEQ ID NO:1; or
• b. D659, E756 and/or D922 corresponding to the CasX protein of SEQ ID NO: 2.
• Embodiment 40. The CasX variant of Embodiment 39, wherein the mutation is a substitution of alanine for the residue.
• Embodiment 41. A variant of a reference guide nucleic acid (gNA) capable of binding a CasX protein, wherein the reference guide nucleic acid comprises a tracrNA sequence and a crNA sequence, wherein:
• a. the tracrNA comprises a scaffold stem loop region comprising a bubble;
• b. the tracrNA and the crNA form a stem and a triplex region; and
• c. the tracrNA and the crNA are fused, and form a fusion stem loop region
• wherein the gNA variant comprises at least one modification compared to the reference guide nucleic acid sequence, and the variant exhibits one or more improved characteristics compared to the reference guide RNA.
• Embodiment 42. The gNA variant of Embodiment 41, comprising a tracrRNA stem loop comprising the sequence -UUU-N_3-20-UUU- (SEQ ID NO: 4403).
• Embodiment 43, The gNA variant of Embodiment 41 or 42, comprising a crRNA sequence with -AAAG- in a location 5′ to a targeting sequence of the gNA variant.
• Embodiment 44. The gNA variant of Embodiment 43, wherein the -AAAG- sequence is immediately 5′ to the targeting sequence.
• Embodiment 45. The gNA variant of any one of Embodiments 41-44, wherein the gNA variant further comprises a targeting sequence wherein the targeting sequence is complementary to the target DNA sequence.
• Embodiment 46. The gNA variant of any one of Embodiments 41-45, wherein the one or more improved characteristics is selected from the group consisting of improved stability, improved solubility, improved resistance to nuclease activity, increased folding rate of the NA, decreased side product formation during folding, increased productive folding, improved binding affinity to a CasX protein, improved binding affinity to a target DNA, improved gene editing, and improved specificity.
• Embodiment 47. The gNA variant of Embodiment 46, wherein the one or more of the improved characteristics of the CasX variant is at least about 1.1 to about 100,000-fold improved relative to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 48, The CasX variant of Embodiment 46 or 47, wherein one or more of the improved characteristics of the CasX variant is at least about 10 to about 100-fold improved relative to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 49. The gNA variant of any one of Embodiments 41-48, wherein the at least one modification comprises at least one nucleotide substitution in a region of the gNA valiant compared to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 50. The gNA variant of Embodiment 41-49, wherein the at least one modification comprises substitution of at least 1. to 4 nucleotides in a region of the gNA variant compared to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 51. The gNA variant of any one of Embodiments 41-50, wherein the at least one modification comprises at least one nucleotide deletion in a region of the gNA variant compared to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5,
• Embodiment 52. The gNA variant of Embodiments 41-51, wherein the at least one modification comprises deletion of 1 to 4 nucleotides in a region of the gNA variant compared to the reference gNA of SEQ ID NO: 4 or SEQ NO: 5.
• Embodiment 53, The gNA variant of any one of Embodiments 41-52, wherein the at least one modification comprises at least one nucleotide insertion in a region of the gNA variant compared to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 54. The gNA variant of any one of Embodiments 41-53, wherein the at least one modification comprises insertion of 1 to 4 nucleotides in a region of the gNA variant compared to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 55. The gNA variant of any one of Embodiments 41-54, wherein the at least one modification comprises a deletion of at least 1 to 4 nucleotides, an insertion of at least 1 to 4 nucleotides, a substitution of at least 1 to 4 nucleotides, or any combination thereof in a region of the gNA variant compared to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 56. The gNA variant of any one of Embodiments 41-5, comprising a scaffold region at least 60% homologous to SEQ ID NO: 4 or SEQ ID NO: 5.
• Embodiment 57. The gNA variant of any one of Embodiments 41-55, comprising a scaffold. NA stem loop at least 60% homologous to SEQ ID NO: 14.
• Embodiment 58. The gNA variant of any one of Embodiments 41-55, comprising an extended stem loop at least 60% homologous to SEQ I D NO: 14.
• Embodiment 59. The gNA variant of any one of Embodiments 41-55, wherein the gNA variant sequence is at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, or at least 70%, or at least 80% homologous to SEQ D NO: 4.
• Embodiment 60. The gNA variant of any one of Embodiments 41-58, wherein the gNA variant sequence is at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% homologous, or is 100% homologous to a sequence selected from the group of sequences of SEQ ID NOS: 2101-2241.
• Embodiment 61. The gNA variant of any one of Embodiments 41-60, comprising an extended stem loop region comprising fewer than 10,000 nucleotides.
• Embodiment 62. The gNA variant of any one of Embodiments 41-60, wherein the scaffold stem loop or the extended stem loop sequence is replaced with an exogenous stem loop sequence.
• Embodiment 63. The gNA variant of Embodiment t 62, wherein the exogenous stem loop is a hairpin loop that is capable of binding a protein, RNA or DNA molecule.
• Embodiment 64. The gNA variant of Embodiment 62 or 63, wherein the exogenous stem loop is a hairpin loop that increases the stability of the gNA.
• Embodiment 65. The gNA variant of Embodiment 63 or 64, wherein the hairpin loop is selected from MS2, Qβ, U1A, or PP7.
• Embodiment 66. The gNA variant of any one of Embodiments 41-65, further comprising one or more ribozymes.
• Embodiment 67. The gNA variant of Embodiment 66, wherein the one or more ribozymes are independently fused to a temnnus of the gNA variant.
• Embodiment 68. The gNA variant of Embodiment 66 or 67, wherein at least one of the one or more ribozymes are an hepatitis delta virus (HDV) ribozyme, hammerhead ribozyme, pistol ribozyme, hatchet ribozyme, or tobacco ringspot virus (TRSV) ribozyme.
• Embodiment 69. The gNA variant of any one of Embodiments 41-68, further comprising a protein binding motif.
• Embodiment 70. The gNA variant of any one of Embodiments 41-69, further comprising a thermostable stem loop.
• Embodiment 71. The gNA variant of Embodiment 41, comprising the sequence of any one of SEQ ID NO: 2101-2241.
• Embodiment 72. The gNA variant of any one of Embodiments 41-71, further comprising a targeting sequence.
• Embodiment 73. The gNA variant of Embodiment 72, wherein the targeting sequence has 14. 15, 16, 18, 18, 19, 20, 21, 22, 23 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 nucleotides.
• Embodiment 74. The gNA variant of any one of Embodiments 41-73, wherein the gNA is chemically modified.
• Embodiment 75. A gene editing pair comprising a CasX protein and a first gNA.
• Embodiment 76. The gene editing pair of Embodiment 74, wherein the first gNA comprises:
• a. a gNA variant of any one of Embodiments 41-74 and a targeting sequence; or
• b. a reference guide nucleic acid of SEQ ID NOS: 4 or 5 and a targeting sequence,
• wherein the targeting sequence is complementary to the target nucleic acid.
• Embodiment 77. The gene editing pair of Embodiment 74 or 76, wherein the CasX comprises:
• a. a CasX variant of any one of Embodiments 1-40; or
• b. a reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 78. The gene editing pair of any one of Embodiments 74-77, further comprising a second gNA or a nucleic acid encoding the second gNA, wherein the second gNA has a targeting sequence complementary to a different portion of the target nucleic acid compared to the targeting sequence of the first gNA.
• Embodiment 79. The gene editing pair of any one of Embodiments 74-78, wherein the CasX protein and the gNA are capable of associating together in a ribonuclear protein complex (RNP).
• Embodiment 80. The gene editing pair of any one of Embodiments 74-79, wherein the CasX protein and the gNA are associated together in a ribonuclear protein complex (RNP).
• Embodiment 81. The gene editing pair of Embodiment 79 or 80, wherein the RNP is capable of binding a target DNA.
• Embodiment 82. The gene editing pair of any one of Embodiments 79-81, wherein the RNP has a higher percentage of cleavage-competent RNP compared to an RNP of a reference CasX protein and a reference guide nucleic acid.
• Embodiment 83. The gene editing pair of any one of Embodiments 79-82, wherein the RNP is capable of binding and cleaving a target DNA.
• Embodiment 84. The gene editing pair of any one of Embodiments 79-82, wherein e RNP binds a target DNA but does not cleave the target DNA.
• Embodiment 85. The gene editing pair of any one of Embodiments 79-83, wherein the RNP is capable of binding a target DNA and generating one or more single-stranded nicks in the target DNA.
• Embodiment 86. The gene editing pair of any one of Embodiments 79-83 or 85, wherein the gene editing pair has one or more improved characteristics compared to a gene editing pair comprising a reference CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and a reference guide nucleic acid of SEQ ID NOS: 4 or 5,
• Embodiment 87. The gene editing pair of Embodiment 86, wherein the one or more improved characteristics comprises improved CasX:gNA RNP complex stability, improved binding affinity between the CasX and gNA, improved kinetics of RNP complex formation, higher percentage of cleavage-competent RNP, improved. RNP binding affinity to the target DNA, improved unwinding of the target DNA, increased editing activity, improved editing efficiency, improved editing specificity, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, decreased off-target cleavage, improved binding of the non-target strand of DNA, or improved resistance to nuclease activity.
• Embodiment 88. The gene editing pair of Embodiment 86 or 87, wherein the at least one or more of the improved characteristics is at least about 1.1 to about 100,000-fold improved relative to a gene editing pair of the reference CasX protein and the reference guide nucleic acid.
• Embodiment 89. The gene editing pair of any one of Embodiments 86-88, wherein one or more of the improved characteristics of the CasX variant is at least about 10 to about 100-fold improved relative to a gene editing pair of the reference CasX protein and the reference guide nucleic acid.
• Embodiment 90. A method of editing a target DNA. comprising contacting the target DNA with a gene editing pair of any one of Embodiments 74-89, wherein the contacting results in editing of the target DNA.
• Embodiment 91. The method of Embodiment 90, comprising contacting the target DNA with a plurality of gNAs comprising targeting sequences complementary to different regions of the target DNA.
• Embodiment 92. The method of Embodiment 90 or 91, wherein the contacting introduces one or more single-stranded breaks in the target DNA and wherein the editing comprises a mutation, an insertion, or a deletion in the target DNA.
• Enibodiinent 93. The method of Embodiment 90 or 91, wherein the contacting comprises introducing one or more double-stranded breaks in the target DNA and wherein the editing comprises a mutation, an insertion, or a deletion in the target DNA.
• Embodiment 94. The method of any one of Embodiments 90-93, further comprising contacting the target DNA with a nucleotide sequence of a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to the target DNA.
• Embodiment 95. The method of Embodiment 94, wherein the donor template is inserted in the target DNA at the break site by homology-directed repair.
• Embodiment 96. The method of any one of Embodiments 90-95, wherein editing occurs in vitro outside of a cell.
• Embodiment 97. The method of any one of Embodiments 90-95, wherein editing occurs in vitro inside of a cell.
• Embodiment 98. The method of any one of Embodiments 90-95, wherein editing occurs in vivo inside of a cell.
• Embodiinent 99. The method of Embodiments 97 or 98, wherein the cell is a eukaryotic cell.
• Embodiment 100. The method of Embodiment 99, wherein the eukaryotic cell is selected from the group consisting of a plant cell, a fungal cell, a protist cell, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.
• Embodiment 101. The method of Embodiment 99 or 100, wherein the method comprises contacting the eukaryotic cell with a vector encoding or comprising the CasX protein and the gNA, and optionally further comprising the donor template.
• Embodiment 102. The method of Embodiment 101, wherein the vector is an Adeno-Associated Viral (AAV) vector.
• Embodiment 103. The method of Embodiment 102, wherein the AAV is AAV AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AV8, AAV9, AAV10, AAV-Rh74, or AAVRh10.
• Embodiment 104. The method of Embodiment 101, wherein the vector is a lentiviral vector.
• Embodiment 105. The method of Embodiment 101, wherein the vector is a virus-like particle (VLP).
• Embodiment 106. The method of any one of Embodiments 101-105, wherein the vector is administered to a subject at a therapeutically effective dose.
• Embodiment 107. The method of Embodiment 105, wherein the subject is selected from the group consisting of mouse, rat, pig, non-human primate, and human.
• Embodiment 108. The method of Embodiment 107, wherein the subject is a human.
• Embodiment 109. The method of any one of Embodiments 106-108, wherein the vector is administered at a dose of at least about 1×10¹⁰ vector genomes (vg), or at least about 1×10¹¹ vg, or at least about 1×10¹² vg, or at least about 1×10¹³ vg, or at least about 1×10¹⁴ vg, or at least about 1×10¹⁵ vg, or at least about 1×10¹⁶ vg.
• Embodiment 110. The method of any one of Embodiments 106-109, wherein the vector is administered by a route of administration selected from the group consisting of intraparenchymal, intravenous, intra-arterial, intracerebroventricular, intracisternal, intrathecal, intracranial, and intraperitoneal routes.
• Embodiment 111. The method of Embodiment 97, wherein the cell is a prokaryotic cell.
• Embodiment 112. A cell comprising a CasX variant, wherein the CasX variant is a CasX variant of any one of Embodiments 1-40.
• Embodiment 113. The cell of Embodiment 112, further comprising
• a. a gNA variant of any one of Embodiments 41-74, or
• b. a reference guide nucleic acid of SEQ ID NOS: 4 or 5 and a targeting sequence.
• Embodiment 114. A cell comprising a gNA variant of any one of Embodiments 41-74.
• Embodiment 115. The cell of Embodiment 114, further comprising a CasX variant of any one of Embodiments I to Embodiment 35, or a CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO. 3.
• Embodiment 116. The cell of Embodiment 114 or 15, further comprising a donor nucleotide template comprising a sequence that hybridizes with a target DNA.
• Embodiment 117. The cell of Embodiment 116, wherein the donor template ranges in size from 10-10,000 nucleotides.
• Embodiment 118. The cell of Embodiment 116 or 117, wherein the donor template is a single-stranded DNA template or a single stranded RNA template.
• Embodiment 119. The method of Embodiment 116 or 117, wherein the donor template is a double-stranded DNA template.
• Embodiment 120. The cell of any one of Embodiments 112-119, wherein the cell is a. eukaryotic cell.
• Embodiment 121. The cell of any one of Embodiments 112-119, wherein the cell is a prokaryotic cell.
• Embodiment 122. A polynucleotide encoding the CasX variant of any one of Embodiments 1 to 40.
• Embodiment 123. A polynucleotide encoding the gNA variant of any one of Embodiments 41-74.
• Embodiment 124. A vector comprising the polynucleotide of Embodiment 122 and/or 123.
• Embodiment 125. The vector of Embodiment 123, wherein the vector is an Adeno-Associated Viral (AAV) vector.
• Embodiment 126, The method of Embodiment 125, wherein the AAV is AAV AAV2, AAV3, AAV4. AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV-Rh74, or AAVRh10.
• Embodiment 127. The vector of Embodiment 123, wherein the vector is a lentiviral vector.
• Embodiment 128. The vector of Embodiment 124, wherein the vector is a virus-like particle (VLP).
• Embodiment 129. A cell comprising the polynucleotide of Embodiment 122, or the vector of any one of Embodiments 124-128.
• Embodiment 130. A composition, comprising the CasX variant of any one of Embodiments 1 to 35.
• Embodiment 131. The composition of Embodiment 130, further comprising:
• a. a gNA variant of any one of Embodiments 45-74, or
• b. the reference guide RNA of SEQ ID NOS: 4 or 5 and a targeting sequence.
• Embodiment 132. The composition of Embodiment 130 or 131, wherein the CasX protein and the gNA are associated together in a ribonuclear protein complex (RNP).
• Embodiment 133. The composition of any one of Embodiments 130-132, further comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target DNA.
• Embodiment 134. The composition of any one of Embodiments 130-133, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 135. A composition, comprising a gNA variant of any one of Embodiments 41-74.
• Embodiment 136. The composition of Embodiment 135, further comprising the CasX variant of any one of Embodiments 1 to 35, or the CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 137. The composition of Embodiment 136, wherein the CasX protein and the gNA are associated together in a ribonuclear protein complex (RNP).
• Embodiment 138. The composition of any one of Embodiments 135-137, further comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target DNA.
• Embodiment 139. The composition of any one of Embodiments 135-138, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 140. A composition, comprising the gene editing pair of any one of Embodiments 4-89.
• Embodiment 141. The composition of Embodiment 140, further comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target DNA.
• Embodiment 142. The composition of Embodiment. 140 or 141, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 143. A kit, comprising the CasX variant of any one of Embodiments 1 to 35 and a container.
• Embodiment 144. The kit of Embodiment 143, further comprising:
• a. a gNA variant of any one of Embodiments 45-74, or
• b. the reference guide RNA of SEQ ID NOS: 4 or 5 and a targeting sequence.
• Embodiment 145. The kit of Embodiment 143 or 144, further comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target sequence of a target DNA.
• Embodiment 146. The kit of any one of Embodiments 143-145, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 147. A kit, comprising a gNA variant of any one of Embodiments 45-74.
• Embodiment 148. The kit of Embodiment 147, further comprising the CasX variant of any one of Embodiments 1 to 35, or the CasX protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
• Embodiment 149. The kit of Embodiment 147 or 148, further comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target sequence of a target DNA.
• Embodiment 150. The kit of any one of Embodiments 147-149, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 151. A kit, comprising the gene editing pair of any one of Embodiments 74-89.
• Embodiment 152. The kit of Embodiment 151, further comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target DNA.
• Embodiment 153. The kit of Embodiment 151 or 152, further comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing.
• Embodiment 154. A CasX variant comprising any one of the sequences listed in Table 3.
• Embodiment 155. A gNA variant comprising any one of the sequences listed in Table 2.
• Embodiment 156. The gNA variant of Embodiment 155, further comprising a targeting sequence of at least 10 to 30 nucleotides complementary to a target DNA.
• Embodiment 157. The gNA variant of Embodiment 156, wherein the targeting sequence has 20 nucleotides.
• Embodiment 158. The gNA variant of Embodiment 156, wherein the targeting sequence has 19 nucleotides.
• Embodiment 159. The gNA variant of Embodiment 156, wherein the targeting sequence has 18 nucleotides
• Embodiment 160. The gNA variant of Embodiment 156, wherein the targeting sequence has 17 nucleotides
• Embodiment 161. The CasX variant of any one of Embodiments 1 to 40, wherein the CasX protein comprises a first domain from a first CasX protein and second domain from a second CasX protein different from the first CasX protein.
• Embodiment 162. The CasX variant of Embodiment 161, wherein the first domain is selected from the group consisting of the NTSB, TSL, helical I, helical II, OBD, and RuvC domains.
• Embodiment 163. The CasX variant of Embodiment 162, wherein the second domain is selected from the group consisting of the NTSB, TSL, helical I, helical II, OBD, and RuvC domains.
• Embodiment 164. The CasX variant of any one of Embodiments 161 163, wherein the first and second domains are not the same domain.
• Embodiment 165. The CasX variant of any one of Embodiments 161-164 wherein the first CasX protein comprises a sequence of SEQ ID NO: 1 and the second CasX protein comprises a sequence of SEQ ID NO: 2.
• Embodiment 166. The CasX variant of any one of Embodiments 161-164 wherein the first CasX protein comprises a sequence of SEQ ID NO: 1 and the second CasX protein comprises a sequence of SEQ ID NO: 3.
• Embodiment 167. The CasX variant of any one of Embodiments 161-164, wherein the first CasX protein comprises a sequence of SEQ ID NO: 2 and the second CasX protein comprises a sequence of SEQ ID NO: 3.
• Embodiment 168. The CasX variant of any one of Embodiments 1 to 40 or 161-167, wherein the CasX protein comprises at least one chimeric domain comprising a first part from a first CasX protein and a second part from a second CasX protein different from the first CasX protein.
• Embodiment 169. The CasX variant of Embodiment 168, wherein the at least one chimeric domain is selected from the group consisting of the NTSB, TSL, helical I, helical II, OBD, and RuvC domains.
• Embodiment 170. The CasX variant of Embodiment 168 or 169, wherein the first CasX protein comprises a sequence of SEQ ID NO: 1 and the second CasX protein comprises a sequence of SEQ ID NO: 2.
• Embodiment 171. The CasX variant of Embodiment 168 or 169, wherein the first CasX protein comprises a sequence of SEQ ID NO: 1 and the second CasX protein comprises a sequence of SEQ ID NO: 3.
• Embodiment 172. The CasX variant of Embodiment 168 or 169, wherein the first CasX protein comprises a sequence of SEQ ID NO: 2 and the second CasX protein comprises a. sequence of SEQ ID NO: 3.
• Embodiment 173. The CasX variant of Embodiment 168, wherein the at least one chimeric domain comprises a chimeric RuvC domain.
• Embodiment 174. The CasX variant of Embodiment 173, wherein the chimeric RuvC domain comprises amino acids 661 to 824 of SEQ ID NO: I and amino acids 922 to 978 of SEQ ID NO: 2.
• Embodiment 175. The CasX variant of Embodiment 173, wherein the chimeric. RuvC domain comprises amino acids 648 to 812 of SEQ ID NO: 2 and amino acids 935 to 986 of SEQ ID NO: 1.
• Embodiment 176. The gNA variant of any one of Embodiments 41-74, wherein the gNA comprises a first region from a first gNA and a second region from a second gNA.
• Embodiment 177. The gNA variant of Embodiment 176, wherein the first region is selected from the group consisting of a triplex region, a scaffold stem loop, and an extended stem loop.
• Embodiment 178. The gNA variant of Embodiment 176 or 177. wherein the second region is selected from the group consisting of a triplex region, a scaffold stem loop, and an extended stem loop.
• Embodiment 179. The gNA variant of any one of Embodiments 176-178, wherein the first and second regions are not the same region.
• Embodiment 180. The gNA variant of any one of Embodiments 176-179, wherein the first gNA comprises a sequence of SEQ ID NO: 4 and the second gNA comprises a sequence of SEQ ID NO: 5.
• Embodiment 181. The gNA variant of any one of Embodiments 41-74 or 176-180, comprising at least one chimeric region comprising a first part from a first gNA and a second part from a second gNA.
• Embodiment 182. The gNA variant of Embodiment 181, wherein the at least one chimeric region is selected from the group consisting of a triplex region, a scaffold stem loop, and an extended stem loop.
• Embodiment 183. The gNA variant of Embodiment 182, wherein the first gNA comprises a sequence of SEQ ID NO: 4 and the second gNA comprises a sequence of SEQ ID NO: 5.
• The following Examples are merely illustrative and are not meant to limit any aspects of the present disclosure in any way.
EXAMPLES Example 1 Assays Used to Measure sgRNA and CasX Protein Activity
• Several assays were used to carry out initial screens of CasX protein and sgRNA DME libraries and engineered mutants, and to measure the activity of select protein and sgRNA variants relative to CasX reference sgRNAs and proteins, E. coli CRISPRi screen:
• Briefly, biological triplicates of dead CasX DME Libraries on a chloramphenieol (CM) resistant plasmid with a GFP guide RNA on a carbenicillin (Garb) resistant plasmid were transformed (at >5× library size) into MG1655 with genetically integrated and constitutively expressed GFP and RFP (see FIG. 13A-13B). Cells were grown overnight in EZ-RDM+Carb, CM and Anhvdrotetracycline (aTc) inducer. E. coli were FACS sorted based on gates for the top 1% of GFP but not RFP repression, collected, and resorted immediately to further enrich for highly functional CasX molecules. Double sorted libraries were then grown out and DNA was collected for deep sequencing on a highseq. This DNA was also re-transformed onto plates and individual clones were picked for further analysis.
• E.coli Toxin Selection:
• Briefly carbenicillin resistant plasmid containing an arabinose inducible toxin were transformed into E.coli cells and made electrocompetent. Biological triplicates of CasX DME Libraries with a toxin targeted guide RNA on a chloramphenicol resistant plasmid were transformed (at >5× library size) into said cells and grown in LB+CM and arabinose inducer. E. coli that cleaved the toxin plasmid survived in the induction media and were grown to mid log and plasmids with functional CasX cleavers were recovered. This selection was repeated as needed. Selected libraries were then grown out and DNA was collected for deep sequencing on a highseq. This DNA was also re-transformed onto plates and individual clones were picked for further analysis and testing.
Lentiviral Based Screen EGFP Screen:
• Lentiviral particles were produced in HEK293 cells at a confluency of 70%-90% at time of transfection. Cells were transfected using polyethylenimine based transfection of plasmids containing a CasX DME library. Lentiviral vectors were co-transfected with the lentiviral packaging plasmid and the VSV-G envelope plasmids for particle production, Media was changed 12 hours post-transfection, and virus harvested at 36-48 hours post-transfection. Viral supernatants were filtered using 0.45 mm membrane filters, diluted in cell culture media if appropriate, and added to target cells HEK cells with an Integrated GFP reporter. Polybrene was supplemented to enhance transduction efficiency, if necessary. Transduced cells were selected for 24-48 hours post-transduction using puromycin and grown for 7-10 days. Cells were then sorted for GFP disruption & collected for highly functional sgRNA or protein variants (see FIG. 2). Libraries were then Amplified via PCR directly from the genome and collected for deep sequencing on a highseq. This DNA could also be re-cloned and re-transformed onto plates and individual clones were picked for further analysis.
Assaying Editing Efficiency of an HEK EGFP Reporter:
• To assay the editing efficiency of CasX reference sgRNAs and proteins and variants thereof, EGFP HEK293T reporter cells were seeded into 96-well plates and transfected according to the manufacturer's protocol with lipofectamine 3000 (Life Technologies) and 100-200 ng plasmid DNA encoding a reference or variant CasX protein, P2A-puromycin fusion and the reference or variant sgRNA. The next day cells were selected with 1.5 μg/ml puromycin for 2 days and analyzed by fluorescence-activated cell sorting (FACS) 7 days after selection to allow for clearance of EGFP protein from the cells. EGFP disruption via editing was traced using an Attune N×T Flow Cytometer and high-throughput autosampler.
Example 2 Cleavage Efficiency of CasX Reference sgRNA
• The reference CasX sgRNA of SEQ ID NO: 4 (below) is described in WO 2018/064371, the contents of which are incorporated herein by reference.
• 1 ACAUCUGGCG CGUUUAUUCC AUUACUUUGG AGCCAGUCCC AGCGACUAUG UCGUAUGGAC
• 61 GAAGCGCUUA UUUAUCGGAG AGAAACCGAU AAGUAAAACG CAUCAAAG (SEQ ID NO: 4).
• It was found that alterations to the sgRNA reference sequence of SEQ ID NO: 4, producing SEQ ID NO: 5 (below) were able to improve CasX cleavage efficiency.
• 1 UACUGGCGCU UUUAUCUCAU UACUUUGAGA GCCAUCACCA GCGACUAUGU CGUAUGGGUA
• 61 AAGCGCUUAU UUAUCGGAGA GAAAUCCGAU AAAUAAGAAG CAUCAAAG (SEQ ID NO: 5).
• To assay the editing efficiency of CasX reference sgRNAs and variants thereof, EGFP HEK293T reporter cells were seeded into 96-well plates and transfected according to the manufacturer's protocol with lipofectamine 3000 (Life Technologies) and 100-200 ng plasmid DNA encoding a reference CasX protein, P2A-puromycin fusion and the sgRNA. The next day cells were selected with 1.5 μg/ml puromycin for 2 days and analyzed by fluorescence-activated cell sorting (FACS) 7 days after selection to allow for clearance of EGFP protein from the cells, EGFP disruption via editing was traced using an Attune N×T Flow Cytometer and high-throughput autosampler.
• When testing cleavage of an EGFP reporter by CasX reference and sgRNA variants, the following DNA encoding spacer target sequences were used:

• 	E6
  	(TGTGGTCGGGGTAGCGGCTG; SEQ ID NO: 29)
  	and
  	E7
  	(TCAAGTCCGCCATGCCCGAA; SEQ ID NO: 30).

• An example of the increased cleavage efficiency of the sgRNA of SEQ ID NO: 5 compared to the sgRNA of SEQ ID NO: 4 is shown in FIG. 5A. Editing efficiency of SEQ ID NO: 5 was improved 176% compared to SEQ ID NO: 4. Accordingly, SEQ ID NO: 5 was chosen as reference sgRNA for DME and additional sgRNA variant design, described below.
Example 3 Mutagenesis of CasX Reference gRNA Produces Variants with Improved Target Cleavage
• DME of the sgRNA was achieved using two distinct PCR methods. The first method, which generates single nucleotide substitutions, makes use of degenerate oligonucleotides. These are synthesized with a custom nucleotide mix, such that each locus of the primer that is complementary to the sgRNA locus has a 97% chance of being the wild type base, and a 1% chance of being each of the other three nucleotides. During PCR, the degenerate oligos anneal to, and just beyond, the sgRNA scaffold within a small plasmid, amplifying the entire plasmid. The PCR product was purified, ligated, and transformed into E. coli. The second method was used to generate sgRNA scaffolds with single or double nucleotide insertions and deletions. A unique PCR reaction was set up for each base pair intended for mutation: In the case of the CasX scaffold of SEQ ID NO: 5, 109 PCRs were used, These PCR primers were designed and paired such that PCR products either were missing a base pair, or contained an additional inserted base pair. For inserted base pairs. PCR primers inserted a degenerate base such that all four possible nucleotides were represented in the final library.
• Once constructed, both the protein and sgRNA DME libraries were assayed in a screen or selection as described in Example 1 to quantitatively identify mutations conferring enhanced functionality. Any assay, such as cell survival or fluorescence intensity, is sufficient so long as the assay maintains a link between genotype and phenotype. High throughput sequencing of these populations and validating individual variant phenotypes provided information about mutations that affect functionality as assayed by screening or selection. Statistical analysis of deep sequencing data provided detailed insight into the mutation landscape and mechanism of protein function or guide RNA function (see FIG. 3A-3B, FIG. 4A, FIG. 4B, FIG. 4C).
• DME libraries sgRNA RNA variants were made using a reference gRNA of SEQ NO: 5, underwent selection or enrichment, and were sequenced to determine the fold enrichment of the sgRNA variants in the library, The libraries included every possible single mutation. of every nucleotide, and double indels (insertion/deletions). The results are shown in FIGS. 3A-3B, FIG. 4A-4C, and Table 4 below.
• To create a library of base pair substitutions using DME, two degenerate oligonucleotides that each bind to half of the sgRNA scaffold and together amplify the entire plasmid comprising the starting sgRNA scaffold were designed. These oligos were made from a custom nucleotide mix with a 3% mutation rate. These degenerate oligos were then used to PCR amplify the starting scaffold plasmid using standard manufacturing protocols. This PCR product was gel purified, again following standard protocols. The gel purified PCR product was then blunt end ligated and electroporated into an appropriate E. coli cloning strain. Transformants were grown overnight on standard media, and plasmid. DNA was purified via miniprep.
• To generate a library of small insertions and deletions, PCR primers were designed such that the PCR products resulting from amplification of the plasmid comprising the base sgRNA scaffold would either be missing a base pair, or contain an additional inserted base pair. For inserted base pairs, PCR primers were designed in which a degenerate base has been inserted, such that all four possible nucleotides were represented in the final library of pooled PCR products. The starting sgRNA scaffold was then PCR amplified with each set of oligos as their own reaction. Each PCR reaction contained five possible primers, although all primers annealed to the same sequence. For example, Primer 1 omitted a base, in order to create a deletion. Primers 2, 3, 4, and 5 inserted either an A, T, G, or C. However, these five primers all annealed to the same region and hence could be pooled in a single PCR. However, PCRs for different positions along the sgRNA needed to be kept in separate tubes, and 109 distinct PCR reactions were used to generate the sgRNA DME library.
• The resulting 109 PCR products were then run on an agarose gel and excised before being combined and purified. The pooled PCR products were blunt ligated and electroporated into E. coli. Transformants were grown overnight on standard media with an appropriate selectable marker, and plasmid DNA was purified via miniprep. Having created a library of all single small indels, the steps of PCR amplifying the starting plasmid with each set of oligos, purifying, blunt end ligating, transforming into E. coli and mini-prepping can be repeated to obtain a library containing most double small indels. Combining the single indel library and double indel library at a ratio of 1:1000 resulted in a library that represented both single and double indels.
• The resulting libraries were then combined and passed through the DME screening and/or selection process to identify variants with enhanced cleavage activity. DME libraries were screened using toxin cleavage and CRISPRi repression in E. coli, as well as EGFP cutting in lentiviral-transfected HEK293 cells, as described in Example 1. The fold enrichment of scaffold variants in DME libraries that have undergoing screening/selection followed by sequencing is shown below in Table 4. The read counts associated with each of the below sequences in Table 4 were determined (‘annotations’, ‘seq’). Only sequences with at least 10 reads across any sample were analyzed to filter from 15 Million to 600 K sequences. The below ‘seq’ gives the sequence of the entire insert between the two 5′ random 5mer and the 3′ random 5mer. ‘seq_short’ gives the anticipated sequence of the scaffold only. The mutations associated with each sequence were determined through alignment (‘muts’). All modifications are indicated by their [position (0-indexed)].[reference base].[alternate base]. Position 0 indicates the first T of the transcribed gRNA. Sequences with multiple mutations are semicolon separated. The column muts_lindexed, gives the same information but 1-indexed instead of 0-indexed. Each of the modifications are annotated (‘annotated_variants’), as being a single substitution insertion/deletion, double substitution/insertion/deletion, single_del_single_sub (a deletion and an adjacent substitution), a single_sub_single_ins (a substitution and adjacent insertion), ‘outside_ref’ (indicates that the modification is outside the transcribed gRNA), or ‘other’ (any larger substitution/insertion/deletion or some combination thereof). An insertion at position i indicates an inserted base between position i−1 and i (i.e. before the indicated position). To note about variant annotation: a deletion of any one of a consecutive set of bases can he attributed to any of those bases. Thus, a deletion of the T at position −1 is the same sequence as a deletion of the T at position 0. ‘counts’ indicates the sequencing-depth normalized read count per sequence per sample. Technical replicates were combined by taking the geometric mean. log2enrichment gives the median enrichment (using a pseudocount of 10) across each context, or across all samples, after merging for technical replicates. The naive read count was averaged (geometric) between the D2_N and D3_N samples. Finally, the ‘log2enrichment err’ gives the ‘confidence interval’ on the mean log2 enrichment. It is the standard deviation of the enrichment across samples*2/sqrt of the number of samples. Below, only the sequences with median log2enrichment−log2enrichment_err>0 are shown (2704/614564 sequences examined).
• In Table 4. CI indicates confidence interval and MI indicates median enrichment, which indicates enhanced activity.

• TABLE 4
  Median Enrichment of DME Scaffold Variants

  	SEQ ID			95%
  index	NO	muts_lindexed	MI	CI

  7240543	412	27.-.C;76.G-	3.390	2.040
  7240150	413	27.-.C;75.-.C	3.111	1.862
  2584994	414	0.T.-;2.A.C:27.-.C	2.997	1.806
  2618163	415	0.T.-;2.A.C;55.-.G	2.915	0.725
  2655870	416	2.A.C;0.T.-;76.GG-A	2.903	0.391
  2762330	417	2.A.C;0.T.-;55.-.T	2.857	1.290
  7247368	418	27.-.C;86.C.-	2.815	1.637
  2731505	419	2.A.C;0.T.-;75.-.G	2.795	0.625
  2729600	420	2.A.C;0.T.-;76.-.T	2.791	0.628
  2701142	421	2.A.C;0.T.-;87.-.T	2.768	0.559
  2659588	422	2.A.C;0.T.-;75.-.C	2.733	0.477
  2582823	421	0.T.-;2.A.C;27.-.A	2.729	1.669
  3000598	424	1.TA.--;76.G.-	2.704	0.439
  10565036	425	15.-.T;74.-.T	2.681	0.808
  9696472	426	28.-.T;76.GG.-T	2.681	1.715
  2674674	427	2.A.C;0.T.-.86.-.C	2.650	0.772
  7254130	428	27.-.C;75.CG.-T	2.629	1.755
  2977442	429	1.TA.--;55.-.G	2.629	0.887
  2661951	410	2 A.C:0.T-;76.G.-	2.627	0.432
  1937646	431	2.A.C;0.TT.--;75.-.C	2.626	1.328
  2232796	432	0.T.-;55.-.G	2.607	0.777
  2714418	413	0.T.-;2.A.C.81.GA.-T	2.595	0.443
  2700142	434	2.A.C;0.T.-;87.-.G	2.582	0.608
  2667512	435	2.A.C;0.T -;77.GA.--	2.577	0.588
  7239606	436	27.-.C;76.-.A	2.566	1.441
  10563356	437	15.-.T;75.-.G	2.557	1.056
  7181049	438	27.-.A;75.-.C	2.543	1.893
  2720034	439	2.A.C;0.T.-.78.-.C	2.531	0.492
  2265581	440	0.T.-;86.-.C	2.520	0.504
  2256355	441	0.T.-;76.GG.-C	2.516	0.942
  7251229	442	27.-.C;76.-.G	2.516	1.793
  10281529	443	17.-.T;76.GG.-A	2.515	1.104
  2299702	444	0.T.-;74.-.T	2.504	0.392
  2670445	445	2.A.C;0.T.-:85.T.-	2.499	1.225
  2258816	446	0.T.-.76.G.-	2.494	0.475
  7241311	447	27.-.C;77.GA.--	2.493	1.595
  2658150	448	2.A.C;0.T.-;76.GG.-C	2.492	0.585
  2734378	449	2.A.C;0.T.-;74.-.T	2.490	0.485
  2723181	450	2.A.C;0.T.-;76.-.G	2.488	0.421
  2288202	451	0.T.-;81.GA.-T	2.487	0.591
  2278172	452	0.T.-;89.-.C	2.486	0.690
  2997382	453	1.TA.--;76.GG.-A	2.465	1.066
  2255017	454	0.T.-;76.GG.-A	2.463	0.422
  2257399	455	0.T.-;75.-.C	2.460	0.676
  12183183	456	2.A.-;81.GA.-T	2.459	0.736
  7252067	457	27.-.C;76.GG.-T	2.459	2.062
  10525083	458	15.-.T;75.-.C	2.448	1.006
  7253869	459	27.-.C;74.-.T	2.439	1.638
  4303777	460	4.T.-;76.-.T	2.435	0.782
  2741395	461	2.A.C;0.T.-;73.A.-	2.435	0.633
  7250940	462	27.-.C;78.A.-	2.423	2.064
  4302595	463	4.T.-;76.GG.-T	2.422	0.850
  4275786	464	4.T.-;87.-.T	2.420	1.019
  2650980	465	2.A.C;0.T.-;74.-.C	2.414	0.462
  2458336	466	1.TA.-;3.C.A;76.G.-	2.411	1.089
  10284144	467	17.-.T;76.G.-	2.406	1.638
  2726809	468	2.A.C;0.T.-;76.G.-;78.A.T	2.400	0.556
  2280896	469	0.T.-.87.-.T	2.398	0.560
  2673790	470	2.A.C;0.T.-;88.G.-	2.398	1.017
  3188700	471	0.T.-;2.A.G;27.-.C	2.394	1.732
  9632434	472	16.------------	2.394	1.141
  		.CTCATTACTTTG;75.-.G
  3029757	473	1.TA.--;78.A.-	2.392	0.524
  2728393	474	2.A.C;0.T.-76.GG.-T	2.390	0.714
  2300381	475	0.T.-;75.CG.-T	2.385	0.948
  2279969	476	0.T.-;86.C.-	2.382	0.404
  2260011	477	0.T.-;77.-.C	2.379	0.608
  2248579	478	0.T.-;72.-.C	2.377	0.743
  12075394	479	2.A.-;55.-.G	2.377	0.679
  9602743	480	28.-.C;76.GG.-C	2.376	1.681
  2736722	481	2.A.C;0.T.-.73.AT.-C	2.374	1.104
  12117240	482	2.A.-;76.GG.-A	2.372	0.429
  10307397	483	17.-.T;78.-.C	2.365	0.868
  3034775	484	1.TA.--;75.-.G	2.360	0.992
  12030812	485	2.A.-;27.-.A	2.355	1.651
  10530683	486	15.-.T;86.-.A	2.355	0.999
  12202799	487	2.A.-;75.-.G	2.352	0.508
  9687168	488	28.-.T;76.GG.-A	2.351	1.612
  4309853	489	4.T.-;75.CG.-T	2.344	0.845
  4234320	490	4.T.-;75.-.C	2.344	0.820
  2698521	491	2.A.C;0.T.-;88.-.T	2.339	0.685
  2253698	492	0.T.-;75.-.A	2.334	0.918
  2468003	493	1.TA.--;3.C.A;75.-.G	2.330	0.934
  12290253	494	2.A.-;28.-.C	2.326	1.588
  2999382	495	1.TA.--;75.-.C	2.315	0.592
  3227871	496	2.A.G;0.T.-;55.-.G	2.314	0.774
  10521017	497	15.-.T;74.-.C	2.314	0.910
  10089663	498	19.-.T;75.-.G	2.308	1.078
  4274894	499	4.T.-;87.-.G	2.308	0.512
  2466567	500	1.TA.-;3.C.A;78.A.-	2.308	1.291
  2696261	501	2.A.C;0.T.-;89.-.C	2.293	0.681
  2675948	502	2.A.C;0.T.-;89.-.A	2.289	1.259
  10521784	503	15.-.T;74.-.G	2.283	0.905
  12123787	504	2.A.-;76.G.-	2.278	0.492
  10310335	505	17.-.T;76.GG.-T	2.275	0.804
  2295876	506	0.T.-;77.-.T	2.273	0.931
  2697871	507	0.T.-;2.A.C;89.-.T	2.250	0.626
  2735417	508	2.A.C;0.T.-;75.CG.-T	2.249	0.390
  2671836	509	0.T.-;2.A.C;86.-.A	2.245	0.542
  12033345	510	2.A.-;27.-.C	2.235	1.903
  2821484	511	0.T.-;2.A.C;17.-.T	2.235	0.750
  3033813	512	1.TA.--;76.-.T	2.229	0.548
  2291551	513	0.T.-;78.-.C	2.226	0.532
  2716457	514	2.A.C;0.T.-;80.A.-	2.213	0.548
  2697599	515	2.A.C;0.T.-;89.A.-	2.209	1.346
  12125440	516	2.A.-;87.-.A	2.208	1.053
  4273350	517	4.T.-.88.-.T	2.208	1.013
  2298121	518	0.T.-;75.-.G	2.208	0.241
  2652510	519	0.T.-;2.A.C;74.-.G	2.206	0.613
  3006640	520	1.TA.--;86.-.C	2.206	0.584
  10313388	521	17.-.T;74.-.T	2.206	1.036
  10081410	522	19.-.T;87.-.G	2.206	0.589
  3033236	523	1.TA.--;76.GG.-T	2.198	0.669
  7242523	524	27.-.C;86.-.C	2.198	1.973
  7254383	525	27.-.C;73.AT.-C	2.198	1.510
  2264531	526	0.T.-;87.-.A	2.198	0.778
  2727301	527	0.T.-;2.A.C;77.-.T	2.197	1.323
  3019306	528	1.TA.--;87.-.G	2.191	0.534
  4295725	529	4.T.-;78.A.-	2.187	0.609
  10311816	530	17.-.T;75.-.G	2.187	1.507
  12167745	531	2.A.-;87.-.G	2.184	0.736
  12199256	532	2.A.-;76.GG.-T	2.179	0.737
  6477911	533	16.-.C;75.-.G	2.178	0.983
  4274124	534	4.T.-;86.C.-	2.171	0.474
  12206105	535	2.A.-;74.-.T	2.170	0.608
  12166825	536	2.A.-;86.C.-	2.168	0.774
  11956698	537	2.AC.--;4.T.C;86.-.C	2.164	1.360
  2280390	538	0.T.-;87.-.G	2.162	0.479
  2650159	539	2.A.C;0.T.-;74.T.-	2.161	0.517
  10531253	540	15.-.T;87.-.A	2.159	1.130
  2665054	541	2.A.C;0.T.-;79.G.-	2.158	0.562
  8531520	542	75.-.G;86.-.C	2.155	0.582
  2296436	543	0.T.-;76.GG.-T	2.154	0.679
  4249048	544	4.T.-;86.-.C	2.142	0.675
  10547068	545	15.-.T;87.-.G	2.140	0.857
  12168820	546	2.A.-;87.-.T	2.140	0.458
  2466824	547	1.TA.--;3.C.A;76.-.G	2.137	0.989
  3036963	548	1.TA.--;75.CG.-T	2.137	0.479
  10522450	549	15.-.T;75.-.A	2.135	1.003
  10300736	550	17.-.T;87.-.T	2.134	1.348
  3002220	551	1.TA.--;79.G.-	2.131	0.607
  3030471	552	1.TA.--;76.-.G	2.130	0.372
  10523429	553	15.-.T;76.GG.-A	2.130	0.787
  1909254	554	0.TTA.---;3.C.A;75.-.G	2.130	1.147
  3004722	555	1.TA.--;85.T.-	2.124	1.092
  2672731	556	2.A.C;0.T.-;87.-.A	2.121	0.898
  12129733	557	2.A.-;77.GA.--	2.120	0.500
  4250089	558	4.T.-;89.-.A	2.117	0.998
  2688981	559	2.A.C;0.T.-;99.-.G	2.112	0.980
  2995452	560	1.TA.--;74.-.G	2.112	0.611
  12114782	561	2.A.-;75.-.A	2.110	0.500
  2993173	562	1.TA.--;73.-.A	2.104	0.697
  1978344	563	0.T.C;87.-.G	2.100	0.870
  4294004	564	4.T.-;78.-.C	2.099	0.595
  10568306	565	15.-.T;73.A.-	2.096	0.741
  10561545	566	15.-.T;76.GG.-T	2.095	0.554
  2713433	567	2.A.C;0.T.-;82.AA.-T	2.094	0.560
  1863579	568	0.TT. ;75.-.G	2.086	0.787
  3006303	569	1.TA.--;88.G.-	2.086	0.537
  4236935	570	4.T.-;76.G.-	2.081	0.919
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  		.;2.A.C;79.GAGAAA.TTTCT
  		C
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  8470255	1696	78.-.C;132.G.C	0.991	0.219
  2661937	1697	132.G.C;2.A.C;0.T.-;76.G.-	0.990	0.390
  2670761	1698	0.T.-;2.A.C;85.TCC.---	0.990	0.720
  11776916	1699	2.-.C;87.-.A	0.989	0.938
  12747759	1700	0.-.T;77.-.T	0.989	0.938
  15165085	1701	-29.A.G;86.C.-	0.987	0.176
  8212745	1702	86.-.C;129.C.A	0.987	0.509
  2989789	1703	1.TA.--;72.-.A	0.986	0.659
  6531564	1704	17.-.G;87.-.T	0.985	0.962
  12436169	1705	1.TAC.---;87.-.G	0.984	0.678
  3311127	1706	2.A.G;0.T.-;82.A.-	0.984	0.759
  2264270	1707	0.T.-;86.CC.-A	0.983	0.775
  10091719	1708	19.-.T;73.AT.-G	0.982	0.402
  8143233	1709	76.G.-;123.A.C	0.982	0.226
  1248077	1710	-15.T.G;86.-.C	0.981	0.619
  12716866	1711	0.-.T;74.T.-	0.981	0.501
  3303133	1712	2.A.G;0.T.-;89.-.C	0.980	0.929
  9974910	1713	19.-.G;76.GG.-C	0.980	0.702
  8143415	1714	76.G.-;122.A.C	0.980	0.247
  1981670	1715	0.T.C;74.-.T	0.980	0.590
  2302384	1716	0.T.-;73.AT.-G	0.978	0.565
  1809039	1717	-3.TACT.----;78.A.-	0.978	0.801
  13139359	1718	-1.G.-;2.A.C	0.978	0.275
  8538659	1719	75.-G;122.A.C	0.978	0.392
  2651461	1720	0.T.-;2.A.C;74.T.G	0.977	0.582
  3028256	1721	1.TA.--;79.GA.-T	0.977	0.767
  444970	1722	-27.C.A;87.-.G	0.976	0.225
  2271218	1723	132.G.T;0.T.-	0.976	0.376
  13101059	1724	-1.GT.--;76.-.G	0.976	0.320
  15169928	1725	-29.A.G;75.CG.-T	0.976	0.276
  6454149	1726	16.-.C;72.-.C	0.976	0.472
  8519506	1727	76.GG.-T;133.A.C	0.976	0.183
  1936400	1728	0.TT.--;2.A.C;74.T.-	0.975	0.971
  8363289	1729	87.-.T;132.G.T	0.975	0.349
  14646928	1730	-29.A.C;0.T.-;2.A.C;76.-.G	0.975	0.273
  8212907	1731	86.-.C;131.A.C	0.975	0.470
  13097486	1732	-1.GT.--;75.-.C	0.974	0.347
  3272148	1733	2.A.G;0.T.-;77.-.A	0.974	0.592
  8557995	1734	74.-.T;121.C.A	0.973	0.210
  8142576	1735	76.G.-;127.T.G	0.973	0.375
  14816291	1736	-29.A.C.;73.A.-	0.972	0.232
  10080185	1737	19.-.T;89.-.C	0.971	0.565
  1904247	1738	0.TTA.---;3.C.A;75.-.A	0.970	0.749
  6460821	1739	16.-.C;77.GA.--	0.970	0.637
  12738126	1740	0.-.T;87.-.T	0.968	0.578
  8357730	1741	87.-.G;129.C.A	0.968	0.270
  12187919	1742	2.A.-;79.GA.-T	0.968	0.963
  14644862	1743	-29.A.C;0.T.-;2.A.C;76.GG.-C	0.967	0.512
  13101334	1744	-1.GT.--;76.GG.-T	0.967	0.377
  12437308	1745	1.TAC.---;80.A.-	0.966	0.933
  2672055	1746	0.T.-;2.A.C;86.CA	0.966	0.590
  6304109	1747	16.-.A;76.GG.-C	0.966	0.672
  12214091	1748	2.A.-;73.A.T	0.966	0.602
  8511126	1749	76.G.-;78.AG.TC	0.965	0.454
  10473646	1750	16.C.-;76.GG.-T	0.965	0.499
  8561622	1751	74.-.T;82.A.-	0.965	0.362
  1981516	1752	0.T.C;75.C.-	0.964	0.525
  4300894	1753	4.T.-;77.G.T	0.964	0.236
  8084158	1754	74.-.G	0.964	0.402
  8096194	1755	75.-.A;87.-.T	0.964	0.605
  2281085	1756	0.T.-;87.C.T	0.961	0.675
  8063355	1757	74.T.-;86.-.C	0.960	0.507
  3038327	1758	1.TA.--;73.-.G	0.959	0.854
  9976817	1759	19.-.G;79.G.-	0.958	0.737
  13223005	1760	2.A.G;-3.TAGT.----	0.958	0.837
  8542589	1761	75.-.G;98.-.T	0.957	0.875
  3345006	1762	0.T.-;2.A.G;73.A.T	0.957	0.793
  4217628	1763	4.T.-;71.-.C	0.956	0.495
  10068711	1764	19.-.T;76.-.A	0.956	0.689
  10198139	1765	18.-.G;77.-.T	0.956	0.663
  2463484	1766	1.TA.--;3.C.A;87.-.T	0.955	0.695
  8490228	1767	76.-.G;128.T.G	0.955	0.305
  3322121	1768	0.T.-;2.A.G;80.AG.-T	0.955	0.812
  2458850	1769	1.TA.--;3.C. A;79.G.-	0.955	0.858
  6626017	1770	18.C.-;78.A.-	0.954	0.611
  8519520	1771	76.GG.-T;132.G.T	0.954	0.281
  1974653	1772	0.T.C;75.-.A	0.954	0.490
  2683428	1773	120.C.A;2.A.C;0.T.-	0.954	0.253
  4272200	1774	4.T.-;89.A.G	0.954	0.925
  8193481	1775	85.TC.-G	0.953	0.701
  6557686	1776	18.C.A;75.-.G	0.953	0.330
  1860902	1777	0.TT.--;81.GA.-T	0.952	0.515
  2717874	1778	2.A.C;0.T.-;80.AG.-T	0.951	0.611
  2882024	1779	1.-.C;74.-.G	0.951	0.619
  3273132	1780	0.T.-;2.A.G;77.-.C	0.951	0.397
  441958	1781	-27.C.A;76.GG.-A	0.949	0.205
  14811390	1782	-29.A.C;78.A.-	0.949	0.249
  14802094	1783	-29.A.C;86.-.C	0.949	0.461
  10523926	1784	15.-.T;76.-.A	0.948	0.739
  12742835	1785	0.-.T;81.GA.-T	0.948	0.383
  8093342	1786	75.-.A;133.A.C	0.948	0.327
  8490265	1787	76.-.G;129.C.A	0.948	0.322
  2412848	1788	1.-.A;76.-.T	0.947	0.632
  8183422	1789	85.TC.-A	0.947	0.638
  2463159	1790	1.TA.--;3.C.A;88.-.T	0.946	0.552
  8490433	1791	76.-.G;133.A.C	0.946	0.318
  2681222	1792	0.T.-;2.A.C;115.T.G	0.946	0.288
  8480741	1793	78.A.-;132.G.C	0.946	0.202
  2663534	1794	0.T.-;2.A.C;77.G.C	0.946	0.861
  8118132	1795	76.GG.-C;129.C.A	0.946	0.373
  6447398	1796	16.-.C;55.-.G	0.945	0.768
  2285156	1797	0.T.-;82.AA.--	0.945	0.503
  8117520	1798	76.GG.-C;120.C.A	0.945	0.413
  8603147	1799	73.A.-	0.945	0.225
  8537609	1800	75.-.G;124.T.G	0.944	0.366
  2245955	1801	0.T.-;71.-.C	0.944	0.684
  8161116	1802	79.G-	0.942	0.264
  8536998	1803	75.-.G;119.C.A	0.942	0.370
  8537871	1804	75.-.G;127.T.C	0.941	0.334
  8543767	1805	75.-.G;89.A.-	0.941	0.628
  6603080	1806	l8.C.-;55.-.G	0.941	0.707
  13850293	1807	-14.A.C;87.-.G	0.940	0.218
  1852615	1808	0.TT.--;76.-.A	0.938	0.750
  8208020	1809	88.G.-;132.G.C	0.938	0.242
  14918769	1810	-29.A.C;2.A.-;76.GG.-A	0.937	0.353
  8223161	1811	90.-.G	0.937	0.664
  2684123	1812	0.T.-.2.A.C;126.C.A	0.936	0.262
  2883487	1813	1.-.C;76.GG.-C	0.934	0.884
  8089075	1814	75.-C.AA	0.934	0.299
  13746840	1815	-13.G.T;76.G.-	0.934	0.266
  10179608	1816	18.-.G;73.-.A	0.933	0.587
  8357113	1817	87.-.G;119.C.A	0.933	0.238
  2570963	1818	0.T.-;2.A.C;18.C.-	0.932	0.404
  6621548	1819	18.C.-;88.-.T	0.932	0.702
  8543544	1820	75.-.G;89.-.C	0.930	0.331
  8158269	1821	79.G.A	0.928	0.860
  3341556	1822	2.A.G;0.T.-;73.AT.-G	0.928	0.857
  2683151	1823	119.C.A;2.A.C;0.T.-	0.928	0.288
  8543919	1824	75.-.G;88.-.T	0.926	0.543
  2570189	1825	0.T.-;2.A.C;18.-.A	0.926	0.645
  4015474	1826	3.-.C;86.-.C	0.926	0.838
  2731496	1827	0.T.-;2.A.C;75.-.G;132.G.C	0925	0.518
  8480834	1828	78.A.-;131.A.C	0.925	0.257
  3011827	1829	1.TA.--	0.923	0.388
  8592843	1830	70.-.T;86.-.C	0.923	0.501
  8057655	1831	73.-.A	0.923	0.547
  8480787	1832	78.A.-;133.A.C	0.923	0.247
  2249456	1833	0.T.-;72.-.G	0.922	0.820
  8752628	1834	55.-.T;76.GG.-A	0.922	0.503
  2274200	1835	0.T.-.99.-.T	0.921	0.848
  8142972	1836	76.G.-;131.A.C;133.A.C	0.921	0.258
  1252489	1837	-15.T.G;76.GG.-T	0.921	0.236
  14822468	1838	-29.A.C;55.-.T	0.921	0.524
  8357890	1839	87.-.G;131.A.C	0.921	0.275
  8485265	1840	76.-.G;88.G.-	0.920	0.453
  14796763	1841	-29.A.C;74.-.C	0.919	0.375
  14796493	1842	-29.A.C;74.T.-	0.919	0.249
  8558538	1843	74.-.T;133.A.C	0.919	0.281
  7247803	1844	27.-.C;86.CC.-G	0.918	0.915
  10073442	1845	19.-.T;88.GA.-C	0.918	0.552
  12133660	1846	2.A.-;85.TC.-G	0.918	0.916
  2572420	1847	0.T.-;2.A.C;19.-.A	0.917	0.558
  8555076	1848	74.-.T;88.G.-	0.915	0.377
  10607377	1849	16.C.T;75.-.G	0.915	0.789
  3281290	1850	2A.G;0.T.-;88.G.-	0.915	0.699
  12713711	1851	0.-.T;72.-.A	0.915	0.659
  15408234	1852	-30.C.G;0.T.-;2.A.C	0.915	0.291
  12722990	1855	0.-.T;79.G.-	0.915	0.499
  8105716	1854	76.GG.-A;132.G.T	0.914	0.275
  2271180	1855	0.T.-	0.913	0.381
  10289412	1856	17.-.T;90.-.G	0.913	0.695
  14807090	1857	-29.A.C;87.-T	0.912	0.449
  6108421	1858	14.-.A;72.-.C	0.910	0.863
  8141461	1859	76.G.-;119.C.A	0.909	0.263
  14350324	1860	-25.A.C;76.-.G	0.908	0.330
  8538185	1861	130.--T.TAG;133.A.G;75.-.G	0.906	0.421
  8538491	1862	75.-.G;123.A.C	0.906	0.359
  14292135	1863	-25.A.C;0.T.-;2.A.C	0.905	0.255
  2399779	1864	1.-.A;75.-.C	0.904	0.626
  8142947	1865	76.G.-;131.AG.CC	0.903	0.312
  8603195	1866	73.A.-;131.A.C	0.902	0.229
  3329015	1867	2.A.G;0.T.-;78.-.T	0.901	0.635
  2457498	1868	1.TA.--;3.C.A;76.-.A	0.901	0.878
  14799938	1869	-29.A.C;76.G.-;78.A.C	0.901	0.250
  10194359	1870	18.-.G;82.AA.--	0.901	0.723
  2461767	1871	1.TA. ;3.C.A;99.-.G	0.898	0.891
  8128631	1872	75.-.C;131.AG.CC	0.898	0.298
  6130904	1873	14.-.A;75.CG.-T	0.898	0.809
  2885480	1874	1.-.C;77.GA.--	0.897	0.564
  8565409	1875	131.A.C;75.CG.-T	0.896	0.289
  8526599	1876	76.-.T;133.AC	0.895	0.367
  8542268	1877	75.-.G;99.-.G	0.895	0.466
  3296935	1878	0.T.-;2.A.G;98.-.T	0.894	0.819
  8535676	1879	115.T.G;75.-.G	0.892	0.386
  8530925	1880	75.-.G;82.-.A	0.891	0.434
  8142901	1881	76.G.-;134.G.T	0.890	0.290
  8142383	1882	76.G-;125.T.G	0.890	0.343
  2054253	1883	0.TT.-;2.A.G;87.-.T	0.890	0.872
  8001281	1884	71.T.C	0.888	0.608
  6366788	1885	17.-.A;86.C-	0.888	0.797
  12123821	1886	2.A.-;76.G.-;131.A.C	0.887	0.303
  15159066	1887	-29.A.G;74.T.-	0.886	0.228
  10072842	1888	19.-.T;87.-.A	0.886	0.612
  1979426	1889	0.T.C;80.A.-	0.886	0.576
  10193667	1890	18.-.G;82.A.-	0.886	0.828
  1252039	1891	-15.T.G;76.-.G	0.885	0.316
  4247573	1892	4.T.-;87.C.A	0.885	0.526
  6110295	1893	14.-.A;74.-.G	0.884	0.833
  6369429	1894	17.-.A;76.-.T	0.884	0.672
  6476407	1895	16.-.C;78.-.T	0.883	0.612
  2309043	1896	0.T.-;65.GC.-T	0.883	0.649
  10084280	1897	19.-.T;82.AA.-G	0.883	0.750
  2884850	1898	1.-.C;76.G.-;78.A.C	0.882	0.492
  2347258	1899	0.T.-;19.-.G	0.880	0.616
  12737110	1900	0.-T;88.-.T	0.880	0.357
  10557558	1901	15.-.T;78.A.C	0.879	0.710
  1851901	1902	0.TT.--;74.-.G	0.878	0.824
  6621723	1903	18.C.-;86.C.-	0.877	0.845
  10567449	1904	15.-.T;73.A.G	0.876	0.489
  1863878	1905	O.TT.--;75.C-	0.876	0.766
  7832261	1906	55.-.G;132.G.C	0.876	0.807
  15161180	1907	-29.A.G;77.-.A	0.875	0.216
  8545164	1908	75.-.G;82.AA.-G	0.875	0.569
  7830386	1909	55.-.G;86.-.C	0.875	0.744
  6077749	1910	15.TC.-A;76G.-	0.875	0.859
  8148008	1911	76.G.-;86.C.-	0.875	0.187
  2278635	1912	0.T.-;88.-.G	0.874	0.725
  1041817	1913	-17.C.A;75.-.C	0.873	0.246
  2465231	1914	1.TA.--;3.C.A;82.AA.-T	0.873	0.830
  2266703	1915	0.T.-;90.-.G	0.872	0.862
  6625678	1916	18.C.-;78.-.C	0.872	0.580
  8136927	1917	76.G.-;86.-.C	0.872	0.493
  8093375	1918	75.-.A;131.A.C	0.871	0.335
  2454809	1919	1.TA.--;3.C.A;72.-.A	0.870	0.736
  1980576	1920	0.T.C;76.GG.-T	0.870	0.466
  2271158	1921	0.T.-;132.G.C	0.870	0.383
  442251	1922	-27.C.A;75.-.C	0.870	0.273
  2350399	1923	0.T.-;18.-.G	0.869	0.556
  8498008	1924	78.A.G	0.869	0.356
  8080600	1925	74.-G;86.-C	0.868	0.560
  3328595	1926	2.A.G;0.T.-;78.AG.-T	0.868	0.824
  8467079	1927	78.AG.-C	0.868	0.422
  6459918	1928	16.-.C;77.-.A	0.866	0.523
  2265855	1929	0.T.-;88.GA.-C	0.865	0.721
  15161451	1930	-29.A.G;79.G-	0.865	0.291
  8565376	1931	75.CG.-T;133.A.C	0.865	0.308
  2684676	1932	0.T.-;2.A.C;131.A.G	0.864	0.347
  6461858	1933	16.-.C;86.-.A	0.864	0.611
  3011807	1934	1.TA.--;132.G.C	0.863	0.396
  1905700	1935	0.TTA.---;3.C.A;86.-.C	0.863	0.792
  8440297	1936	81.GAA.-TT	0.863	0.410
  8752800	1937	55.-.T;75.-.C	0.862	0.546
  12721020	1938	0.-.T;75.-.C	0.862	0.449
  441780	1939	-27.C.A;75.-.A	0.861	0.300
  10070497	1940	19.-.T;76.G.-;78.A.C	0.861	0.561
  8112403	1941	76.-.A;132.G.T	0.861	0.584
  1002534	1942	-17.C.A;2.A.C;0.T.-	0.861	0.227
  3324612	1943	0.T.-;2.A.G;78.A.C	0.861	0.737
  3030912	1944	1.TA.--;78.A.-;80.A.-	0.861	0.838
  10182195	1945	18.-.G;76.GG.-C	0.860	0.462
  8519380	1946	76.GG.-T;129.C.A	0.860	0.207
  8493521	1947	76.-.G;98.-.T	0.859	0.735
  8128428	1948	75.-.C;128.T.G	0.858	0.241
  1248006	1949	-15.T.G;88.G.-	0.857	0.217
  5585921	1950	10.T.C;76.G.-	0.855	0.371
  6127219	1951	14.-.A;78.A.-	0.855	0.493
  3007558	1952	1.TA.--;90.-.G	0.854	0.711
  10555821	1953	15.-.T;80.AG.-T	0.854	0.843
  12747339	1954	0.-.T;78.A.T	0.854	0.745
  14344892	1955	-25.A.C;75.-.C	0.853	0.296
  10310038	1956	17.-.T;77.-.T	0.853	0.647
  4303315	1957	4.T.-;76.G.T	0.852	0.664
  14786751	1958	-29.A.C;55.-.G	0.851	0.737
  15059318	1959	-29.A.G;0.T.-;2.A.C;76.-.G	0.851	0.285
  15240190	1960	-29.A.G;2.A.-	0.851	0.500
  6468525	1961	16.-.C;91.A.-;93.A.G	0.849	0.652
  2826831	1962	0.T.-;2.A.C;15.-.T;75.-.G	0.849	0.523
  8212871	1963	86.-.C;133.A.C	0.848	0.669
  3318144	1964	2.A.G;0.T.-;82.AA.-T	0.848	0.742
  1246180	1965	-15.T.G;75.-.A	0.847	0.337
  1982591	1966	0.T.C;66.CT.-G	0.847	0.442
  15166880	1967	-29.A.G;81.GA.-T	0.847	0.253
  1904171	1968	0.TTA.---;3.C.A;74.-.G	0.846	0.783
  14635061	1969	-29.A.C;0.T.-	0.846	0.382
  8565091	1970	75.CG.-T;126.C.A	0.845	0.207
  2725821	1971	0.T.-;2.A.C;77.GA.--;80.A.T	0.845	0.837
  4259960	1972	4.T.-;130.T.G	0.844	0.800
  3135495	1973	1.T.G;3.C.-;75.-.G	0.844	0.791
  14345120	1974	-25.A.C;76.G.-	0.844	0.259
  10071193	1975	19.-.T;81.G.-	0.844	0.779
  6476304	1976	16.-.C;78.AG.-T	0.844	0.661
  15175052	1977	-29.A.G;55.-.T	0.844	0.629
  8519203	1978	76.GG.-T;126.C.A	0.843	0.233
  8173991	1979	77.GA.--	0.843	0.383
  12746208	1980	0.-.T;76.-.G	0.842	0.435
  8133056	1981	75.-.C;87.-.T	0.842	0.419
  8526626	1982	76.-.T;131.A.C	0.841	0.223
  1252968	1983	-15.T.G;75.C.-	0.841	0.361
  14646713	1984	-29.A.C;0.T.-;2.A.C;80.A.-	0.840	0.513
  6304778	1985	16.-.A;77.-.A	0.840	0.462
  8479746	1986	78.A.-;120.C.A	0.838	0.293
  12763666	1987	0.-.T;55.-.T	0.838	0.783
  2684656	1988	0.T.-;2.A.C;131.A.C;133.A.C	0.838	0.207
  14800177	1989	-29.A.C;79.G.-	0.837	0.233
  8128118	1990	75.-.C;124.T.G	0.837	0.256
  13797685	1991	-14.A.C;0.T.-;2.A.C	0.836	0.250
  4259801	1992	4.T.-;128.T.G	0.836	0.763
  6612829	1993	18.C.-;76.G-	0.833	0.708
  448172	1994	-27.C.A;73.A.-	0.833	0.216
  1246589	1995	-15.T.G;76.GG.-C	0.833	0.560
  14796144	1996	-29.A.C;73.-.A	0.832	0.441
  6611642	1997	18.C.-;76.GG.-A	0.831	0.704
  3040392	1998	1.TA.--;73.A.T	0.831	0.517
  1938331	1999	0.TT.--;2.A.C;79.G.-	0.831	0.783
  10528065	2000	15.-.T;79.GA.-C	0.831	0.713
  3261986	2001	0.T.-;2.A.G;74.T.G	0.830	0.736
  8131593	2002	75.-.C;99.-.G	0.830	0.553
  14255597	2003	-24.G.T;2.A.-	0.830	0.570
  14879001	2004	-29.A.C;15.-.T;75.-.G	0.829	0.805
  14918841	2005	-29.A.C;2.A.-;76.GG.-C	0.829	0.732
  2290589	2006	0.T.-;79.GA.-T	0.829	0.726
  2951795	2007	1.TA.--;16.-.C	0.829	0.306
  9987799	2008	19-.G;86.-.G	0.827	0.731
  15455726	2009	-30.C.G;78.A.-	0.827	0.282
  14812695	2010	-29.A.C;77.-.T	0.826	0.575
  8202480	2011	87.-.A;131.A.C	0.825	0.570
  8066107	2012	74.T.-;121.C.A	0.825	0.204
  14807234	2013	-29.A.C;86.-.G	0.824	0.174
  10085211	2014	19.-.T;80.A-	0.824	0.633
  8180233	2015	81.GA.-C	0.823	0.428
  1044371	2016	-17.C.A;87.-.G	0.821	0.293
  10286908	2017	17.-.T;85.TC.-A	0.821	0.502
  10250881	2018	18.C.T;75.-.G	0.820	0.593
  2463586	2019	1.TA.--;3.C.A;86.-.G	0.820	0.682
  6554412	2020	18.C.A;76.G.-	0.819	0.318
  8485725	2021	76.-.G;98.-.A	0.818	0.716
  2271237	2022	0.T.-;131.A.C	0.817	0.352
  2564816	2023	0.T.-;2.A.C;17.-.A	0.816	0.601
  8357229	2024	87.-.G;120.C.A	0.816	0.329
  12747630	2025	0.-.T;76.G.-;78.A.T	0.816	0.796
  9972115	2026	19.-.G;73.-.A	0.816	0.802
  8212329	2027	86.-C;121.C.A	0.815	0.514
  14654311	2028	-29.A.C;1.TA.--;76.G.-	0.815	0.380
  1864798	2029	0.TT.--;73.AT.-G	0.814	0.762
  8117352	2030	76.GG.-C;119.C.A	0.813	0.433
  8479512	2031	78.A.-;119.C.A	0.812	0.224
  8133372	2032	75.-.C;82.A.-	0.812	0.357
  10468894	2033	16.C.-;87.-.G	0.812	0.667
  8489702	2034	76.-.G;121.C.A	0.812	0.335
  14919783	2035	-29.A.C;2.A.-	0.812	0.513
  8198335	2036	86.C.A	0.811	0.799
  8105698	2037	76.GG.-A;133.A.C	0.811	0.269
  13845556	2038	-14.A.C;76.GG.-C	0.809	0.491
  3011864	2039	1.TA.--;132.G.T	0.809	0.352
  13222066	2040	2.A.G;-3.TAGT.----;76.GG.-A	0.809	0.597
  6471171	2041	16.-.C;82.A.-	0.808	0.510
  8526572	2042	132.G.C;76.-.T	0.808	0.259
  8352868	2043	86.C.-;131.A.C	0.807	0.226
  10198068	2044	18.-.G;76.G.-;78.A.T	0.807	0.436
  8137025	2045	76.G.-;89.-.A	0.804	0.538
  8629413	2046	66.CT.-G;88.G-	0.803	0.320
  8105428	2047	76.GG.-A;126.C.A	0.803	0.240
  7947397	2048	66.CT.-A.87.-.G	0.802	0.362
  7835793	2049	55.-.G;76.GG.-T	0.802	0.735
  8140338	2050	76.G.-;116.T.G	0.802	0.306
  12722736	2051	0.-.T;77.-.C	0.801	0.427
  8757065	2052	55.-.T.86.C.-	0.801	0.559
  2398681	2053	1.-.A;75.-.A	0.801	0.641
  4011043	2054	3.-.C;74.-.C	0.799	0.713
  14920334	2055	-29.A.C;2.A.-;86.C.-	0.799	0.460
  13845318	2056	-14.A.C;76.GG.-A	0.799	0.188
  3427589	2057	0.T.-;2.A.G;19.-.G	0.799	0.416
  14806422	2058	-29A.C;89.A.-	0.798	0.702
  15165304	2059	-29.A.G;87.-.T	0.797	0.463
  2125941	2060	0.TTA. ;3.C.G;89.A.-	0.797	0.791
  15168973	2061	-29.A.G;76.-.T	0.796	0.380
  8538239	2062	75.-.G;131.AG.CC	0.796	0.429
  8528721	2063	76.GGA.-TT	0.796	0.447
  7834109	2064	55.-.G;86.-.G	0.794	0.596
  8476335	2065	78.A.-;98.-.A	0.794	0.528
  8352802	2066	132.G.C;86.C.-	0.794	0.214
  10372832	2067	18.CA.-T;74.-T.	0.794	0.724
  8752727	2068	55.-.T;76.GG.-C	0.793	0.681
  6460172	2069	16.-.C;77.-.C	0.792	0.474
  1245743	2070	-15.T.G;74.T.-	0.792	0.347
  6469515	2071	16.-.C;88.-.T	0.792	0.645
  15241028	2072	-29.A.G;2.A.-;78.A.-	0.792	0.398
  2711056	2073	0.T.-;2.A.C;82.A.G	0.791	0.747
  1974296	2074	0.T.C;74.T.-	0.790	0.533
  8637058	2075	66.CT.-G;86.-.G	0.789	0.254
  8526611	2076	76.-.T;132.G.T	0.788	0.323
  8144153	2077	76.G.-;119.C.T	0.788	0.240
  10566620	2078	15.-.T;73.A.C	0.788	0.613
  8557775	2079	74.-.T;119.C.A	0.788	0.230
  8462867	2080	79.GA.-T	0.787	0.613
  8549438	2081	75.C-	0.787	0.425
  8558414	2082	74.-.T;129.C.A	0.787	0.255
  8105581	2083	76.GG.-A;129.C.A	0.787	0.259
  2281703	2084	0.T.-;86.C.T	0.786	0.719
  2400499	2085	1.-.A;76.G.-;78.A.C	0.785	0.482
  14920368	2086	-29.A.C;2.A.-;87.-.G	0.785	0.602
  8543253	2087	75.-.G;91.A.-;93.A.G	0.785	0.452
  8488707	2088	76.-.G;116.T.G	0.785	0.283
  9979217	2089	19.-.G;86.-.C	0.783	0.612
  15162226	2090	-29.A.G;86.-.A	0.783	0.522
  12146137	2091	2.A.-;116.T.G	0.783	0.429
  5454231	2092	8.G.C;76.G.-	0.782	0.646
  2288382	2093	0.T.-;77.GA.--;83.A.T	0.781	0.648
  8549424	2094	75.C.-;132.G.C	0.781	0.386
  6461529	2095	16.-.C;85.T.-	0.781	0.720
  1090544	2096	2.A.-	0.781	0.530
  2282648	2097	0.T.-;84.-.T	0.779	0.667
  12149194	2098	2.A.-;131.A.G	0.779	0.440
  8142223	2099	76.G.-;124.T.G	0.779	0.273
  8199575	2100	86.CC.-A	0.779	0.611
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  8093073	2286	126.C.A;75.-.A	0.778	0.370
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  8083653	2293	74.-.G;121.C.A	0.775	0.434
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  13750813	2295	-13.G.T;75.-.G	0.774	0.496
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  14654654	2426	-29.A.C;1.TA.--	0.703	0.363
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  7490581	2428	36.C.A;76.GG.-C	0.703	0.439
  15452184	2429	-30.C.G;86.-.C	0.702	0.465
  8089736	2430	75.-.A;87.-.A	0.702	0.404
  3161365	2431	0.T.-;2.A.G;14.-.A	0.702	0.700
  8215458	2432	88.GA.-C	0.702	0.286
  2455947	2433	1.TA.--;3.C.A;73.-.A	0.702	0.693
  827787	2434	-21.C.A;76.G.-	0.702	0.246
  3574182	2435	2.-.A;55.-.G	0.701	0.681
  8504697	2436	78.-.T	0.701	0.457
  8147538	2437	76.G.-;91.A.-;93.A.G	0.701	0.391
  8436856	2438	81.GA.-T;132.G.C	0.700	0.199
  8110287	2439	76.-.A;86.-.C	0.700	0.448
  8598693	2440	70.-.T;87.-.T	0.700	0.315
  4260194	2441	4.T.-;129.C.T	0.699	0.510
  8059622	2442	73.-.A;87.-.G	0.699	0.389
  8586230	2443	73.AT.-G	0.699	0.265
  8126524	2144	75.-.C;115.T.G	0.699	0.336
  10084621	2445	19.-.T;82.AA.-T	0.699	0.642
  10607021	2446	16.C.T;78A.-	0.698	0.567
  8212230	2447	86.-.C;120.C.A	0.698	0.505
  2664493	2448	0.T.-;2.A.C;79.G.A	0.698	0.640
  2203429	2449	0.T.-;18.C-	0.698	0.407
  8605503	2450	73.A.-;86.C.-	0.697	0.200
  13852662	2451	-14.A.C;78.A.-	0.697	0.309
  8546163	2452	75.C.-;86.-.C	0.697	0.445
  446575	2453	-27.C.A;76.-.G	0.696	0.351
  8065997	2454	74.T.-;120.C.A	0.696	0.234
  11888602	2455	2.A.C;75.-.G	0.696	0.515
  8536608	2456	75.-.G;118.T.C	0.694	0.323
  14797194	2457	-29.A.C;74.-.G	0.694	0.384
  15166776	2458	-29.A.G;82.AA.-T	0.694	0.237
  14800643	2459	-29.A.C;77.GA.--	0.693	0.379
  8030604	2460	72.-.C;86.-.C	0.692	0.345
  2464748	2461	1.TA.--;3.C.A;82.AA.-C	0.692	0.574
  8493269	2462	76 -.G;99.-.G	0.691	0.356
  8549456	2463	75.C.-;133.A.C	0.691	0.458
  2307776	2464	0.T.-;66.CT.--	0.690	0.673
  6306305	2465	16.-.A;86.-.C	0.690	0.602
  8126956	2466	75.-.C;116.T.G	0.690	0.278
  14809754	2467	-29.A.C;81.GA.-T	0.688	0.296
  8212714	2468	86.-.C;128.T.G	0.688	0.369
  1251890	2469	-15.T.G;78.A.-	0.687	0.319
  8518607	2470	76.GG.-T;119.C.A	0.687	0.191
  8057702	2471	73.-.A;131.A.C	0.686	0.432
  3024866	2472	1.TA.--;82.AA.-G	0.686	0.454
  8367599	2473	86.-.G;133.A.C	0.686	0.157
  8431922	2474	82.AA.-T	0.686	0.217
  8144351	2475	76.G.-;117.G.T	0.685	0.239
  8538257	2476	75.-.G;131.A.C;133.A.C	0.685	0.419
  8543064	2477	75.-.G;91.A.-	0.685	0.640
  15455856	2478	-30.C.G;76.-.G	0.685	0.299
  12149015	2479	2.A.-;130.T.G	0.685	0.459
  2685087	2480	0.T.-;2.A.C;122.A.C	0.684	0.234
  8084140	2481	74.-.G;132.G.C	0.683	0.396
  8142757	2482	76.G.-;130.T.C;132.G.C	0.683	0.272
  8538197	2483	75.-.G;134.G T	0.683	0.368
  15058053	2484	-29.A.G;0.T.-;2.A.C;76.GG.-C	0.683	0.336
  8066567	2485	74.T.-;129.C.A	0.681	0.266
  441402	2486	-27.C.A;74.T.-	0.681	0.300
  1042785	2487	-17.C.A;86.-.C	0.679	0.335
  8490149	2488	76.-.G;127.T.G	0.678	0.293
  1905560	2489	0.TTA.---;3.C.A;87.-.A	0.678	0.635
  8352170	2490	86.C.-;120.C.A	0.678	0.182
  1252598	2491	-15.T.G;76.-.T	0.678	0.235
  2400384	2492	1.-.A;77.-.A	0.678	0.356
  8087722	2493	74.-.G;86.C.-	0.676	0.432
  8101522	2494	75.-C.AG	0.676	0.285
  8087834	2495	74.-.G;87.-.T	0.676	0.449
  8431908	2496	82.AA.-T;132.G.C	0.676	0.225
  14645411	2497	-29.A.C;0.T.-;2.A.C;86.-.C	0.676	0.635
  2835829	2498	0.T.-;2.A.C;6.G.T	0.675	0.298
  8438736	2499	81.GAA.-TC	0.674	0.360
  8065838	2500	74.T.-;119.C.A	0.673	0.209
  15171004	2501	-29.A.G;73.A.-	0.673	0.259
  8084203	2502	74.-.G;131.A.C	0.673	0.327
  15161712	2503	-29.A.G;77.GA.--	0.672	0.388
  6613064	2504	18.C.-;77.-.A	0.672	0.551
  12315000	2505	2.A.-;15.-.T;75.-.G	0.672	0.635
  14246167	2506	-24.G.T;75.-.G	0.672	0.308
  15051656	2507	-29.A.G;0.T.-	0.671	0.366
  8469914	2508	78.-.C;121.C.A	0.671	0.232
  8352836	2509	86.C.-;133.A.C	0.670	0.207
  8554990	2510	74.-.T;87.-.A	0.670	0.490
  830076	2511	-21.C.A;75.-.G	0.670	0.422
  8538376	2512	75.-.G;126.C.G	0.670	0.370
  15451096	2513	-30.C.G;75.-.C	0.670	0.236
  1290476	2514	-15.T.G;2.A.-	0.669	0.658
  14644913	2515	-29.A.C;0.T.-;2.A.C;75.-.C	0.668	0.335
  8481064	2516	78.A.-;123.A.C	0.667	0.232
  12726534	2517	0.-.T;86.-.C	0.666	0.531
  14814019	2518	-29.A.C;75.C.-	0.666	0.397
  15450607	2519	-30.C.G;75.-.A	0.665	0.225
  8512477	2520	76.G.-;78.A.T;132.G.C	0.665	0.478
  1247921	2521	-15.T.G;87.-.A	0.665	0.476
  6461965	2522	16.-.C;86.CC.-A	0.664	0.620
  14815751	2523	-29.A.C;73.A.G	0.663	0.362
  8557906	2524	74.-.T;120.C.A	0.663	0.196
  8174025	2525	77.GA.--;132.G.T	0.663	0.265
  1979872	2526	0.T.C;78.-.C	0.663	0.404
  8148116	2527	76.G.-;87.-.T	0.662	0.584
  8055441	2528	73.-.A;86.-.C	0.662	0.471
  15162449	2529	-29.A.G;88.G.-	0.662	0.206
  8522485	2530	76.GGA.-TC	0.662	0.401
  3081068	2531	1.TA.--;18.-.G	0.662	0.556
  8117952	2532	76.GG.-C;126.C.A	0.661	0.381
  6469397	2533	16.-.C;89.-.T	0.661	0.591
  8181855	2534	85.TCC.-AA	0.661	0.568
  1044315	2535	-17.C.A;86.C.-	0.661	0.167
  14920528	2536	-29.A.C;2.A.-;82.A.-	0.659	0.536
  8518772	2537	76.GG.-T;120.C.A	0.659	0.283
  15058093	2538	-29.A.G;0.T.-;2.A.C;75.-.C	0.658	0.434
  8057683	2539	132.G.T;73.-.A	0.657	0.434
  2459622	2540	1.TA.--;3.C.A;86.-.A	0.656	0.656
  8069836	2541	74.T.-;86.C.-	0.656	0.293
  3320802	2542	2.A.G;0.T.-;80.A.-	0.656	0.611
  14919186	2543	-29.A.C;2.A.-;77.GA.--	0.655	0.360
  8207846	2544	88.G.-;126.C.A	0.655	0.244
  447068	2545	-27.C.A;76.-.T	0.655	0.227
  8603132	2546	73.A.-;132.G.C	0.654	0.247
  8755264	2547	55.-.T;132.G.C	0.654	0.548
  443309	2548	-27.C.A;86.-.C	0.653	0.447
  8548846	2549	75.C-;121.C.A	0.653	0.455
  8150297	2550	77.-.A;132.G.T	0.652	0.274
  8603165	2551	73.A.-;133.A.C	0.652	0.298
  12312790	2552	16.C.-;2.A.-	0.652	0.524
  10248608	2553	18.C.T;76.G.-	0.651	0.536
  1046713	2554	-17.C.A;75.CG.-T	0.651	0.263
  8638044	2555	66.CT.-G;82.AA.-T	0.651	0.287
  3315325	2556	0.T.-;2.A.G;82.AA.-C	0.650	0.605
  12314014	2557	2.A.-;15.-.T;76.G-	0.649	0.574
  8494400	2558	76.-.G;86.C.-	0.649	0.187
  14920881	2559	-29.A.C;2.A.-;80.A.-	0.648	0.517
  14243707	2560	-24.G.T;76.G.-	0.648	0.185
  12148911	2561	2.A.-;129.C.A	0.647	0.601
  12149062	2562	2.A.-;132.G.C	0.646	0.502
  8600526	2563	73.A.-;88.G.-	0.645	0.440
  8538871	2564	75.-.G;121.C.T	0.645	0.402
  8603181	2565	73.A.-;132.G.T	0.645	0.289
  15450764	2566	-30.C.G;76.GG.-A	0.644	0.211
  12149230	2567	2.A.-;129.C.G	0.643	0.340
  8558338	2568	74.-.T;127.T.G	0.643	0.272
  8367575	2569	86.-.G;132.G.C	0.642	0.146
  14647726	2570	-29.A.C;0.T.-;2.A.C;66.CT.-G	0.641	0.378
  8490463	2571	76.-.G;131.AG.CC	0.640	0.222
  12123507	2572	2.A.-;76.G.-;121.C.A	0.640	0.452
  8352850	2573	86.C.-;132.G.T	0.640	0.245
  12191691	2574	2.A.-;78.A.-;132.G.T	0.639	0.499
  8638264	2575	66.CT.-G;80.A.-	0.639	0.282
  1195928	2576	-15.T.G;1.TA.--	0.639	0.361
  1979286	2577	0.T.C;81.GA.-T	0.639	0.548
  8207662	2578	88.G.-;121.C.A	0.638	0.120
  6460643	2579	16.-.C;81.G.-	0.638	0.572
  2686745	2580	0.T.-;2.A.C;113.A.C	0.638	0.276
  1045705	2581	-17.C.A;78.A.-	0.638	0.262
  8600457	2582	73.A.-;87.-.A	0.636	0.454
  7948057	2583	66.CT.-A;76.-.G	0.636	0.380
  10091271	2584	19.-T;73.AT.-C	0.636	0.542
  442030	2585	-27.C.A;76.-.A	0.636	0.592
  844891	2586	2.A.-;-21.C.A	0.633	0.622
  10516019	2587	15.-.T;71.-.C	0.633	0.534
  12016332	2588	2.A.-;18.C-	0.632	0.463
  8073253	2589	74.-.C;132.G.C	0.632	0.356
  8357699	2590	87.-.G;128.T.G	0.630	0.335
  2684905	2591	0.T.-;2.A.C;123.A.C	0.630	0.301
  2684593	2592	0.T.-;2.A.C;134.G.T	0.630	0.258
  12149142	2593	2.A.-;132.G.T	0.630	0.481
  2881692	2594	1.-.C;74.-.C	0.628	0.531
  5590003	2595	87.-.G;10.T.C	0.628	0.471
  12123808	2596	132.G.T;2.A.-;76.G.-	0.628	0.327
  8212595	2597	86.-.C;126.C.A	0.627	0.514
  8173470	2598	77.GA.--:121.C.A	0.627	0.292
  8034488	2599	72.-.C;82.A.-	0.627	0.141
  2411142	2600	1.-.A;78.-.C	0.626	0.400
  8096384	2601	75.-.A;82.A.-	0.626	0.418
  2723173	2602	0.T.-;2.A.C;76.-.G;132.G.C	0.626	0.320
  8118097	2603	76.GG.-C;128.T.G	0.625	0.405
  8543409	2604	75-.G;91.AA.-G	0.625	0.400
  14812614	2605	-29.A.C;76.G.-;78.A.T	0.625	0.410
  6476723	2606	16.-.C;76.G.-;78.A.T	0.624	0.568
  8519286	2607	76.GG.-T;127.T.G	0.624	0.239
  8501650	2608	78.AG.-T	0.623	0.440
  8208050	2609	88.G.-;133.A.C	0.623	0.206
  8549499	2610	75.C.-;131.A.C	0.623	0.381
  12009703	2611	2.A.-;17.-.A	0.623	0.617
  8128850	2612	75.-.C;123.A.C	0.623	0.272
  1862825	2613	0.TT.-;78.-.T	0.622	0.588
  6368672	2614	17.-.A;78.-.C	0.622	0.607
  8519348	2615	76.GG.-T;128.T.G	0.622	0.277
  1041692	2616	-17.C.A;76.GG.-C	0.622	0.482
  8018631	2617	72.-.A	0.621	0.469
  8066533	2618	74.T.-;128.T.G	0.619	0.261
  8436892	2619	81.GA.-T;132.G.T	0.619	0.154
  8636610	2620	66.CT.-G;89.A.-	0.618	0.524
  2884910	2621	1.-.C;77.-.C	0.617	0.494
  8143053	2622	76.G.-;129.C.T	0.617	0.285
  8356385	2623	87.-.G;115.T.G	0.616	0.348
  8561418	2624	74.-.T;87.-.T	0.616	0.531
  6467416	2625	16.-.C;99.-.G	0.615	0.507
  2723199	2626	0.T.-;2.A.C;76.-.G;132.G.T	0.615	0.389
  13746674	2627	-13.G.T;75.-.C	0.614	0.317
  15736191	2628	-32.G.T;76.G-	0.614	0.181
  2950619	2629	1.TA. ;17.T.C	0.613	0.330
  1250048	2630	-15.T.G;87.-.G	0.612	0.301
  8519441	2631	76.GG.-T;130.T.G	0.611	0.227
  8174044	2632	77.GA.--;131.A.C	0.611	0.368
  8083913	2633	74.-.G;126.C.A	0.610	0.361
  6554290	2634	18.C A;75.-.C	0.610	0.248
  8481228	2635	78.A.-;122.A.C	0.610	0.293
  14004700	2636	-19.G.T;0.T.-.2.A.C	0.610	0.268
  481605	2637	-27.C.A;2.A.-	0.610	0.487
  2262447	2638	0.T.-;81.GA.-C	0.608	0.518
  2683891	2639	0.T.-;2.A.C;124.T.G	0.608	0.300
  2685505	2640	0.T.-;2.A.C;120.C.T	0.608	0.287
  827692	2641	-21.C.A;75.-.C	0.608	0.315
  13101663	2642	-1.GT.--;74.-.T	0.607	0.272
  2271017	2643	0.T.-;128.T.G	0.607	0.345
  8066699	2644	74.T.-;133.A.C	0.607	0.229
  8118193	2645	76.GG.-C;130.T.G	0.607	0.534
  8073290	2646	74.-.C;132.G.T	0.606	0.307
  1117646	2647	-16.C.A;75.-.C	0.606	0.417
  444910	2648	-27.C.A;86.C.-	0.605	0.107
  8563682	2649	75.CG.-T;115.T.G	0.605	0.210
  14645196	2650	-29.A.C;0.T.-;2.A.C;77.GA.--	0.604	0.451
  14663089	2651	-29.A.C;0.T.-;2.A.G;76.-.G	0.604	0.579
  8480843	2652	78.A.-;131.A.C;133.A.C	0.603	0.221
  15241063	2653	-29.A.G;2.A.-;76.-.G	0.603	0.535
  8128359	2654	75.-.C;127.T.G	0.603	0.246
  12202830	2655	2.A.-;75.-.G;131.A.C	0.602	0.300
  2516661	2656	1.T.C;76.-.G	0.602	0.569
  8600854	2657	73.A.-;98.-.A	0.601	0.555
  15158807	2658	-29.A.G;73.-.A	0.600	0.594
  12147720	2659	2.A.-;120.C.A	0.600	0.524
  14344554	2660	-25.A.C;76.GG.-A	0.600	0.212
  3133295	2661	1.T.G;3.C.-;74.T.-	0.600	0.541
  3601058	2662	2.-.A;76.GG.-T	0.599	0.520
  8562045	2663	74.-.T;82.AA.-T	0.599	0.257
  8080686	2664	74.-.G;89.-.A	0.599	0.542
  8116266	2665	76.GG.-C;115.T.G	0.599	0.439
  8528148	2666	76.-.T;86.C.-	0.598	0.268
  14809572	2667	-29.A.C;82.AA.-T	0.597	0.169
  1041548	2668	-17.C.A;76.GG.-A	0.597	0.348
  13847372	2669	-14.A.C;86.-.C	0.597	0.440
  2654872	2670	0.T.-;2.A.C;75.C.A	0.596	0.361
  8543705	2671	75.-G;89.A.G	0.596	0.481
  8150315	2672	77.-.A;131.A.C	0.595	0.217
  13854171	2673	-14.A.C;74.-.T	0.595	0.255
  8084187	2674	74.-.G;132.G.T	0.595	0.378
  1249988	2675	-15.T.G;86.C.-	0.594	0.264
  10308807	2676	17.-.T;78.A.-;80.A.-	0.593	0.538
  8093276	2677	75.-.A;130.T.G	0.593	0.294
  15069677	2678	-29.A.G;0.T.-;2.A.G;75.-.G	0.593	0.429
  2884699	2679	1.-.C;77-.A	0.593	0.444
  14921605	2680	-29.A.C;2.A-;74.-.T	0.592	0.536
  8448153	2681	80.A.-;132.G.C	0.592	0.175
  8140966	2682	76.G.-;118.T.C	0.591	0.209
  8161100	2683	79.G.-;132.G.C	0.591	0.221
  15165008	2684	-29.A.G;88.-.T	0.590	0.294
  15058006	2685	-29.A.G;0.T.-;2.A.C;76.GG.-	0.590	0.449
  		A
  14647360	2686	-29.A.C;0.T.-;2.A.C;75.CG.-T	0.589	0.365
  8207961	2687	88.G.-;129.C.A	0.588	0.254
  2684707	2688	0.T.-;2.A.C;129.C G	0.587	0.249
  12177699	2689	2.A.-;82.A.-;84.A.T	0.587	0.578
  8495115	2690	76.-.G;80.A.G	0.587	0.277
  8173741	2691	77.GA.--;126.C.A	0.586	0.262
  8044380	2692	72.-.G;87.-.G	0.586	0.496
  2270366	2693	0.T.-;120.C.A	0.585	0.348
  15456767	2694	-30.C.G;74.-.T	0.585	0.259
  12752882	2695	0.-T-.73.AT.-G	0.584	0.561
  4217308	2696	4.T.-;71.T.C	0.584	0.515
  14810890	2697	-29.A.C;78.AG.-C	0.583	0.368
  13853442	2698	-14.A.C;76.GG.-T	0.583	0.211
  8448176	2699	80.A.-	0.583	0.209
  8103057	2700	76.GG.-A;98.-.A	0.582	0.554
  8141130	2701	76.G.-;118.T.G	0.581	0.262
  8133120	2702	75.-.C;86.-.G	0.581	0.269
  14921140	2703	-29.A.C;2.A.-;76.-.G	0.581	0.464
  1046627	2704	-17.C.A;74.-.T	0.581	0.238
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  		T.TAG;133.A.G;2.A.C;0.T.-
  15486653	2745	-30.C.G;2.A.-	0.567	0.457
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  		T.TAG;133.A.G;76.GG.-C
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  8565224	2898	75.CG.-T;128.T.G	0.494	0.258
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  8602683	2925	73.A.-;121.C.A	0.483	0.181
  1250113	2926	-15.T.G;87.-.T	0.483	0.353
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  15241190	2935	-29.A.G;2.A.-;76.GG.-T	0.480	0.448
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  14795119	2940	-29.A.C;72.-.C	0.478	0.366
  8549156	2941	126.C.A;75.C.-	0.478	0.401
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  442714	2943	-27.C.A;79.G.-	0.476	0.336
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  13098412	2949	-1.GT.--;86.-.C	0.474	0.202
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  2728409	2952	0.T.-;2.A.C;76.GG.-T;132.G.T	0.469	0.458
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  8538739	2956	75.-.G;122.A.G	0.467	0.335
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  8602922	2958	73.A-;126.C.A	0.466	0.283
  8558390	2959	74.-.T;128.T.G	0.465	0.206
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  8495023	2961	78.A.-;82.A.G	0.463	0.212
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  443194	2964	-27.C.A;87.-.A	0.461	0.399
  8586216	2965	73.AT.-G;132.G.C	0.461	0.251
  8492129	2966	76.-.G;113.A G	0.460	0.274
  8602593	2967	73.A.-;120.C.A	0.460	0.167
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  8018666	2969	72.-.A;131.A.C	0.459	0.406
  2658141	2970	0.T.-;2.A.C;76.GG.-	0.459	0.418
  		C;132.G.C
  2270855	2971	0.T.-;126.0.A	0.458	0.340
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  8357785	2973	87.-.G;130.T.G	0.457	0.321
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  8538425	2975	75.-.G;26.C.T	0.456	0.392
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  8512529	3249	76.G.-;78.A.T;131.A.C	0.257	0.192
  8519060	3250	76.GG.-T;124.T.G	0.255	0.178
  1045581	3251	-17.C.A;78.-.C	0.254	0.161
  13844608	3252	-14.A.C;74.T.-	0.252	0.231
  13171509	3253	-1.G.T;76.GG.-T	0.251	0.179
  8336250	3254	89.-.C:121.C.A	0.248	0.177
  15455277	3255	-30.C.G;80.A.-	0.246	0.216
  8353027	3256	86.C.-;123.A.C	0.246	0.146
  8161013	3257	79.G.-;128.T.G	0.245	0.184
  8105760	3258	76.GG -A;129.C.G	0.244	0.201
  8558713	3259	74.-.T;123.A.C	0.243	0.218
  2681904	3260	0.T.-;2.A.C;116.T.C	0.243	0.228
  8558310	3261	74.-.T;127.T.C	0.239	0.165
  2684449	3262	0.T.-;2.A.C;130.T.C;132.G.C	0.235	0.191
  15052207	3263	-29.A.G;0.T.-;75.-.G	0.233	0.229
  8524468	3264	76.G.T;78.A.-	0.232	0.184
  7490514	3265	36.C.A;76.GG.-A	0.231	0.201
  8633217	3266	66.CT.-G;132.G.T	0.225	0.188
  8069615	3267	74.T.-;89.-.C	0.224	0.182
  15451403	3268	-30.C.G;77.-.A	0.224	0.142
  8520167	3269	76.GG.-T;119.C.T	0.222	0.182
  10994911	3270	8.G.T;76.G.-	0.222	0.186
  2272784	3271	0.T.-;113.A.G	0.218	0.188
  8100983	3272	75.C.A;87.-.G	0.209	0.207
  13851721	3273	-14.A.C;82.AA.-T	0.209	0.191
  8084086	3274	74.-.G;130.T.C	0.207	0.200
  8564034	3275	75.CG.-T;116.T.G	0.206	0.195
  1117838	3276	-16.C.A;75.CG.-T	0.205	0.200
  14023671	3277	-19.G.T;76.GG.-T	0.205	0.189
  8519544	3278	76.GG.-T;131.A.C;133.A.C	0.201	0.159
  8633185	3279	66.CT.-G	0.200	0.137
  14817545	3280	-29.A.C;66.CT.-G	0.199	0.147
  1482006	3281	-9.T.C;76.G.-	0.199	0.183
  14524849	3282	-28.G.T;75.-.C	0.198	0.181
  8470132	3283	78.-.C;127.T.G	0.197	0.192
  7738954	3284	51.C.A;76.G.-	0.189	0.175
  1247296	3285	-15.T.G;79.G.-	0.189	0.163
  8519864	3286	76.GG.-T;122.A.G	0.188	0.125
  1117512	3287	-16.C.A;76.GG.-T	0.185	0.166
  15171788	3288	-29.A.G;66.CT.-G	0.184	0.119
  8601732	3289	73.A.-;115.T.G	0.183	0.174
  6556220	3290	18.C.A;86.C.-	0.182	0.124
  8633071	3291	66.CT.-G;129.C.A	0.175	0.164
  8499488	3292	78.A.-;80.A.G	0.171	0.166
  8519321	3293	76.GG.-T;128.T.C	0.169	0.133
  14348190	3294	-25.A.C;86.C.-	0.165	0.107
  321013	3295	-28.G.C;74.-.T	0.164	0.163

• Approximately 140 modified gRNAs were generated, some by DME and some by targeted engineering, and assayed for their ability to disrupt expression of a target GFP reporter construct by creation of indels. Sequences for these gRNA variants are shown in Table 2. These modified gRNAs exclude modifications to the spacer region, and instead comprise different modified scaffolds (the portion of the sgRNA that interacts with the CRISPR protein). sRNA scaffolds generated by DME include one or more deletions, substitutions, and insertions, which can consist of a single or several base pairs. The remaining gRNA variants were rationally engineered based on knowledge of thermostable RNA structures, and are either terminal fusions of ribozymes or insertions of highly stable stem loop sequences. Additional gRNAs were generated by combining gRNA variants. The results for select gRNA variants are shown in Table 5 below.

• TABLE 5
  Ability of select gRNA variants to disrupt GFP expression

  		Normalized
  		Editing
  SEQ ID		Activity (ave, 2
  NO:	NAME (Description)	spacers n = 6)	Std. dev.

  5	X2 reference	—	—
  2101	phage replication stable	1.42	0.22
  2102	Kissing loop b1	1.17	0.11
  2103	Kissing loop a	1.18	0.03
  2104	32, uvsX hairpin	1.89	0.11
  2105	PP7	1.08	0.04
  2106	64, trip mut, extended stem truncation	1.69	0.18
  2107	hyperstable tetraloop	1.36	0.11
  2108	C18G	1.22	0.42
  2109	T17G	1.27	0.04
  2110	CUUCGG loop	1.24	0.22
  2111	MS2	1.12	0.25
  2112	-1, A2G, -78, G77T	1.00	0.18
  2113	QB	1.44	0.25
  2114	45, 44 hairpin	0.24	0.41
  2115	U1A	1.02	0.05
  2116	A14C, T17G	0.86	0.01
  2117	CUUCGG loop modified	0.75	0.04
  2118	Kissing loop b2	0.99	0.06
  2119	-76:78, -83:87	0.97	0.01
  7120	-4	0.93	0.03
  2121	extended stem truncation	0.73	0.02
  2124	-98:100	0.66	0.05
  2125	-1:5	0.45	0.05
  2126	-2163	0.57	0.07
  2127	=+G28, A82T, -84	0.56	0.04
  2128	=+51T	0.52	0.03
  2129	-1:4, +G5A, +G86,	0.09	0.21
  2130	2174	0.34	0.09
  2131	+g72	0.34	0.24
  2132	shorten front, CUUCGG loop modified extend	0.65	0.02
  	extended
  2133	A14C	0.37	0.03
  2134	-1:3, +G3	0.45	0.16
  2135	=+C45, +T46	0.42	0.04
  2136	CUUCGG loop modified, fun start	0.38	0.03
  2137	-74:75	0.18	0.04
  2138	{circumflex over ( )}T45	0.21	0.05
  2139	-69, -94	0.24	0.09
  2140	-94	0.01	0.01
  2141	modified CUUCGG, minus Tin 1st triplex	0.04	0.03
  2142	-1:4, +C4, A14C, T17G, +G72, -76:78, -83:87	0.16	0.03
  2143	T1C, -73	0.06	0.06
  2144	Scaffold uuCG, stem uuCG. Stem swap, t shorten	0.01	0.09
  2145	Scaffold uuCG, stem uuCG. Stem swap	0.04	0.03
  2146	0.0090408	0.06	0.04
  2147	no stem Scaffold uuCG	-0.11	0.02
  2148	no stem Scaffold uuCG, fun start	-0.06	0.02
  2149	Scaffold uuCG, stem uuCG, fun start	-0.02	0.02
  2150	Pseudoknots	-0.01	0.01
  2151	Scaffold uuCG, stem uuCG	-0.05	0.01
  2152	Scaffold uuCG, stem uuCG, no start	-0.04	0.07
  2153	Scaffold uuCG	-0.12	0.07
  2154	+GCTC36	-0.20	0.05
  2155	G quadriplex telomere basket+ ends	-0.21	0.02
  2156	G quadriplex M3q	-0.25	0.04
  2157	G quadriplex telomere basket no ends	-0.17	0.04
  2159	Sarcin-ricin loop	0.40	0.03
  2160	uvsX, C18G	1.94	0.06
  2161	truncated stem loop, C18G, trip mut (T10C)	1.97	0.16
  2162	short phage rep, C18G	1.91	0.17
  2163	phage rep loop, C18G	1.72	0.13
  2164	+G18, stacked onto 64	1.44	0.08
  2165	truncated stem loop, C18G, -1 A2G	1.63	0.40
  2166	phage rep loop, C18G, trip mut (T10C)	1.76	0.12
  2167	short phage rep, C18G, trip mut (T10C)	1.20	0.09
  2168	uvsX, trip mut (T10C)	1.54	0.12
  2169	truncated stem loop	1.50	0.10
  2170	+A17, stacked onto 64	1.54	0.13
  2171	3′ HDV genomic ribozyme	1.13	0.13
  2172	phage rep loop, trip mut (T10C)	1.39	0.10
  2173	-79:80	1.33	0.05
  2174	short phage rep, trip mut (T10C)	1.19	0.10
  2175	extra truncated stem loop	1.08	0.05
  2176	T17G, C18G	0.94	0.09
  2177	short phage rep	1.11	0.05
  2178	uvsX, C18G, -1 A2G	0.62	0.08
  2179	uvsX, C18G, trip mut (T10C), -1 A2G, HDV -99	1.06	0.08
  	G65T
  2180	3′ HDV antigenomic ribozyme	1.20	0.07
  2181	uvsX, C18G, trip mut (T10C), -1 A2G, HDV	0.95	0.03
  	AA(98:99)C
  2182	3′ HDV ribozyme (Lior Nissim, Timothy Lu)	1.08	0.01
  2183	TAC(1:3)GA, stacked onto 64	0.92	0.04
  2184	uvsX, -1 A2G	1.46	0.13
  2185	truncated stem loop, C18G, trip mut (T10C), -1	0.80	0.02
  	A2G, HDV -99 G65T
  2186	short phage rep, C18G, trip mut (T10C), -1 A2G,	0.80	0.05
  	HDV -99 G65T
  2187	3′ sTRSV WT viral Hammerhead ribozyme	0.98	0.03
  2188	short phage rep, C18G, -1 A2G	1.78	0.18
  2189	short phae rep, C18G, trip mut (T10C), -1 A2G,	0.81	0.08
  	3′ genomic HDV
  2190	phage rep loop, C18G, trip mut (T10C), -1 A2G,	0.86	0.07
  	HDV -99 G65T
  2191	3′ HDV ribozyme (Owen Ryan, Jamie Cate)	0.78	0.04
  2192	phage rep loop, C18G, -1 A2G	0.70	0.08
  2193	{circumflex over ( )}C55	0.78	0.03
  2194	-78, G77T	0.73	0.07
  2195	{circumflex over ( )}G1	0.73	0.10
  2196	short phage rep, -1 A2G	0.66	0.11
  2197	truncated stern loop, C18G, trip mut (T10C), -1	0.68	0.09
  	A2G
  2198	-1, A2G	0.54	0.07
  2199	truncated stem loop, trip mut (T10C), -1 A2G	0.40	0.03
  2200	uvsX, C18G, trip mut (T10C), -1 A2G	0.35	0.11
  2201	phage rep loop, -1 A2G	0.96	0.05
  2202	phage rep loop, trip mut (T10C), -1 A2G	0.49	0.06
  2203	phase rep loop, C18G, trip mut (T10C), -1 A2G	0.73	0.13
  2204	truncated stem loop, C18G	0.59	0.02
  2205	uvsX, trip mut (T10C), -1 A2G	0.56	0.08
  2206	truncated stem loop, -1 A2G	0.89	0.07
  2207	short phage rep, trip mut (T10C), -1 A2G	0.37	0.12
  2208	5′HDV ribozme (Owen Ryan, Jamie Cate)	0.39	0.03
  2209	5′HDV genomic ribozyme	0.35	0.06
  2210	truncated stem loop, C18G, trip mut (T10C), -1	0.24	0.04
  	A2G, HDV AA(98:99)C
  2211	5′env25 pistol ribozyme(with an added	0.33	0.07
  	CUUCGG loop)
  2212	5′HDV antigenomic ribozyme	0.17	0.01
  2213	3′ Hammerhead ribozyme (Lior Nissim, Timothy	0.09	0.02
  	Lu) guide scaffold scar
  2214	+A27, stacked onto 64	0.03	0.03
  2215	5′Hammerhead ribozyme Lior Nissim, Timothy	0.18	0.03
  	Lu) smaller scar
  2216	phage rep loop, C18G, trip mut (T10C), -1 A2G,	0.13	0.04
  	HDV AA(98:99)C
  2217	-27, stacked onto 64	0.00	0.03
  2218	3′ Hatchet	0.09	0.01
  2219	3′ Hammerhead ribozyme (Lior Nissim, Timothy	0.05	0.03
  	Lu)
  2220	5′Hatchet	0.04	0.03
  2221	5′HDV ribozyme (Lior Nissim, Timothy Lu)	0.08	0.01
  2222	5′Hammerhead ribozyme (Lior Nissim, Timothy	0.22	0.01
  	Lu)
  2223	3′ HH15 Minimal Hammerhead ribozyme	0.01	0.01
  2224	5′ RBMX recruiting motif	-0.08	0.03
  2225	3′ Hammerhead ribozyme (Lior Nissim, Timothy	-0.04	0.02
  	Lu) smaller scar
  2226	3′ env25 pistol ribozyme (with an added	-0.01	0.01
  	CUUCGG loop)
  2227	3′ Env-9 Twister	-0.17	0.02
  2228	+ATTATCTCATTACT25	-0.18	0.27
  2229	5′Env-9 Twister	-0.02	0.01
  2230	3′ Twisted Sister 1	-0.27	0.02
  2231	no stem	-0.15	0.03
  2232	5′HH15 Minimal Hammerhead ribozyme	-0.18	0.04
  2233	5′Hammerhead ribozyme (Lior Nissim, Timothy	-0.14	0.01
  	Lu) miide scaffold scar
  2234	5′Twisted Sister 1	-0.14	0.04
  2235	5′sTRSV WT viral Hammerhead ribozyme	-0.15	0.02
  2236	148, =+G55, stacked onto 64	3.40	0.18
  2239	175, trip mut, extended stem truncation, with [T]	1.18	0.09
  	deletion at 5′ end

• Although guide stability can he measured thermodynamically (for example, by analyzing inciting temperatures) or kinetically (for example, using optical tweezers to measure folding strength), without wishing to be hound by any theory it is believed that a more stable sgRNA bolsters CRISPR editing efficiency. Thus, editing efficiency was used as the primary assay for improved guide function.
• The activity of the gRNA scaffold variants was assayed using E6 and E7 spacers as described above, targeting CFP. The starting sgRNA scaffold in this case was a reference Planctomyces CasX tracr RNA fused to a Planctomyces crispr RNA (crRNA) using a “GAAA” stem loop (SEQ ID NO: 5). This sgRNA scaffold was used a base for DME and rationally engineered mutations. The activity of variant gRNAs shown in Table 6 was normalized to the activity of this starting, or base, sgRNA scaffold.
• The sgRNA scaffold was cloned into a small (less than 3 kilobase pair) plasmid with a 3′ type Ii restriction enzyme site for dropping in different spacers. The spacer region of the sgRNA is the part of the sgRNA interacts with the target DNA, and does not interact directly with the CasX protein. Thus, scaffold engineering should be spacer independent. One way to achieve this is by executing sgRNA DME and testing engineered sgRNA variants using several distinct spacers, such as the E6 and E7 spacers targeting GFP. This reduces the possibility of creating an sgRNA scaffold variant that works well with one spacer sequence targeting one genetic target, but not other spacer sequences directed to other targets. For the data shown in Table, 6, the E6 and E7 spacer sequences targeting GFP were used. Repression of GFP expression by sgRNA variants was normalized to GFP repression by the sgRNA starting scaffold of SEQ ID NO: 5 assayed with the same spacer sequence(s).
• Activity of select sgRNA variants generated by DME and rational engineering is shown in FIGS. 5A-5E, mean change in activity is shown in Table 6, and sgRNA variant sequences are provided in Table 2. sgRNA variants with increased activity were tested in HEK293 cells as described in Example 1. FIG. 5C shows that select sgRNA variant have improved GFP editing when assayed in HEK293 cells. FIG. 5D shows that in some cases, activity can be improved by appending ribozyme sequences. FIG. 5E shows that sgRNA variants comprising combinations of changes, for example those generated by DME or replacing stem loop sequences, can further improve editing activity.
Example 4 Mutagenesis of CasX Protein Produces Improved Variants
• A selectable, mammalian-expression plasmid was constructed that included a reference, also referred to herein as starting or base, CasX protein sequence, an sgRNA scaffold, and a destination sequence that can be replaced by spacer sequences. In this case, the starting CasX protein was Stx2 (SEQ ID NO: 2), the wild type Planctomycetes CasX sequence and the scaffold was the wild type sgRNA scaffold of SEQ ID NO: 5. This destination plasmid was digested using the appropriate restriction enzyme following manufacturer's protocol. Following digestion, the digested DNA was purified using column purification according to manufacturer's protocol. The E6 and E7 spacer oligos targeting GFP were annealed in 10 uL of annealing buffer. The annealed oligos were ligated to the purified digested backbone using a Golden Gate ligation reaction. The Golden Gate ligation product was transformed into chemically competent E. coli bacterial cells and plated onto LB agar plates with the appropriate antibiotic. Individual colonies were picked, and the GFP spacer insertion was verified via Sanger sequencing.
• The following methods were used to construct a DME library of CasX protein variants. The functional Plm CasX protein, which is a 978 residue multi-domain protein (SEQ ID NO: 2) can function in a complex with a 108 bp sgRNA scaffold (SEQ ID NO: 5), with an additional 3′ 20 bp variable spacer sequence, which confers DNA binding specificity. Construction of the comprehensive mutation library thus required two methods: one for the protein, and one for the sgRNA. Plasmid recombineering was used to construct a DME protein library of CasX protein variants. PCR-based mutagenesis was used to construct an RNA library of the sgRNA. Importantly, the DME approach can make use of a variety of molecular biology techniques. The techniques used for genetic library construction can be variable, while the design and scope of mutations encompasses the DME method.
• In designing DME mutations for the reference CasX protein, synthetic oligonucleotides were constructed as follows: for each codon, three types of oligonucleotides were synthesized. First, the substitution oligonucleotide replaced the three nucleotides of the codon with one of 19 possible alternative codons which code for the 19 possible amino acid mutations. 30 base pair flanking regions of perfect homology to the target gene allow programmable targeting of these mutations. Second, a similar set of 20 synthetic oligonucleotides encoded the insertion of single amino acids. Here, rather than replace the codon, a new region consisting of three base pairs was inserted between the codon and the flanking homology region. Twenty different sets of three nucleotides were inserted, corresponding to new codons for each of the twenty amino acids. Larger insertions can be built identically but will contain an additional three, six, or nine base pairs, encoding all possible combinations of two, three, or four amino acids. Third, an oligonucleotide was designed to remove the three base pairs comprising the codon, thus deleting the amino acid. As above, oligonucleotides can be designed to delete one, two, three, or four amino acids. Plasmid recombineering was then used to recombine these synthetic mutations into a target gene of interest, however other molecular biology methods can be used in its place to accomplish the same goal.
• Table 6 shows the fold enrichment of CasX protein variant DME libraries created from the reference protein of SEQ ID NO: 2, which were then subjected to DME selection/screening processes.
• In Table 6 below, the read counts associated with each of the listed variants was determined. Each variant was defined by its position (0-indexed), reference base, and alternate base. Only sequences with at least 10 reads (summed) across samples were analyzed, to filter from 457K variants to 60K variants. An insertion at position i indicates an inserted base between position i−1 and i (i.e. before the indicated position). ‘counts’ indicates the sequencing-depth normalized read count per sequence per sample. Technical replicates were combined by taking the geometric mean. ‘log2enrichment’ gives the median enrichment (using a pseudocount of 10) across each context, or across all samples, after merging for technical replicates. Each context was normalized by its own naive sample. Finally, the ‘log2enrichment_err’ gives the ‘confidence interval’ on the mean log2 enrichment. It is the std. deviation of the enrichment across samples 2/sqrt of the number of samples. Below, only the sequences with median log2enrichment−log2enrichment_err>0 are shown (60274 sequences examined).
• The computational protocol used to generate Table 6 was as follows: each sample library was sequenced on an Illumina. HiSeq for 150 cycles paired end (300 cycles total). Reads were trimmed to remove adapter sequences, and aligned to a reference sequence. Reads were filtered if they did not align to the reference, or if the expected number of errors per read was high, given the phred base quality scores. Reads that aligned to the reference sequence, but did not match exactly, were assessed for the protein mutation that gave rise to the mismatch, by aligning the encoded protein sequence of the read to the protein sequence of the reference at the aligned location. Any consecutive variants were grouped into one variant that extended multiple residues, The number of reads that support any given variant was determined for each sample. This raw variant read count per sample was normalized by the total number of reads per sample (after filtering for low expected number of errors per read, given the phred quality scores) to account for different sequencing depths. Technical replicates were combined by finding the geometric mean of variant normalized read count (shown below, ‘counts’). Enrichment was calculated for each sample by diving by the naive read count (with the same context—i.e. D2, D3, DDD). To downweight the enrichment associated with low read count, a pseudocount of 10 was added to the numerator and denominator during the enrichment calculation. The enrichment for each context is the median across the individual gates, and the enrichment overall is the median enrichment across the gates and contexts. Enrichment error is the standard deviation of the log2 enrichment values, divided by the sqrt of the number of values per variant, multiplied by 2 to make a 95% confidence interval on the mean.
• Heat maps of DME variant enrichment for each position of the reference CasX protein are shown in FIGS. 7A-7I and FIGS. 8A-8C. Fold enrichment of DME variants with single substitutions, insertions and deletions of each amino acid of the reference CasX protein of SEQ ID NO: 2 are shown. FIGS. 7A-7I and Table 6 summarize the results when the DME experiment was run at 37° C. FIGS. 8A-8C summarize the results when the same experiment was run at 45° C. A comparison of the data in FIGS. 7A-7I and FIGS. 8A-8C shows that running the same assay at two temperatures enriches for different variants. A comparison of the two temperatures thus indicates which amino acid residues and changes are important for thennostability and folding, and these amino acids can then be targeted to produce CasX protein variants with improved themmstability and folding.

• TABLE 6
  Fold enrichment of CasX DME variants.

  Pos.	Ref.	Alt.	Med. Enrich.	95% CI	Pos.	Ref.	Alt.	Med. Enrich.	95% CI

  11	R	N	3.123689614	1.666090155	877	V	D	1.738762289	0.688664606
  13	--	AS	2.772897791	0.812692873	459	K	W	1.696823829	0.67904004
  13	--	AG	2.740825108	1.138556052	891	E	K	1.6928634	0.819015932
  12	-	V	2.739405927	1.743064315	9	-	T	1.667698181	0.626564384
  13	--	TS	2.69239793	1.005397595	19	-	R	1.664532235	0.885325268
  12	-	Y	2.676525308	1.621386271	11	R	P	1.655382042	1.234907956
  754	FE	LA	2.638126094	0.709679147	793	-	L	1.585086754	0.91714318
  13	-	L	2.63160466	1.131924801	931	S	L	1.583295371	0.643295534
  14	V	S	2.616515776	1.515637887	12	--	AG	1.580094246	1.037517499
  877	V	G	2.558943878	1.132565008	770	M	P	1.577648056	1.061356917
  21	-	D	2.295527175	0.893253582	791	L	E	1.551380949	0.823309399
  12	--	PG	2.222956581	1.243693989	21	-	A	1.542633652	0.760237264
  824	V	M	2.181465681	1.137291381	814	F	H	1.510927821	0.672796928
  12	-	Q	2.102167857	1.396704669	12	-	C	1.506305374	0.730799624
  13	L	E	2.049540302	0.886997965	791	L	S	1.505731571	0.598349327
  12	R	A	2.046419725	1.229773759	792	--	AS	1.474378912	0.833339427
  889	S	K	2.030682939	0.721857305	12	-	L	1.46896091	0.783746198
  791	-	Q	1.996189679	0.799796529	795	T	-	1.465811841	0.744738295
  21	-	S	1.907167641	0.736834562	792	-	Q	1.462809015	0.586506727
  14	-	A	1.89090961	1.25865759	11	R	S	1.459875087	0.740946571
  11	R	M	1.88125645	0.779897343	11	R	T	1.450818176	0.908088492
  856	Y	R	1.83253552	0.74976479	738	A	V	1.397545277	0.638310372
  707	A	Q	1.830052571	0.555234229	791	-	Y	1.382702158	0.877495368
  16	-	D	1.826796594	1.168291076	384	E	P	1.36783963	0.775382596
  17	S	G	1.799890039	0.536675637	793	--	ST	1.351743597	0.608183464
  931	S	M	1.798321904	1.171026479	738	A	T	1.349932545	0.581386051
  13	L	V	1.782912682	0.513630591	781	W	Q	1.342276465	0.719454459
  11	--	AS	1.782444935	0.75642805	17	-	G	1.340746587	0.878053267
  856	Y	K	1.748619552	0.651026121	12	--	AS	1.333635165	1.19716917
  796	--	AS	1.742437726	0.859039085	771	A	Y	1.292995852	0.871463205
  792	-	E	1.290525566	1.195462062	979	L-E[stop]	VSSK (SEQ	1.125229136	0.372301096
  							ID NO: 3797)
  921	A	M	1.28763891	0.560591034	936	R	Q	1.117866436	0.745233062
  979	LE[stop]GS-	VSSKDL	1.282505495	0.371661154	979	LE[stop]GS-	VSSKDLQAS	1.111969193	0.311410682
  		(SEQ ID NO:				PGIK (SEQ ID	N (SEQ ID
  		3804)				NO: 3279)	NO: 3813)
  770	M	Q	1.279910431	1.186538897	396	Y	Q	1.105278825	0.646150998
  16	--	AG	1.271874994	0.55951096	979	LE[stop]GSP	VSSKDL	1.104849849	0.260693612
  							(SEQ ID NO:
  							3804)
  384	E	N	1.247124467	0.607911368	353	L	F	1.103922948	0.510520582
  979	L-	VS	1.239823793	0.315337927	979	LE[stop]GS-	VSSKDLQA	1.100880851	0.345695892
  						PG (SEQ ID	(SEQ ID NO:
  						NO: 3251)	3810)
  979	LE[stop]	VSS	1.233215135	0.36262523	697	Y	H	1.097977697	0.419010874
  658	--D	APG	1.220851584	0.979760686	796	--	PG	1.095168865	0.816765224
  979	L-E	VSS	1.21568584	0.37106558	4	--	TS	1.088089915	0.693109756
  385	E	S	1.210243487	0.826999735	10	R	K	1.085472062	0.382234839
  979	LE[stop]GS-	VSSKDLQAS	1.208612972	0.286427519	790	G	M	1.066566819	0.686227232
  	PGIK (SEQ ID	NK (SEQ ID
  	NO:	NO: 3814)
  	3279)[stop]
  793	--	SA	1.192367811	0.72089465	921	A	K	1.056315246	0.70226115
  739	R	A	1.188987234	0.611670208	696	-	R	1.049001055	0.880941583
  795	--	AS	1.183930928	0.90542554	9	I	L	1.039309233	0.528320595
  979	LE[stop]GS-P	VSSKDLQ	1.180100725	0.35995062	979	LE[stop]GSPG	VSSKDLQAS	1.037884742	0.299531766
  		(SEQ ID NO:				IK (SEQ ID	NK (SEQ ID
  		3809)				NO:	NO: 3814)
  						3279)[stop]N
  977	V	K	1.17977084	0.720108501	13	-	S	1.031062599	0.727357338
  658	--D	AAS	1.173300666	0.50353561	384	E	R	1.028117481	0.683537724
  14	--	TS	1.173232132	0.700156049	21	K	D	1.019445543	0.748518701
  10	-	V	1.164019233	1.085055677	978	[stop]	G	1.016498062	0.514955543
  375	E	K	1.163948709	0.891802018	979	L-E[stop]G	VSSKD (SEQ	1.016126075	0.353515679
  							ID NO: 3800)
  795	--	AG	1.14629929	0.481029275	10	R	N	1.010184099	0.846798556
  979	LE[stop]GSPG	VSSKDLQ	1.143633475	0.340695621	794	--	PG	1.00924007	0.987312969
  	(SEQ ID NO:	(SEQ ID NO:
  	3251)	3809)
  979	LE	VS	1.142516835	0.386398408	741	L	W	0.851844349	0.594072278
  877	V	Q	1.141917178	0.655790093	24	-	W	0.835220929	0.745009807
  791	L	Q	1.004388299	0.361910793	755	E	[stop]	0.833955657	0.31600491
  792	P	G	1.002325281	0.805296973	928	I	T	0.832425124	0.307759846
  877	V	C	0.995089773	0.566724231	979	LE[stop]GS-	VSSKDLQAS	0.822335062	0.317179456
  						PGI (SEQ ID	(SEQ ID NO:
  						NO: 3278)	3812)
  476	C	Y	0.984546648	0.686487573	781	W	K	0.810589018	0.686153856
  19	--	PG	0.984071689	0.738694244	791	L	R	0.806201856	0.611654466
  979	LE[stop]GSPG	VSSKDLQA	0.972011014	0.292930615	979	LE[stop]GSPG	VSSKDLQAS	0.80600706	0.220866187
  	I (SEQ ID NO:	(SEQ ID NO:				IK (SEQ ID	N (SEQ ID
  	3278)	3810)				NO:	NO: 3813)
  						3279)[stop]
  752	L	P	0.971338521	0.459371253	711	E	Q	0.793874739	0.38732268
  12	R	C	0.969988229	0.745286116	703	T	N	0.791134752	0.735228799
  12	R	Y	0.962112567	0.714384629	793	S	-	0.7821232	0.523699668
  979	LE[stop]GSPG	VSSKDLQAS	0.960035296	0.298173201	385	E	K	0.781091846	0.579724424
  	IK (SEQ ID	(SEQ ID NO:
  	NO: 3279)	3812)
  18	--	PG	0.952532997	0.782330584	955	R	M	0.780963169	0.340474646
  778	M	I	0.945963409	0.345538178	469	-	N	0.775656135	0.541879732
  798	S	P	0.942103893	0.470224487	788	Y	T	0.770125047	0.581859138
  16	D	G	0.941159649	0.341870864	705	Q	R	0.76633283	0.261069709
  22	A	Q	0.937573643	0.676316271	9	--	TS	0.763723778	0.674640849
  754	FE	IA	0.935796963	0.660936674	979	LE[stop]GS	VSSKD (SEQ	0.761764547	0.205465156
  							ID NO: 3800)
  1	Q	K	0.935474248	0.373656765	715	A	K	0.761122086	0.540516283
  14	V	F	0.932689058	0.742246472	384	E	K	0.760859162	0.22641046
  8	K	I	0.928472117	0.521050669	591	QG	R-	0.757963418	0.374903235
  384	E	G	0.920571639	0.452302777	316	R	M	0.757086682	0.310302995
  732	D	T	0.912254061	0.759438627	770	M	T	0.753193128	0.319236781
  658	D	Y	0.894131769	0.312165116	384	E	Q	0.752976137	0.602376709
  211	L	P	0.887315174	0.318877781	17	S	E	0.752400908	0.414988963
  14	V	A	0.885138345	0.699864156	755	E	D	0.74863141	0.212934852
  979	LE[stop]G	V--S	0.884897395	0.252782429	12	R	-	0.743504623	0.648509511
  13	-	F	0.883212774	0.713984249	938	Q	E	0.741570425	0.469451701
  979	LE[stop]G	VSSK (SEQ	0.881127427	0.417135617	657	I	V	0.73806027	0.256874713
  	ID NO: 3797)
  386	D	K	0.879045429	0.728272074	656	G	C	0.659813316	0.293973226
  5	R	I	0.871114116	0.317513506	4	K	N	0.656251908	0.302190904
  660	--	AS	0.862493953	0.798632847	774	Q	E	0.654737733	0.134116674
  877	V	M	0.855677916	0.267740831	-1	S	C	0.652333059	0.118222939
  -1	S	T	0.735179004	0.144429929	21	--	AS	0.651563705	0.48650799
  2	E	[stop]	0.734071396	0.323713248	185	L	P	0.649897837	0.225081568
  384	E	A	0.733775595	0.660142332	38	P	T	0.648698083	0.350485275
  891	E	Y	0.733458673	0.465192765	936	R	H	0.648045448	0.423309347
  643	V	F	0.732765961	0.577614171	813	G	C	0.644003475	0.310838653
  796	-	C	0.732364738	0.485790322	786	L	M	0.643153738	0.314936636
  280	L	M	0.731787266	0.258239226	942	K	N	0.639528926	0.249553292
  695	-	K	0.730902961	0.509205112	293	Y	H	0.636816244	0.207205991
  343	W	L	0.725824372	0.292120452	542	F	L	0.635949082	0.181128276
  3	------	IKRINK (SEQ	0.721338414	0.470264314	303	W	L	0.635588216	0.261903568
  		ID NO: 3475)
  732	D	N	0.71945188	0.416870981	979	LE	V[stop]	0.635165807	0.329009453
  687	---	PTH	0.716433371	0.159856315	578	P	H	0.634392073	0.324298942
  176	A	D	0.71514177	0.206626688	687	--	PT	0.633217575	0.355316701
  485	W	L	0.713411462	0.238105577	886	K	N	0.632562679	0.231080349
  22	A	D	0.710738042	0.32510753	20	K	R	0.632186797	0.237509121
  193	L	P	0.709349304	0.242633498	248	L	P	0.631068881	0.180279623
  899	R	M	0.707875506	0.298429738	18	N	S	0.630660766	0.266585824
  886	KG	R-	0.706803824	0.286241441	836	M	V	0.630065132	0.266534124
  796	--	TS	0.697218521	0.492426198	116	K	N	0.629540403	0.234219411
  329	P	H	0.696817542	0.314817482	847	EG	GA	0.628295048	0.299740787
  273	L	P	0.696199602	0.349703999	912	L	P	0.627137425	0.187179246
  31	L	M	0.696080627	0.331245769	92	P	H	0.626243107	0.350245614
  645	-	E	0.692307595	0.590013131	299	Q	K	0.623386276	0.302029469
  9	I	Y	0.689813642	0.667593375	707	A	T	0.622086487	0.275515174
  9	1	N	0.688953393	0.257809633	669	L	M	0.620453868	0.351072046
  919	H	R	0.688781806	0.363439859	789	E	D	0.617920878	0.216264385
  687	P	H	0.684782236	0.310607479	916	F	S	0.617302977	0.309372822
  332	P	H	0.672484781	0.326219913	55	P	li	0.616365993	0.329695842
  796	-	N	0.672333697	0.64437503	936	R	G	0.615282844	0.189389227
  421	W	L	0.667702097	0.291970479	595	F	L	0.615176885	0.154670433
  875	E	[stop]	0.66617872	0.287006304	0	M	1	0.612039515	0.303853593
  378	L	K	0.664474618	0.393361359	925	A	P	0.581907283	0.186614282
  891	E	Q	0.663650921	0.312291932	659	R	L	0.580864225	0.319384189
  926	L	M	0.661737644	0.525550321	306	L	P	0.578183307	0.210431982
  381	L	R	0.609889042	0.420808291	676	P	Q	0.577757554	0.308473522
  945	T	A	0.609683347	0.258353939	877	V	E	0.57724394	0.294796776
  389	K	N	0.609647876	0.274048697	19	T	A	0.576889973	0.198407278
  755	E	G	0.607714844	0.078377344	14	V	D	0.574902804	0.437270334
  559	I	M	0.606040482	0.27336203	887	G	Q	0.574717855	0.519529758
  825	L	P	0.604240507	0.192490062	935	L	V	0.573813105	0.185021716
  733	M	T	0.603960776	0.340233556	961	W	L	0.573698555	0.253700288
  664	P	T	0.60370266	0.234348448	23	--	GP	0.572198674	0.570313308
  10	R	T	0.602483957	0.372156893	541	R	L	0.571508027	0.254421711
  964	F	L	0.60175279	0.17004436	288	E	D	0.571482463	0.24542675
  911	C	S	0.601303891	0.279730674	742	L	V	0.570384839	0.3027928
  788	Y	G	0.600935917	0.580949772	931	S	T	0.570369019	0.120673525
  447	Q	K	0.600543047	0.297568309	623	-------	RRTRQDE	0.569913903	0.141118873
  							(SEQ ID NO:
  							3684)
  13	L	P	0.599989903	0.236688663	27	P	H	0.569605452	0.285015385
  193	L	M	0.599332216	0.309308194	28	M	T	0.56885021	0.216863369
  114	P	H	0.599262194	0.344450733	907	E	[stop]	0.567613159	0.345163987
  660	G	R	0.599221963	0.319640645	577	D	Y	0.567493308	0.253952459
  894	S	T	0.599084973	0.166490359	672	P	H	0.566921749	0.31335168
  904	P	H	0.59783828	0.349499416	669	L	P	0.564276636	0.224594167
  782	L	T	0.595786463	0.513346845	52	E	D	0.564250133	0.246311739
  944	Q	K	0.595243666	0.351818545	46	N	T	0.563094073	0.208662987
  207	P	H	0.595218482	0.277632613	5	R	G	0.560139309	0.15069426
  151	H	N	0.595188624	0.277503327	912	L	V	0.559515875	0.111973397
  495	A	K	0.594637604	0.315764586	40	L	M	0.558605774	0.239058063
  -1	S	P	0.594582952	0.377333364	923	Q	[stop]	0.558515774	0.34688202
  480	L	E	0.594055289	0.432259346	979	L- E[stop]G	VSSKE (SEQ	0.557263947	0.22994802
  							ID NO: 3826)
  469	E	A	0.594025118	0.30338267	41	R	T	0.555902565	0.199937528
  11	R	G	0.59320688	0.163279008	179	E	[stop]	0.555817911	0.245362937
  85	W	L	0.591691074	0.2708118	344	W	L	0.555474112	0.286390208
  15	K	E	0.587925122	0.149546484	703	T	R	0.53396819	0.160757401
  755	E	K	0.586636571	0.217538569	962	Q	E	0.533896042	0.302336405
  337	Q	R	0.585098232	0.172195554	764	Q	H	0.53385913	0.24340782
  877	V	A	0.584567684	0.258968272	793	S	T	0.533306619	0.17379091
  793	--	TS	0.583269098	0.45091329	6	I	M	0.533192185	0.188523563
  670	I	R	0.582033902	0.112618756	467	L	P	0.533022246	0.179464215
  63	R	M	0.554978749	0.336590825	244	Q	[stop]	0.532045714	0.262393061
  1	Q	R	0.554755158	0.207724233	8	K	N	0.531704561	0.294399975
  9	I	V	0.554053334	0.219348804	508	F	V	0.529042378	0.192146822
  914	C	[stop]	0.552658801	0.347714953	665	A	P	0.529013767	0.174049723
  836	M	I	0.551813626	0.180327214	46	NL	T[stop]	0.529006897	0.272198259
  856	Y	H	0.549262192	0.369311354	3	I	V	0.528916598	0.14506718
  620	L	M	0.548957556	0.322210662	518	W	S	0.528332889	0.199792834
  926	L	P	0.547714601	0.450095044	792	P	A	0.528028079	0.112407207
  377	L	P	0.546553821	0.20366425	13	L	A	0.526728857	0.318983292
  920	A	S	0.545992524	0.484867291	56	Q	K	0.526387006	0.188452852
  961	W	[stop]	0.544371204	0.244581668	878	N	S	0.526073971	0.27887921
  746	V	G	0.543151726	0.512718498	213	Q	E	0.525578421	0.16885346
  554	---	RFY	0.542549772	0.20487223	748	Q	H	0.525406412	0.200108279
  664	P	H	0.542466431	0.281534858	15	K	N	0.525094369	0.273038164
  5	R	[stop]	0.541304946	0.166704906	954	K	N	0.524763966	0.208680978
  803	Q	K	0.540975244	0.291121648	835	W	L	0.524725836	0.26540236
  652	M	I	0.540953074	0.217563311	847	E	D	0.524019387	0.23897504
  326	KG	R-	0.540593574	0.402287668	608	L	M	0.523890883	0.248052068
  789	E	[stop]	0.540122225	0.236046287	932	W	R	0.523129128	0.299781077
  889	S	L	0.539927241	0.375365013	21	K	N	0.522953217	0.250998038
  10	R	I	0.539433301	0.326816988	790	G	[stop]	0.5229473	0.262740975
  725	K	N	0.539088606	0.178127049	707	A	D	0.522560362	0.214610237
  603	L	P	0.538897648	0.229282796	954	K	V	0.522546614	0.349200627
  15	K	R	0.538786311	0.154390287	952	T	A	0.521534511	0.149679645
  541	R	G	0.537572295	0.133876643	892	A	D	0.521298872	0.228218092
  632	L	M	0.537440995	0.246129141	847	-------	EGQITYY	0.521149636	0.115331328
  							(SEQ ID NO:
  							3388)
  665	A	S	0.536996011	0.286216687	7	N	I	0.521103862	0.202836314
  650	K	E	0.536939626	0.139863469	917	E	K	0.509268127	0.386629094
  932	W	L	0.536075206	0.314946873	12	R	I	0.509210198	0.267908359
  684	L	M	0.535519584	0.338883641	326	K	N	0.508325806	0.277854988
  918	T	R	0.535067274	0.304580877	802	A	W	0.507146644	0.398619961
  10	R	G	0.534873359	0.3557865	627	Q	H	0.506946344	0.17779761
  575	F	L	0.534865272	0.139851134	705	Q	K	0.506601342	0.205329495
  737	T	G	0.534759369	0.303617666	935	L	P	0.505173269	0.279127846
  907	E	G	0.534688762	0.240107856	636	L	P	0.504912592	0.279575261
  702	R	M	0.520743818	0.247227864	378	L	V	0.504856105	0.146721248
  901	S	G	0.520379757	0.143482219	770	M	I	0.502407214	0.148647414
  560	N	H	0.519240936	0.286066696	302	I	T	0.502263164	0.328365742
  350	V	M	0.518159753	0.277778553	584	P	H	0.501836401	0.188263444
  535	F	L	0.518099748	0.153008763	962	Q	H	0.501557133	0.21210836
  512	Y	H	0.517168474	0.223506594	909	F	L	0.501216251	0.397907118
  278	1	M	0.516794992	0.238648894	522	G	C	0.50035512	0.232143601
  746	V	A	0.51672383	0.202625874	233	M	I	0.500272986	0.246898577
  664	P	R	0.516702968	0.252959416	284	P	R	0.499965267	0.18413971
  -1	S	A	0.516689693	0.142459137	639	E	D	0.499845638	0.16815712
  298	A	D	0.51645727	0.257163483	351	K	E	0.49917291	0.274793088
  361	G	C	0.515521808	0.242033529	12	R	S	0.498984129	0.193129295
  424	1	V	0.515355817	0.185117148	920	A	V	0.498509984	0.394258252
  907	E	D	0.514835248	0.277377403	709	E	[stop]	0.498173203	0.222297538
  923	Q	E	0.514826301	0.324456465	443	S	H	0.498010803	0.445232627
  413	W	L	0.514728329	0.241932097	27	P	L	0.497724007	0.373177387
  748	Q	R	0.514571576	0.240563892	849	Q	K	0.497661989	0.259123161
  591	Q	H	0.514415886	0.331792035	793	-	Q	0.497102388	0.47673495
  1	Q	E	0.514404075	0.263908964	750	A	G	0.496799617	0.243940432
  171	P	T	0.513803013	0.237477165	26	G	C	0.496365725	0.228107532
  544	K	R	0.512919851	0.163480182	706	A	D	0.494947511	0.225683587
  677	-------	LSRFKD	0.511837147	0.194279796	431	L	P	0.494543065	0.192514906
  		(SEQ ID NO:
  		3577)
  377	L	M	0.511718619	0.274965484	13	LV	AS	0.494489513	0.367074627
  1	Q	H	0.511496323	0.29357307	0	M	V	0.49405414	0.206071479
  202	R	M	0.511365875	0.303187834	614	R	I	0.494053835	0.209299062
  422	E	[stop]	0.511043687	0.224103239	248	L	M	0.49299868	0.24880607
  922	E	[stop]	0.510570886	0.450135707	81	L	M	0.492127571	0.369172442
  407	-------	KKHGED	0.510425363	0.211479415
  		(SEQ ID NO:
  		3500)
  8	K	A	0.510125467	0.417426274	921	D	Y	0.479522102	0.330930172
  300	I	M	0.510084254	0.178542003	17	S	R	0.479410291	0.242870401
  668	A	P	0.509985424	0.202934866	23	G	C	0.47738757	0.286426817
  418	-	D	0.49144742	0.21486801	892	A	G	0.477302415	0.253000116
  914	C	R	0.490784001	0.353820866	832	A	T	0.47606534	0.23451824
  3	I	S	0.490305334	0.219289736	421	W	[stop]	0.475666945	0.216973062
  781	W	L	0.490256264	0.225567162	316	R	S	0.47464939	0.264534919
  234	G	[stop]	0.489800943	0.231905474	681	K	N	0.474468269	0.192816933
  369	A	V	0.489746571	0.142680124	22	A	V	0.474221933	0.206217506
  685	G	C	0.48966455	0.174412352	691	L	M	0.473867575	0.189071763
  498	A	S	0.489397172	0.173872708	95	L	V	0.473859579	0.188485586
  746	V	D	0.488692506	0.484120982	827	K	N	0.47365473	0.198868181
  666	--	AG	0.488446913	0.383322789	858	R	M	0.473407136	0.257236194
  309	W	L	0.487964134	0.209151088	519	Q	P	0.472315609	0.224391717
  979	----	VSSK (SEQ	0.486810051	0.287650542	95	L	P	0.471361064	0.162277972
  		ID NO: 3797)
  27	P	R	0.486771244	0.185539954	976	A	T	0.470889659	0.109031
  583	L	M	0.486474099	0.232216764	782	L	I	0.470558203	0.125178365
  760	G	R	0.485722591	0.195838563	723	A	S	0.469929973	0.218713854
  596	I	T	0.485474246	0.130718203	24	K	R	0.469399175	0.236250784
  189	G	[stop]	0.484957086	0.271997616	748	Q	E	0.46890075	0.291020418
  884	W	L	0.48469466	0.210361106	686	---	NPT	0.468711675	0.157459195
  162	E	[stop]	0.484515492	0.270313618	1	Q	L	0.468380179	0.341181409
  405	L	P	0.484058533	0.143471721	466	G	V	0.467982153	0.207162352
  815	T	A	0.483688268	0.140346764	346	---	MVC	0.467747954	0.140593808
  875	E	D	0.483680843	0.230122106	746	V	L	0.467699466	0.162488099
  703	T	K	0.483561705	0.243688021	101	Q	K	0.467562845	0.263058522
  35	V	A	0.48268809	0.163074127	99	V	L	0.467355555	0.098627209
  320	K	E	0.482629615	0.202594011	354	I	M	0.46704321	0.243813968
  203	E	D	0.482289135	0.173584261	826	E	[stop]	0.466802563	0.164892155
  202	R	S	0.482184999	0.1640178	150	P	L	0.466773068	0.200507693
  613	G	C	0.482001189	0.220237462	476	C	R	0.466682009	0.123054893
  220	A	P	0.481251117	0.159715468	38	P	H	0.466309116	0.291701454
  920	A	G	0.481026982	0.321704418	120	E	[stop]	0.465867266	0.21730484
  874	E	Q	0.480905869	0.250463545	370	G	R	0.465477814	0.252126933
  192	A	G	0.480770514	0.112319124	7	N	K	0.465102103	0.221573061
  578	P	T	0.48002354	0.203348553	920	A	P	0.45449471	0.288443793
  515	A	P	0.480000762	0.142980394	701	Q	H	0.453812486	0.146230302
  55	P	T	0.465075846	0.236340763	891	E	[stop]	0.453785945	0.233457013
  681	K	E	0.464515385	0.142005053	133	C	W	0.453639333	0.137405208
  781	W	C	0.464433122	0.295451154	370	G	V	0.453597184	0.202403506
  946	N	D	0.463522655	0.373105851	548	E	D	0.453077345	0.109679349
  368	L	M	0.463023353	0.266615533	689	H	D	0.453055551	0.09160837
  0	M	T	0.462868938	0.232012879	931	S	R	0.45302365	0.382294772
  737	T	A	0.462760296	0.301960654	133	C	[stop]	0.452586533	0.10138833
  847	----	EGQI (SEQ	0.462759431	0.219565444	868	E	[stop]	0.452282618	0.301898798
  		ID NO: 3385)
  0	M	K	0.462242932	0.245616902	33	V	L	0.451975838	0.159872004
  711	E	[stop]	0.461879161	0.191719959	266	D	Y	0.451699485	0.165335876
  357	K	N	0.461332764	0.184353442	497	E	D	0.451539434	0.154482619
  434	H	D	0.461154018	0.191223379	661	E	[stop]	0.45138977	0.234896635
  910	V	E	0.460870605	0.281013173	897	K	N	0.451376493	0.172130787
  922	E	D	0.460080408	0.286351122	894	S	G	0.451201568	0.216541569
  480	L	D	0.459795711	0.404684507	46	N	K	0.450854268	0.293319843
  772	E	G	0.459510918	0.312503946	42	E	[stop]	0.450047213	0.226279727
  369	A	P	0.459368992	0.154954523	20	K	N	0.449773662	0.196721642
  148	G	C	0.459321913	0.21989387	285	H	N	0.44861581	0.243329874
  565	E	[stop]	0.459284191	0.257970072	47	L	V	0.448453393	0.267732388
  472	K	N	0.458126194	0.217353923	953	D	E	0.448187279	0.183598076
  19	T	K	0.458002489	0.250652905	8	K	E	0.447865624	0.173510738
  550	F	L	0.457885561	0.135416611	255	K	N	0.447654062	0.257753112
  642	E	D	0.457477443	0.18048994	965	Y	[stop]	0.447638184	0.206848878
  761	F	L	0.457399802	0.126293846	381	L	V	0.447548148	0.24623578
  104	P	H	0.457206235	0.205670388	938	Q	K	0.44750144	0.297903846
  588	G	C	0.457151433	0.254991865	719	S	C	0.4472033	0.232249869
  516	F	L	0.456927783	0.127509134	89	Q	K	0.447094951	0.222907496
  147	K	N	0.456444496	0.280029247	735	R	L	0.447058488	0.220193339
  651	P	H	0.456356549	0.186081926	673	E	G	0.446968171	0.213951556
  2	E	D	0.456056175	0.35763481	126	G	C	0.446802066	0.204738022
  643	V	G	0.455368156	0.295796806	919	H	D	0.446668628	0.327432207
  524	K	N	0.45482233	0.143701874	23	G	V	0.446595867	0.2102612
  18	N	K	0.454706199	0.199478283	733	M	1	0.446594817	0.174646778
  5	R	T	0.45449471	0.277079709	490	R	G	0.435740618	0.182925074
  310	Q	E	0.446297431	0.123674296	789	E	G	0.435579914	0.162786893
  729	L	V	0.445993097	0.433135394	603	--	LE	0.43556049	0.202470667
  455	W	L	0.445597501	0.281894997	442	R	S	0.435504028	0.210966357
  215	G	V	0.445352945	0.205217458	714	R	I	0.435462316	0.200883442
  135	P	T	0.44528202	0.217449002	8	K	R	0.435212211	0.195908908
  936	R	T	0.445259832	0.32221387	854	N	D	0.43513717	0.067943636
  519	Q	K	0.444720886	0.28933765	335	E	[stop]	0.434927464	0.21407853
  656	G	R	0.444552088	0.279063867	915	G	R	0.434895859	0.195491247
  613	G	R	0.444378039	0.117584873	762	G	C	0.434868342	0.215911162
  16	D	Y	0.44433236	0.241975919	3	I	T	0.434607673	0.107252687
  5	R	K	0.443724261	0.262708705	406	E	[stop]	0.434574625	0.271888642
  3	I	M	0.443191661	0.128675121	710	V	A	0.434488312	0.161462791
  523	V	L	0.443126307	0.088900743	594	E	Q	0.434478655	0.199232108
  760	G	C	0.442544743	0.174174731	601	L	M	0.433295669	0.21298138
  27	P	T	0.442229152	0.271402709	194	---	DFY	0.433205	0.315807396
  694	G	D	0.441607057	0.430247861	79	A	S	0.433187114	0.14702693
  695	E	D	0.440698297	0.174763691	913	NC	FS	0.432811714	0.214195068
  96	M	I	0.440309501	0.212758418	955	R	S	0.432632415	0.15138175
  234	G	V	0.44028737	0.19450919	793	------	SKTYL (SEQ	0.432421193	0.207758327
  							ID NO: 3715)
  385	E	D	0.440128169	0.19408182	171	P	H	0.432364213	0.194710101
  744	Y	H	0.439198298	0.25211241	560	N	S	0.432346515	0.239882019
  519	Q	H	0.438343378	0.164581049	370	---	GYK	0.432297106	0.219290605
  385	E	[stop]	0.438258279	0.212771705	321	P	Q	0.432271564	0.211438092
  793	S	R	0.438010456	0.160112082	979	LE[stop]GS-	VSSKDLRA	0.432126183	0.250028634
  						PG (SEQ ID	(SEQ ID NO:
  						NO: 3251)	3820)
  726	A	S	0.437983799	0.129329735	21	K	E	0.431813708	0.20570077
  953	D	Y	0.437888499	0.29124605	348	C	W	0.431395847	0.285738532
  203	E	[stop]	0.437866757	0.193004717	712	Q	E	0.430794328	0.137430622
  887	G	V	0.437831028	0.150855683	867	V	A	0.430546539	0.112438125
  189	G	R	0.437816984	0.195105194	902	H	N	0.430482041	0.210989962
  672	P	L	0.437768207	0.1420574	232	C	R	0.430431738	0.130635142
  906	Q	R	0.437668081	0.257388395	164	E	[stop]	0.43010378	0.307258004
  887	G	R	0.436446894	0.261046568	926	L	V	0.42049552	0.169568285
  6	I	T	0.436255483	0.311769796	873	S	R	0.420222785	0.189220359
  751	M	R	0.436212653	0.194544034	823	R	G	0.420141589	0.140425724
  115	V	A	0.436134597	0.191229151	703	T	A	0.419927183	0.299947391
  348	C	R	0.429790014	0.254295816	265	K	N	0.419762272	0.205398427
  13	L	R	0.429496589	0.209797858	904	P	L	0.419717349	0.24717221
  11	R	W	0.429311947	0.298268587	315	G	A	0.419275038	0.167267502
  944	Q	E	0.429084418	0.194128082	346	M	I	0.418933456	0.153077303
  974	K	E	0.428778767	0.120819051	301	V	A	0.418922077	0.253824177
  935	L	M	0.428357966	0.408223034	545	I	M	0.418607437	0.264461321
  131	Q	E	0.427961752	0.108783149	676	P	T	0.41817469	0.167866208
  961	W	R	0.427770336	0.153009954	516	F	S	0.418152987	0.18301751
  508	F	L	0.427277307	0.150834085	790	G	V	0.417872524	0.17800118
  732	D	Y	0.427260152	0.232782252	890	G	V	0.417424955	0.242331279
  876	S	G	0.427219565	0.1654476	684	L	P	0.41697175	0.237298169
  36	M	I	0.426965901	0.18021585	369	A	T	0.416965887	0.158164268
  699	E	[stop]	0.426936027	0.247620152	890	G	R	0.416918523	0.30183511
  624	R	G	0.426915666	0.161800086	515	A	T	0.416763488	0.158965629
  687	-----	PTHTL (SEQ	0.426399688	0.235010897
  		ID NO: 3626)
  176	A	G	0.425859136	0.154112817	903	R	G	0.416689964	0.149830948
  256	K	N	0.425760398	0.195398586	898	K	[stop]	0.416641263	0.154852179
  904	P	A	0.425684716	0.273763449	632	L	V	0.416523782	0.131108293
  859	Q	K	0.425619083	0.166409301	126	G	D	0.41639346	0.171080754
  222	G	[stop]	0.425285813	0.299517445	151	H	R	0.41621118	0.192083944
  20	K	E	0.425128158	0.147645138	480	L	P	0.4153828	0.153349872
  327	G	C	0.425002655	0.239317573	569	M	T	0.415261579	0.12705723
  530	L	P	0.423859206	0.240275284	819	A	S	0.414776737	0.173259385
  175	E	Q	0.423850119	0.242087732	212	E	[stop]	0.414560972	0.214325617
  797	L	P	0.423394833	0.254739368	104	P	T	0.414121539	0.241680787
  351	K	M	0.423313443	0.177944606	765	G	A	0.413859942	0.202334164
  912	L	M	0.423204978	0.27824291	862	--	VK	0.413059952	0.195129021
  188	F	L	0.422539663	0.187750751	210	P	A	0.412638448	0.228860931
  850	I	M	0.422459968	0.218452121	824	V	A	0.412207035	0.173953175
  391	K	N	0.422162984	0.158915852	736	N	K	0.411883437	0.18403448
  894	-	S	0.42194087	0.23660887	13	L	H	0.411795935	0.405614507
  758	S	R	0.420859106	0.119214586	844	L	V	0.411372197	0.244473235
  941	K	N	0.420814047	0.266042931	973	W	L	0.403521777	0.16358494
  381	L	P	0.42076192	0.122089029	976	A	S	0.403444209	0.261893297
  564	G	C	0.411344604	0.228204596	180	L	P	0.403389637	0.163854455
  694	G	R	0.41123482	0.211796515	220	A	S	0.402957864	0.279961071
  977	V	L	0.411157664	0.380351062	894	------	SLLKK (SEQ	0.402797711	0.216370575
  							ID NO: 3720)
  142	E	K	0.410509302	0.15102557	739	R	I	0.402772732	0.234602886
  4	K	E	0.410380978	0.274892917	548	E	[stop]	0.402765683	0.262561545
  890	G	D	0.410337543	0.240602631	764	Q	K	0.402617217	0.220740512
  409	H	D	0.410132391	0.22531365	723	A	D	0.402461227	0.236080429
  563	S	C	0.409998896	0.206123321	934	F	L	0.402458138	0.384373835
  793	S	N	0.409457982	0.067541166	42	E	D	0.401939693	0.171540664
  705	Q	H	0.409365382	0.15278139	956	A	G	0.401859954	0.23877341
  515	A	D	0.409252018	0.206051204	771	A	D	0.401428057	0.231350403
  382	S	R	0.408669778	0.157144259	15	K	M	0.401237871	0.256454456
  97	S	N	0.408564877	0.109922347	298	A	V	0.401000777	0.140487597
  624	R	I	0.40845718	0.228955853	128	A	P	0.400992369	0.173078759
  568	P	T	0.408066084	0.284742394	511	Q	H	0.400978135	0.171613013
  702	R	S	0.408063786	0.129537489	26	G	V	0.400800405	0.212307845
  796	Y	N	0.40788333	0.311628718	591	------	QGREFI (SEQ	0.400574847	0.190655853
  							ID NO: 3636)
  897	K	R	0.407876662	0.136002906	156	G	S	0.400389686	0.306653761
  292	A	V	0.407642755	0.163883385	728	N	S	0.400298817	0.177178828
  741	L	Q	0.407532982	0.11928093	917	------	ETHADE	0.400170477	0.15562198
  							(SEQ ID NO:
  							3401)
  315	G	C	0.407147181	0.218556644	640	R	G	0.399931978	0.200741
  -1	S	Y	0.407080752	0.324937034	254	I	M	0.39981124	0.209846066
  945	T	I	0.407011152	0.285905433	644	L	P	0.399481964	0.165702888
  695	E	[stop]	0.406081569	0.227028835	549	A	S	0.399416255	0.189530269
  956	A	S	0.405686952	0.185566124	528	L	V	0.399354304	0.147818268
  752	L	M	0.405575007	0.172103348	502	I	V	0.399285899	0.256373682
  45	E	[stop]	0.405531899	0.162357698	79	A	D	0.399080303	0.154917165
  487	G	C	0.405450681	0.290615306	753	I	M	0.399024046	0.268887392
  310	Q	R	0.405123752	0.12048192	588	G	D	0.398941525	0.112261489
  791	L	P	0.404916001	0.108993438	873	S	G	0.392619693	0.143564629
  767	R	I	0.404746394	0.223610078	414	G	D	0.392615344	0.149137614
  538	G	C	0.404409405	0.233295785	237	A	G	0.392578525	0.167793454
  584	P	A	0.403953066	0.108926305	479	E	[stop]	0.392365621	0.272905538
  552	A	D	0.403929388	0.192995621	752	L	V	0.392234134	0.171880044
  648	N	D	0.403814843	0.290734901	692	R	I	0.391963575	0.221910688
  722	Y	H	0.398538883	0.164012123	683	s	Y	0.39187962	0.197184801
  550	-	G	0.398527591	0.353355602	568	P	s	0.391506615	0.094807068
  133	C	R	0.398285042	0.283233819	114	P	T	0.391456539	0.163794482
  591	--	QG	0.398079043	0.133460692	341	V	A	0.391246425	0.087691935
  877	V	L	0.398057665	0.212468549	50	K	R	0.39108021	0.159163965
  958	V	A	0.398007545	0.130004197	698	K	R	0.390885992	0.181654156
  903	R	I	0.39789959	0.321002606	979	L-	V[stop]	0.3907803	0.18994351
  118	G	D	0.397657151	0.192339782	932	W	G	0.390757599	0.185057669
  745	A	S	0.397594938	0.285476509	519	Q	R	0.390675235	0.117792262
  914	C	F	0.397278541	0.29475166	140	K	E	0.390615529	0.123713502
  461	---	SFV	0.39704755	0.20205322	40	L	P	0.390579865	0.194510846
  637	---	TFE	0.396824735	0.209304074	978	-	[stop]	0.390537744	0.255501032
  855	R	M	0.396780958	0.191874811	509	S	T	0.390466368	0.117704569
  142	E	[stop]	0.396624103	0.229993954	465	E	[stop]	0.390424913	0.211758729
  108	D	N	0.396298431	0.15939576	88	F	S	0.390363974	0.156430305
  730	-------	ADDMVRN	0.395727458	0.207712648	429	E	[stop]	0.390336598	0.135919503
  		(SEQ ID NO:
  		3305)
  241	T	I	0.395690613	0.131948289	783	---	TAK	0.390178711	0.143499076
  641	R	I	0.395315387	0.202249461	442	R	M	0.390097432	0.262199628
  364	F	L	0.395209211	0.112951976	453	T	A	0.389911631	0.312187594
  739	R	G	0.395162717	0.191317885	923	Q	H	0.389855175	0.353446475
  446	A	S	0.39510798	0.254001902	666	V	A	0.389840585	0.169825945
  593	R	[stop]	0.395071199	0.196636879	499	E	D	0.38958943	0.172940321
  168	L	P	0.39502304	0.27101743	930	R	G	0.389517964	0.2357312
  890	G	C	0.394653545	0.224530018	847	------	EGQITY	0.389324278	0.122951036
  							(SEQ ID NO:
  							3387)
  677	--	LS	0.394551417	0.187547463	846	V	L	0.389120343	0.259313474
  47	L	R	0.394492318	0.238759289	908	K	N	0.38907418	0.225076472
  339	N	S	0.394482682	0.152047471	975	P	T	0.388901662	0.256059318
  316	R	G	0.394439897	0.159274636	783	T	R	0.381262501	0.118770396
  206	H	N	0.394299838	0.156799046	916	F	V	0.380756944	0.281228145
  651	P	A	0.394024946	0.151434436	450	A	T	0.38074186	0.136570467
  441	R	G	0.393551449	0.150649913	906	Q	E	0.380700478	0.285392821
  325	L	P	0.393343386	0.140601419	29	K	[stop]	0.380574061	0.171976662
  589	K	N	0.3926379	0.261890195	936	R	I	0.38042421	0.204558309
  149	K	N	0.38882454	0.171027465	754	F	I	0.380277272	0.145574058
  691	L	P	0.388805401	0.14397393	315	G	S	0.380117687	0.143338421
  207	P	A	0.387921412	0.102883658	89	Q	[stop]	0.379768129	0.102222221
  11	-	S	0.387747808	0.379461072	289	G	C	0.379664161	0.235845043
  638	F	L	0.387272475	0.168477543	750	A	T	0.379378398	0.182932261
  558	V	L	0.386662896	0.254612529	216	G	C	0.379274317	0.176888646
  816	I	V	0.386659025	0.185203822	303	W	C	0.379215164	0.182222922
  680	F	L	0.386638685	0.211225716	295	N	K	0.379144284	0.378487654
  329	P	T	0.386489681	0.220048383	919	H	Y	0.379137691	0.321018649
  576	D	G	0.386151413	0.113653327	726	A	D	0.379067543	0.145080733
  225	G	V	0.386137184	0.239109613	133	C	S	0.378841599	0.162936296
  22	A	G	0.385839168	0.336984972	497	E	[stop]	0.378292682	0.202801468
  146	D	E	0.385277721	0.095712474	444	E	K	0.378042967	0.318660643
  507	G	R	0.385233777	0.212044464	693	I	M	0.378036899	0.225823359
  523	V	I	0.385109283	0.152511446	587	F	L	0.377947216	0.117981043
  501	S	G	0.385073546	0.140125388	291	E	D	0.377733323	0.142365006
  763	R	L	0.38502172	0.191531655	85	W	S	0.377648166	0.097279693
  705	Q	E	0.384851421	0.17568818	165	R	M	0.377647305	0.161201002
  82	H	D	0.383907018	0.103874584	569	M	I	0.377387614	0.195898876
  794	K	N	0.383803253	0.195192527	247	I	T	0.37729282	0.165305688
  979	LE[stop]GSPG	VSSKDLR	0.38375861	0.240184851	513	-	N	0.377106209	0.14731404
  	(SEQ ID NO:	(SEQ ID NO:
  	3251)	3819)
  894	S	R	0.383344078	0.273603195	754	F	L	0.376911731	0.164266559
  639	E	[stop]	0.383174826	0.193125393	21	K	[stop]	0.376868031	0.199468055
  655	I	M	0.383102617	0.208514699	268	A	T	0.376839819	0.129211081
  261	L	V	0.382856978	0.19611714	672	P	T	0.376830532	0.204970386
  480	L	R	0.382841683	0.252187108	735	R	[stop]	0.376814295	0.09621637
  489	L	V	0.38262991	0.16124555	147	K	E	0.376789616	0.140417542
  134	Q	E	0.382580711	0.180510987	904	P	R	0.37666328	0.185106225
  650	--	PA	0.382487274	0.372015728	712	Q	H	0.376030218	0.227827888
  630	P	H	0.381699363	0.211396524	92	P	T	0.368981275	0.236532466
  21	K	R	0.381603442	0.1634713	292	A	T	0.36879806	0.193425471
  677	---	LSR	0.381372384	0.163400905	465	E	D	0.368752489	0.224455423
  284	P	T	0.381276843	0.171865261	189	--------	GQRALDFY	0.368745456	0.227136846
  							(SEQ ID NO:
  							3448)
  2	E	V	0.375325693	0.197955097	805	T	A	0.368671629	0.11272788
  184	S	I	0.375300851	0.252137747	947	K	E	0.368551642	0.227968732
  163	H	D	0.3751698	0.208290707	148	G	D	0.36788165	0.139635081
  677	L	P	0.375131489	0.090158552	129	C	W	0.367758112	0.199915902
  44	L	P	0.374906966	0.249472829	129	C	[stop]	0.367708546	0.192643557
  606	G	V	0.374739683	0.285964981	98	R	T	0.367673403	0.174398036
  937	S	G	0.374669762	0.248499289	478	C	W	0.367598979	0.111931907
  727	K	N	0.374273348	0.164838535	228	L	M	0.367328433	0.24869867
  734	V	A	0.374244799	0.121134147	547	P	H	0.367324308	0.220855574
  902	H	Q	0.374087073	0.175219897	105	K	N	0.367245695	0.155463083
  398	F	L	0.373909011	0.239653674	597	W	R	0.367058721	0.142955463
  845	K	N	0.373742099	0.158752661	328	F	L	0.366955458	0.100787228
  822	D	N	0.373424135	0.138952336	469	E	[stop]	0.366917206	0.180496612
  136	L	M	0.372880562	0.202180857	130	S	T	0.366622403	0.127263853
  543	K	E	0.372880222	0.146877967	283	Q	E	0.366530641	0.247989672
  244	Q	H	0.372873077	0.184616643	958	V	L	0.366470474	0.270699212
  403	L	R	0.372697479	0.330913239	673	E	Q	0.366346139	0.219545941
  679	R	I	0.372176403	0.370324076	118	G	C	0.366255984	0.265748809
  738	A	D	0.372074442	0.291834989	848	G	V	0.366195099	0.200861406
  155	F	L	0.371845015	0.114679195	923	Q	L	0.366184575	0.233234243
  174	P	R	0.371603352	0.137168151	357	K	R	0.366148171	0.185792239
  919	H	N	0.371556993	0.327290993	623	------	RRTRQD	0.365486053	0.26101804
  							(SEQ ID NO:
  							3683)
  944	Q	H	0.37144256	0.338788753	85	W	C	0.365346783	0.146084706
  164	E	G	0.370935537	0.216755032	376	-----	ALLPY (SEQ	0.365321474	0.191317647
  							ID NO: 3319)
  197	S	G	0.370856052	0.178568608	356	E	D	0.365050343	0.136074432
  840	N	K	0.370814634	0.142530771	262	A	S	0.365012551	0.204615446
  13	L	M	0.370495333	0.29466367	774	Q	K	0.359747336	0.182131652
  488	D	N	0.370055302	0.226946737	439	E	D	0.359587685	0.134619305
  929	A	P	0.370027168	0.168555798	198	I	T	0.359370526	0.173615874
  580	L	V	0.36995513	0.139984948	156	G	C	0.359055571	0.173590319
  135	P	A	0.369933138	0.10604161	399	G	C	0.358922413	0.255017848
  342	D	Y	0.369924443	0.189241086	59	S	T	0.358703019	0.109042363
  959	ET	AV	0.369879201	0.114167508	93	V	M	0.358615623	0.161948363
  557	T	A	0.369640872	0.087836911	674	G	[stop]	0.358503233	0.220631194
  6	I	V	0.369460173	0.192497769	539	K	N	0.358074633	0.087009621
  765	G	S	0.3649426	0.100657536	709	E	D	0.357944736	0.136689683
  717	----	GYSR (SEQ	0.364903794	0.186125273	120	E	G	0.357933511	0.168382586
  		ID NO: 3457)
  199	H	Y	0.364586783	0.168211628	494	F	L	0.357874746	0.139367085
  796	Y	H	0.364521403	0.145575579	272	G	V	0.357428523	0.207170798
  237	A	P	0.364453395	0.150681341	527	N	I	0.357320226	0.086164887
  768	T	A	0.36435574	0.18512185	236	V	A	0.357249373	0.125737046
  513	N	D	0.364305814	0.16260499	974	K	N	0.357242055	0.190403244
  823	RV	LS	0.364237044	0.11377221	10	RR	PG	0.356712463	0.324298272
  656	G	A	0.364010939	0.135958583	39	D	Y	0.356585187	0.235756832
  276	P	T	0.363878534	0.201304545	579	N	S	0.3558347	0.181516226
  214	I	V	0.363876419	0.142178855	214	I	M	0.355779849	0.142887254
  300	I	V	0.363823907	0.234997169	843	E	[stop]	0.355689249	0.225441771
  769	F	S	0.363687361	0.079831237	526	----	LNLY (SEQ	0.355597159	0.179351732
  							ID NO: 3563)
  182	T	R	0.363686071	0.201742372	667	I	M	0.355548811	0.239632986
  677	L	V	0.363578004	0.138045802	559	I	V	0.355478406	0.171281999
  796	Y	C	0.363566923	0.281557418	706	A	S	0.355431605	0.116949175
  5	R	S	0.363258223	0.211185531	11	RR	TS	0.35536352	0.272262643
  298	A	S	0.36320777	0.211187305	865	L	Q	0.355287262	0.164676142
  594	E	[stop]	0.36278807	0.205352129	946	N	K	0.355277474	0.180093688
  105	K	R	0.362205009	0.140104618	689	HI	PV	0.355052108	0.144577201
  907	E	Q	0.362024887	0.226228418	898	K	N	0.354894826	0.200062158
  509	S	G	0.361807445	0.13953396	950	--	GN	0.354845909	0.167057981
  110	R	I	0.361752083	0.138681372	332	P	T	0.354796362	0.20270742
  406	E	Q	0.361750488	0.303638253	323	Q	E	0.354759964	0.249399571
  470	A	V	0.361349462	0.10686226	42	E	A	0.354721226	0.213005644
  4	K	[stop]	0.36129388	0.179352157	644	L	V	0.351676716	0.163471035
  362	K	E	0.361196668	0.232368389	78	K	E	0.35167205	0.128519193
  713	R	G	0.3607467	0.181817788	272	G	C	0.351365895	0.208785029
  857	K	N	0.360715256	0.172046815	157	--------	RCNVSEHE	0.351115058	0.126463217
  							(SEQ ID NO:
  							3661)
  120	E	D	0.36030686	0.214810208	883	S	R	0.351093302	0.143213807
  277	K	E	0.36002957	0.210892547	917	E	V	0.350763439	0.206641731
  477	RCELK (SEQ	SFSSH (SEQ	0.360015336	0.177473578	843	E	D	0.350569244	0.142523946
  	ID NO: 3285)	ID NO: 3696)
  532	I	T	0.359759307	0.145072322	870	D	Y	0.350431061	0.194706521
  22	A	T	0.354629728	0.083320918	393	F	V	0.35027948	0.168738586
  948	T	S	0.354488334	0.198422577	162	E	K	0.350236681	0.12523983
  16	D	E	0.354450775	0.187189495	119	N	D	0.350147467	0.235898677
  170	S	Y	0.354344814	0.160709939	306	L	M	0.349889759	0.165537841
  862		VKDLS (SEQ	0.354059938	0.179170942	110	R	T	0.349523294	0.289863999
  		ID NO: 3781)
  249	E	[stop]	0.354016591	0.294486267	976	A	D	0.34941868	0.241042383
  531	I	M	0.353941253	0.095481374	914	C	W	0.349231308	0.169568161
  266	D	H	0.35392753	0.237329699	115	V	M	0.349160578	0.17839763
  859	Q	E	0.353923377	0.126451964	863	K	N	0.348978081	0.175915912
  113	I	V	0.353631334	0.187941798	830	K	R	0.348789882	0.11782242
  136	L	P	0.353572714	0.240617705	564	G	S	0.348654331	0.240781896
  503	L	M	0.353400839	0.174768283	647	S	I	0.348570495	0.163208612
  51	P	R	0.353321532	0.126698252	617	E	D	0.348384104	0.103608149
  179	E	D	0.353270131	0.108592116	262	A	T	0.348231917	0.222328473
  31	L	V	0.353260601	0.168619621	713	R	I	0.348163293	0.202182526
  502	I	F	0.353258477	0.139633145	893	L	P	0.348133135	0.24849422
  378	L	M	0.353221613	0.189998728	202	R	G	0.347997162	0.177282082
  890	G	A	0.353138339	0.149947604	806	S	Y	0.347673828	0.200543155
  913	N	K	0.353092797	0.294888192	391	K	R	0.347608788	0.122435715
  956	A	D	0.352997131	0.204713576	683	S	C	0.34755615	0.102168244
  158	C	W	0.352758393	0.130405614	446	A	T	0.347296208	0.236243043
  157	----	RCNV (SEQ	0.352566351	0.116984328	282	P	A	0.347073665	0.253113968
  		ID NO: 3658)
  771	A	G	0.352390901	0.141133059	580	L	P	0.347062657	0.078573865
  227	A	G	0.352335693	0.141777326	895	L	P	0.347059979	0.152424473
  202	RE	G-	0.352321171	0.210660545	929	A	T	0.34702013	0.306789031
  99	V	F	0.352314021	0.162936095	555	F	L	0.343270194	0.098281937
  643	V	E	0.352268894	0.209333581	294	N	D	0.343264324	0.126839815
  41	R	I	0.352205261	0.321737078	553	N	D	0.342736197	0.153294035
  387	R	P	0.352184692	0.159814147	893	L	M	0.342736077	0.179172833
  539	K	E	0.351957196	0.146275596	951	N	K	0.342592943	0.278844401
  478	C	F	0.351788403	0.313141443	51	P	T	0.342576973	0.1929364
  942	K	E	0.351775756	0.256493816	649	I	T	0.342534817	0.270208479
  36	M	I	0.351715805	0.097577134	175	E	D	0.342455704	0.202360388
  108	D	Y	0.347014656	0.291577591	823	R	S	0.341965728	0.273152096
  258	E	[stop]	0.34694757	0.281979872	219	C	R	0.341954249	0.136482174
  673	E	A	0.346691172	0.265253287	283	Q	R	0.341949927	0.224313066
  950	G	D	0.346646349	0.128298199	444	E	[stop]	0.341881438	0.217688103
  792	P	T	0.346487957	0.236073016	649	I	V	0.341655494	0.148589673
  673	E	[stop]	0.346388527	0.198074161	854	N	K	0.341614877	0.157948422
  150	P	R	0.34632855	0.278480507	514	C	S	0.34160113	0.231141571
  456	L	P	0.345951509	0.161500864	623	----	RRTR (SEQ	0.341527608	0.187073234
  							ID NO: 3681)
  790	G	R	0.345911786	0.179210019	585	L	M	0.341496703	0.21431877
  647	S	T	0.345819661	0.158521168	211	--	LE	0.341207432	0.169230112
  542	F	S	0.345619595	0.191970857	544	K	E	0.341142267	0.208342511
  841	G	D	0.345447865	0.129392183	478	C	R	0.341091687	0.148433288
  57	P	A	0.345371652	0.147875225	858	R	G	0.340977066	0.206052559
  578	P	R	0.345346371	0.12075926	172	H	D	0.340873936	0.298188428
  793	S	I	0.345235059	0.262377638	16	D	A	0.340771918	0.308121625
  453	T	S	0.345118763	0.097101409	525	K	N	0.340626838	0.147516442
  651	P	R	0.345088622	0.208316961	532	I	V	0.340576058	0.099088927
  556	Y	[stop]	0.345070339	0.114662396	520	K	[stop]	0.34056167	0.228510512
  86	E	[stop]	0.344943839	0.21976554	743	Y	[stop]	0.340397436	0.102396798
  646	S	G	0.344888595	0.154435246	344	W	C	0.340364668	0.176812201
  592	G	C	0.34478874	0.240350052	220	A	G	0.340276978	0.133945921
  49	K	N	0.344659946	0.130706516	186	G	V	0.340265085	0.116877863
  586	A	D	0.344294219	0.15117877	694	G	C	0.340225482	0.309935909
  166	L	V	0.34415435	0.139737754	411	E	Q	0.340144727	0.282548314
  726	A	P	0.344144415	0.164178243	406	E	G	0.340120492	0.140875629
  666	V	L	0.344130904	0.155760915	573	F	L	0.340030507	0.166015227
  749	D	H	0.344052929	0.242192495	52	E	[stop]	0.336207682	0.211986135
  486	Y	C	0.34395063	0.130965705	299	Q	E	0.336024324	0.156699489
  134	Q	K	0.343594633	0.210709609	183	YS	WM	0.335855997	0.179538112
  91	D	H	0.34352508	0.153686099	194	D	Y	0.335755348	0.131644969
  40	LR	PV	0.343506493	0.155292328	213	Q	R	0.335726769	0.209853061
  12	R	T	0.343490891	0.187270573	802	A	D	0.33571172	0.168573673
  653	N	D	0.343487264	0.148663517	163	H	N	0.33571123	0.197315666
  52	E	Q	0.343438912	0.247941408	943	Y	C	0.335604909	0.172843558
  8	K	Q	0.343298615	0.279455517	118	G	S	0.335544316	0.125891126
  458	A	G	0.339794018	0.171435317	758	S	G	0.335513561	0.149050456
  675	C	[stop]	0.339687357	0.208292109	941	K	[stop]	0.335374859	0.192348189
  576	D	Y	0.339621402	0.21774439	279	-------	TLPPQPH	0.335305655	0.144688363
  							(SEQ ID NO:
  							3755)
  787	A	S	0.339526186	0.318305548	632	LF	PV	0.335263893	0.113883053
  537	G	C	0.339454064	0.174110887	894	------	SLLKKR	0.335263893	0.141289409
  							(SEQ ID NO:
  							3721)
  185	--	LG	0.339451721	0.186103153	943	Y	[stop]	0.335115123	0.291608446
  844	L	P	0.339318044	0.191881119	38	P	R	0.33481965	0.113021039
  712	Q	K	0.339288003	0.193891353	616	I	F	0.334790976	0.107803908
  591	Q	R	0.339223049	0.160616368	134	Q	H	0.334549336	0.158461695
  169	L	P	0.339210958	0.127439702	186	G	C	0.334321874	0.156717674
  923	-----	QAALN (SEQ	0.339143383	0.169170821	184	S	G	0.334296555	0.223929833
  		ID NO: 3631)
  623	R	S	0.339131953	0.245088648	765	G	C	0.33423513	0.213904011
  589	K	Q	0.33901987	0.177422866	687	P	T	0.334191461	0.22545553
  522	G	V	0.338985606	0.226282565	803	---	QYT	0.33418367	0.096860089
  204	S	T	0.338673547	0.170845305	374	Q	R	0.334175524	0.104826318
  698	K	E	0.338580473	0.129708045	455	W	C	0.334165051	0.186741008
  497	E	V	0.338306724	0.13489235	552	-----	ANRFY (SEQ	0.333923423	0.258649392
  							ID NO: 3327)
  23	G	S	0.338162596	0.15304761	407	K	R	0.333913165	0.142719617
  29	K	R	0.337989172	0.147861886	175	E	K	0.333834455	0.196225639
  716	G	V	0.337974681	0.202399788	610	-----	LANGR (SEQ	0.333428825	0.102899397
  							ID NO: 3536)
  703	T	S	0.337889214	0.141977828	127	F	I	0.329561201	0.268089932
  979	LE[stop]GSPG	VSSKDLE	0.337814175	0.168342402	837	T	S	0.329510402	0.099725089
  	(SEQ ID NO:	(SEQ ID NO:
  	3251)	3805)
  240	L	M	0.3377179	0.151631422	704	I	T	0.329114566	0.113551049
  950	G	C	0.337265205	0.234973706	387	R	L	0.328928103	0.199189713
  7	N	S	0.337036852	0.185037778	171	P	R	0.328685191	0.279786527
  64	A	P	0.336967696	0.255179815	767	R	T	0.328611454	0.173820273
  795	T	S	0.336837648	0.117371137	597	W	L	0.328585458	0.282536549
  480	L	Q	0.336803159	0.213915334	955	R	G	0.328533511	0.252801289
  600	L	V	0.336801383	0.230766925	629	E	[stop]	0.328472442	0.226070443
  175	E	[stop]	0.336712437	0.187755487	699	E	G	0.328340286	0.161755276
  63	R	S	0.336640982	0.183725757	564	G	A	0.328244232	0.11512512
  394	A	P	0.336388779	0.125201204	129	C	F	0.327975914	0.184885596
  230	----	DACM (SEQ	0.333428825	0.108521075	26	G	S	0.327861024	0.174859434
  		ID NO: 3341)
  848	G	S	0.333406808	0.165245749	199	H	N	0.327823226	0.25447122
  630	P	R	0.333389309	0.182782946	701	Q	R	0.327746296	0.151982714
  442	R	G	0.333281333	0.186150848	186	G	D	0.327613843	0.101552272
  836	M	T	0.33320739	0.215623837	422	E	D	0.327579534	0.227939955
  222	G	V	0.333139545	0.173506426	924	A	T	0.327501843	0.29494568
  21	K	T	0.333022379	0.190202016	176	A	P	0.32741005	0.239900376
  696	S	I	0.332955668	0.138037632	499	E	K	0.327284744	0.159757942
  635	A	T	0.332902532	0.130552446	546	K	R	0.327156617	0.166513946
  551	E	G	0.332833114	0.158314375	556	Y	H	0.327151432	0.118520339
  780	D	Y	0.332787267	0.203141483	548	---	EAF	0.326965289	0.171181066
  47	L	M	0.332771785	0.228474741	901	S	I	0.326880206	0.320148616
  347	V	L	0.332766547	0.164853137	14	V	I	0.326870011	0.276842054
  841	G	C	0.332584425	0.2483922	814	F	L	0.32685269	0.084563864
  593	R	I	0.332546881	0.22140312	157	------	RCNVSE	0.326801479	0.200654893
  							(SEQ ID NO:
  							3660)
  749	D	Y	0.332359902	0.199451757	250	H	R	0.326584294	0.078102923
  27	P	S	0.332358372	0.306966339	730	A	V	0.326443401	0.110931779
  276	P	H	0.332221583	0.26420075	497	E	Q	0.326193187	0.212891542
  293	Y	[stop]	0.332046234	0.133526657	536	K	R	0.326129704	0.20597101
  3	I	N	0.332004357	0.072687293	906	Q	P	0.326073598	0.193779388
  642	----	EVLD (SEQ	0.331972419	0.22538863	243	Y	D	0.326001836	0.130392708
  		ID NO: 3404)
  620	L	P	0.331807594	0.15763111	786	L	Q	0.32241581	0.22201146
  456	L	V	0.331754102	0.143226803	4	K	M	0.32231147	0.124043743
  130	S	G	0.331571239	0.167684126	781	W	R	0.322196176	0.263818038
  629	E	K	0.33154282	0.153428302	182	T	I	0.322044203	0.109310181
  950	G	V	0.331464709	0.229681218	888	R	G	0.322001059	0.172130189
  328	F	Y	0.331454046	0.090600532	388	K	N	0.321769292	0.13958088
  303	W	S	0.331070804	0.245928403	504	D	Y	0.321517406	0.182186572
  421	W	C	0.330779828	0.216037825	260	R	I	0.321461619	0.146534668
  351	K	R	0.330630005	0.142537112	695	E	Q	0.321451268	0.199405121
  498	A	T	0.33049042	0.166213318	960	T	A	0.321351275	0.243570837
  937	S	T	0.330380882	0.231058955	496	I	F	0.321275456	0.162860461
  592	OR	DN	0.329593548	0.300041765	454	D	H	0.321034191	0.123925099
  798	S	F	0.325769587	0.320454472	859	Q	H	0.321009248	0.15665955
  882	S	G	0.325732755	0.141569252	432	S	I	0.32093586	0.219919612
  759	R	G	0.325319087	0.080028833	120	E	Q	0.320905282	0.134126668
  576	D	V	0.325192282	0.239519469	359	E	[stop]	0.320840565	0.172779106
  309	W	[stop]	0.325098891	0.096106342	474	E	[stop]	0.320753733	0.198938474
  554	R	I	0.325075441	0.185726803	609	K	R	0.320654761	0.097190768
  483	Q	H	0.324598695	0.153049426	654	L	P	0.320340402	0.21351518
  979	E	VSSKDQ	0.324398559	0.118712651	344	W	G	0.32013599	0.133467654
  		(SEQ ID NO:
  		3823)
  834	G	C	0.324348652	0.175539945	629	E	D	0.319764058	0.097801219
  719	S	Y	0.324298439	0.22105488	631	A	D	0.319695703	0.120854121
  842	K	R	0.324267597	0.102772814	124	S	Y	0.319588026	0.148095027
  97	S	T	0.324252325	0.240123255	244	Q	R	0.319581236	0.174412151
  172	H	N	0.324047776	0.168532939	338	A	D	0.319500211	0.171228389
  692	R	G	0.324024313	0.134914995	634	V	L	0.3194918	0.113193905
  39	D	V	0.324012084	0.186802864	91	D	N	0.319468455	0.231799127
  776	T	I	0.323918216	0.153171775	740	D	E	0.319448668	0.093677265
  652	M	T	0.323898442	0.13705991	942	K	R	0.319440348	0.184998826
  611	A	V	0.323836429	0.18975125	146	D	Y	0.319268754	0.209601725
  658	D	G	0.323834837	0.116577804	513	N	K	0.319264079	0.180017602
  158	C	[stop]	0.323773158	0.093674966	366	Q	H	0.318971922	0.184226775
  887	G	A	0.32369757	0.19151617	477	R	G	0.318963003	0.179227033
  337	Q	H	0.323607141	0.165283008	947	K	R	0.318930494	0.25585521
  319	A	D	0.323458799	0.152084781	478	C	S	0.318576968	0.151506435
  215		GGNSCA	0.323334457	0.165215546	94	G	A	0.315344942	0.125574217
  		(SEQ ID NO:
  		3431)
  351	K	N	0.323273003	0.138737748	509	S	R	0.315237336	0.198196247
  878	-	I	0.323133111	0.265099492	715	A	S	0.314795788	0.184022977
  597	W	C	0.323039345	0.210227048	639	E	G	0.314490675	0.131536259
  85	W	G	0.3230112	0.140970302	485	W	R	0.314444162	0.077460473
  830	K	E	0.322976082	0.171606667	529	Y	[stop]	0.314338149	0.096977512
  193	--	LD	0.322600674	0.167338288	773	R	M	0.314128132	0.191934874
  350	V	A	0.32248331	0.252994511	227	A	D	0.313893012	0.086820124
  443	S	G	0.318453544	0.181417518	865	L	V	0.313870986	0.093939035
  766	K	E	0.318255467	0.119279294	25	T	S	0.313828907	0.165926738
  557	T	S	0.318254881	0.136960287	206	H	R	0.313540953	0.153060153
  39	D	E	0.318241109	0.177504749	33	V	I	0.313378588	0.092743144
  586	A	S	0.318046156	0.197164692	736	N	S	0.313292021	0.139875641
  270	A	P	0.317952258	0.133471459	613	G	A	0.313219371	0.139952239
  707	A	S	0.317797903	0.176472631	472	K	R	0.313201874	0.163543589
  173	K	N	0.317699885	0.158843579	149	---	KPH	0.313073613	0.111009375
  676	P	R	0.317616441	0.273323665	966	R	I	0.313069041	0.220268045
  409	H	N	0.31739526	0.238962249	847	E	[stop]	0.312986862	0.248850102
  878	N	D	0.317341485	0.123856244	892	A	V	0.312917635	0.236911004
  967	K	E	0.317328223	0.198885809	322	L	P	0.312907638	0.167614176
  405	L	M	0.317316848	0.232382071	947	K	N	0.312809501	0.23804854
  759	R	T	0.317284234	0.210047842	820	D	Y	0.312669916	0.196444965
  505	I	M	0.317274558	0.129635964	627	Q	E	0.312477809	0.180929549
  612	N	D	0.317252502	0.181380961	20	K	T	0.312450252	0.306509245
  862	V	A	0.317158438	0.090072044	914	C	G	0.312434698	0.246328459
  295	-N	LS	0.317076665	0.155046903	793	S	G	0.312385644	0.182436917
  165	R	G	0.317047785	0.17842685	411	E	D	0.312132984	0.213313342
  760	G	D	0.316786277	0.162885521	901	S	R	0.311953255	0.163461395
  244	Q	K	0.316600083	0.246636704	393	F	L	0.311946018	0.192991506
  238	S	Y	0.316596499	0.171458712	757	L	P	0.311927617	0.117197609
  475	F	L	0.316549309	0.192939087	702	R	G	0.311688104	0.266620819
  829	K	N	0.316494901	0.154808851	589	K	R	0.311588343	0.136320933
  28	M	I	0.31630177	0.188404934	717	G	R	0.311565735	0.080863714
  186	G	A	0.316262682	0.1767869	286	T	S	0.311321567	0.240949263
  679	R	G	0.316180477	0.112760057	150	P	T	0.311291496	0.13427262
  925	A	G	0.315901657	0.192750307	107	I	L	0.307707331	0.205313283
  892	A	P	0.315901657	0.129374073	776	T	A	0.307705621	0.113209696
  642	E	A	0.315758891	0.205380131	306	L	V	0.307515106	0.116397313
  629	E	G	0.315702888	0.119743865	651	P	T	0.307457933	0.189846398
  642	E	G	0.315673565	0.11044042	155	F	Y	0.307385155	0.165676404
  104	P	R	0.315607101	0.202791238	229	S	T	0.307373154	0.086318269
  807	K	E	0.315573228	0.117464708	517	I	V	0.307363772	0.108604289
  599	D	E	0.315416693	0.115740153	334	V	A	0.306982037	0.139604112
  578	P	A	0.311263999	0.106013626	614	R	K	0.306921623	0.187827913
  41	R	G	0.311016733	0.286865829	824	V	L	0.306719384	0.210851946
  781	W	S	0.310870839	0.281958829	723	A	V	0.306692766	0.140247988
  382	S	I	0.310857774	0.22558917	711	E	G	0.306675894	0.224133351
  723	A	T	0.310856537	0.118165477	499	E	Q	0.306671973	0.224590082
  451	A	G	0.310527551	0.159640493	104	P	S	0.306640385	0.162249455
  568	P	L	0.310447286	0.186724922	3	I	L	0.306608196	0.194776786
  216	G	S	0.310362762	0.143843218	702	R	K	0.306541295	0.149431609
  216	G	R	0.310272111	0.119909677	954	K	E	0.306525004	0.187285491
  89	Q	R	0.310167676	0.139047602	842	---	KEL	0.306410776	0.206532128
  433	K	R	0.310161393	0.097615554	466	G	C	0.30635382	0.179163452
  21	KA	NC	0.310061242	0.098851828	979	-----	VSSKD (SEQ	0.306277048	0.179502088
  							ID NO: 3799)
  							[stop]
  141	L	P	0.309573602	0.118441502	830	K		0.306086752	0.154175951
  425	D	Y	0.309531408	0.253195982	243	Y	F	0.306073033	0.15669665
  579	N	D	0.309484128	0.137585893	88	F	L	0.305867737	0.156711191
  825	L	V	0.309431153	0.160157183	149	K	E	0.305762803	0.092392237
  464	I	M	0.309049855	0.208541437	102	P	H	0.305663323	0.198476248
  710	V	L	0.309047105	0.126001585	554	----	RFYT (SEQ	0.305511625	0.122801047
  							ID NO: 3665)
  671	D	H	0.309035221	0.209514286	720	-	R	0.305347434	0.161540535
  735	R	P	0.309028904	0.132025621	128	A	G	0.305254739	0.159245241
  819	A	G	0.308778739	0.188847749	122	L	P	0.305222365	0.154910099
  2	E	G	0.308512084	0.159248809	792	P	S	0.305214901	0.160903917
  109	Q	H	0.308384304	0.180580793	312	L	P	0.305192803	0.183880511
  66	L	V	0.308337109	0.160085063	299	Q	[stop]	0.305119863	0.096364942
  93	V	L	0.308334538	0.186355769	668	A	T	0.305069729	0.135204642
  621	Y	[stop]	0.308307714	0.182192979	962	Q	R	0.302114892	0.192863031
  0	M	L	0.308276685	0.236934633	656	G	S	0.301941181	0.160658808
  857	K	E	0.308118374	0.128063493	526	L	P	0.301907253	0.200130867
  264	L	I	0.308089176	0.231951197	181	V	L	0.301627326	0.141701986
  646	S	T	0.307934288	0.163215891	602	S	G	0.301374384	0.168690577
  461	S	T	0.307923977	0.13026743	2	E	K	0.301361669	0.293245611
  937	S	N	0.307902696	0.280386833	46	N	S	0.301357514	0.121526311
  774	Q	L	0.30782826	0.179585187	71	T	S	0.301285774	0.182156883
  427	K	N	0.307771318	0.212433986	887	G	D	0.301271887	0.117733719
  422	E	G	0.307743696	0.21393123	121	R	S	0.301231571	0.167844846
  639	E	Q	0.304680843	0.266883075	108	D	V	0.301094262	0.261979025
  812	C	[stop]	0.304671385	0.223383408	979	LE[stop]GS-	VSSKDLQA	0.301043	0.222937332
  						PGI (SEQ ID	(SEQ ID NO:
  						NO: 3278)	3810)[stop]
  856	--	YK	0.304562199	0.117931145	73	Y	[stop]	0.300976299	0.109164204
  959	-------	ETWQSFY	0.304562199	0.204359044	645	D	H	0.300832783	0.189820783
  		(SEQ ID NO:
  		3403)
  640	R	[stop]	0.304365031	0.131009317	972	---	VWK	0.300386808	0.146545616
  968	KL	S[stop]	0.304328899	0.221090558	127	F	S	0.300342022	0.146847301
  24	K	N	0.304215048	0.239991354	571	V	A	0.300337937	0.156010497
  858	R	T	0.304052714	0.1448623	386	D	N	0.300273532	0.259491112
  530	L	M	0.303970715	0.250168829	381	L	M	0.300116697	0.157006178
  269	S	R	0.303928294	0.209763505	493	P	A	0.299995588	0.227049942
  251	Q	E	0.303459913	0.190095434	199	H	R	0.299830107	0.074234175
  340	E	Q	0.30343193	0.10804688	642	E	[stop]	0.299768631	0.20842894
  623	-	R	0.303430789	0.233394445	352	K	[stop]	0.299555207	0.106916877
  880	D	Y	0.30324465	0.244720194	314	I	V	0.299339024	0.237860572
  223	P	A	0.303031527	0.177373299	696	S	T	0.299269551	0.19370537
  899	R	T	0.302967154	0.112177355	554	R	G	0.299260223	0.263070996
  60	N	D	0.30295183	0.177064719	413	W	S	0.298889603	0.120871006
  966	R	S	0.302926375	0.099801177	973	W	[stop]	0.298886432	0.173734887
  687	P	A	0.302859855	0.188291569	1	Q	[stop]	0.298848883	0.253324527
  821	Y	C	0.302780706	0.154234626	59	S	G	0.298416382	0.178538741
  628	D	Y	0.302709978	0.176578494	717	G	[stop]	0.298317755	0.217662606
  952	--------	TDKRAFVE	0.302629733	0.089246659	348	C	S	0.298274049	0.13599769
  		(SEQ ID NO:
  		3741)
  540	L	V	0.302623885	0.094608809	707	A	G	0.298173789	0.189062395
  855	R	T	0.302608606	0.19469877	345	D	Y	0.295298688	0.153403354
  59	S	I	0.302606901	0.165051866	469	E	G	0.295269456	0.193145904
  272	G	D	0.302541592	0.185286895	495	A	T	0.295248074	0.179130836
  284	P	H	0.302498547	0.213421981	929	A	G	0.295233981	0.250007265
  342	--	TS	0.302413033	0.240972915	435	I	T	0.2952095	0.10707736
  43	R	W	0.302283296	0.149981215	586	A	T	0.295123473	0.125804414
  760	G	A	0.302207311	0.130376601	627	Q	R	0.295089748	0.147312376
  766	K	N	0.302181165	0.136382512	17	S	I	0.295022842	0.203345294
  478	CE	AQ	0.298056287	0.28697996	96	M	V	0.29492941	0.118289949
  915	G	A	0.298020743	0.21282862	83	V	M	0.294841632	0.151911965
  969	L	M	0.297993119	0.288243926	721	K	[stop]	0.294783263	0.121804362
  953	D	V	0.297929214	0.145206254	550	F	S	0.294772324	0.160417343
  485	W	G	0.297911414	0.242181721	538	G	A	0.29474804	0.174345187
  676	P	A	0.297863971	0.089640148	462	F	L	0.294742725	0.14185505
  4	K	T	0.297828559	0.161108285	822	D	H	0.294658575	0.162957386
  631	A	G	0.297777083	0.103836414	213	QI	PV	0.294575907	0.193654425
  250	H	P	0.29766948	0.081415922	658	D	N	0.294502464	0.107952026
  11	-	R	0.29755173	0.242218951	309	W	S	0.294338009	0.284836107
  274	A	T	0.297540582	0.172279995	835	W	C	0.294317109	0.120763755
  918	T	K	0.297381988	0.249593921	607	S	Y	0.294194742	0.192145848
  43	R	L	0.297375059	0.247052829	853	Y	[stop]	0.294188525	0.116100881
  51	P	A	0.29736536	0.241677851	895	L	M	0.294152124	0.189733578
  64	A	T	0.297190007	0.136022098	298	AQ	DR	0.294067945	0.080730567
  617	E	Q	0.297156994	0.256789508	221	S	T	0.293988985	0.161830985
  468		K	0.297121715	0.218726347	854	-----	NRYKRQ	0.29389502	0.164228467
  							(SEQ ID NO:
  							3597)
  705	Q	[stop]	0.297097391	0.129530594	184	---	SLG	0.29389502	0.133943716
  538	G	D	0.297030166	0.143641253	24	K	E	0.293893146	0.087429384
  697	Y	[stop]	0.29694611	0.165401562	903	R	T	0.293855808	0.156130706
  30	T	N	0.296922856	0.20113666	649	I	M	0.293844709	0.213121389
  374	Q	E	0.296916876	0.294201034	646	S	N	0.293718938	0.053702828
  429	E	G	0.296692622	0.12956891	751	M	T	0.293692865	0.188828745
  617	E	G	0.296673186	0.100617287	138	V	A	0.293692865	0.172441917
  174	P	L	0.296325925	0.125090192	421	W	R	0.293643119	0.202965718
  476	C	W	0.296243077	0.108583652	891	E	D	0.290888227	0.199229012
  536	K	[stop]	0.296174047	0.204485045	663	I	T	0.290884576	0.159824412
  340	E	[stop]	0.296106359	0.228363644	86	E	G	0.290735509	0.164271816
  263	N	S	0.295761788	0.153417105	950	-------	GNTDKRA	0.290646329	0.08439848
  							(SEQ ID NO:
  							3447)
  292	A	D	0.295588873	0.132003236	910	V	A	0.290614659	0.192165123
  524	K	E	0.295588726	0.123024834	130	S	R	0.290579337	0.126556505
  252	K	E	0.295509892	0.130412924	286	T	A	0.290569747	0.161258253
  360	D	H	0.295426779	0.169820671	412	D	Y	0.290563856	0.192946257
  771	A	T	0.295409018	0.21146028	390	G	C	0.290531408	0.226107283
  960	T	S	0.295303172	0.200733126	96	M	T	0.290483084	0.117441458
  885	T	A	0.293639992	0.136222429	796	Y	F	0.290480726	0.145066767
  372	K	N	0.293601801	0.159631501	617	E	[stop]	0.290459043	0.254049857
  899	R	W	0.293409271	0.197663789	520	K	Q	0.290432231	0.149193863
  323	Q	R	0.293396269	0.187618952	238	S	C	0.29036146	0.125809391
  787	A	V	0.293181255	0.111256021	510	K	N	0.290307315	0.121616244
  97	S	G	0.29311892	0.120983434	751	M	I	0.290086322	0.117481113
  523	V	A	0.293107836	0.144403198	764	Q	E	0.290043861	0.213865459
  606	GS	-A	0.293095145	0.176419666	239	F	L	0.290032145	0.120563078
  647	S	G	0.293070849	0.180316262	750	A	S	0.290021488	0.169783417
  401	L	M	0.293059235	0.238931791	509	S	N	0.290010303	0.173158694
  706	A	T	0.293004089	0.157196701	791	L	V	0.28993006	0.240441646
  167	I	M	0.292976512	0.174804994	976	A	P	0.289917569	0.129909297
  239	F	Y	0.292846447	0.244049066	970	K	E	0.289792346	0.088055606
  532	I	M	0.292790974	0.132047771	370	G	S	0.289754414	0.116500268
  362	K	N	0.292779584	0.196868197	229	S	I	0.289718863	0.192569781
  531	I	F	0.292690193	0.245999103	126	G	S	0.289695476	0.136718855
  551	E	D	0.292676692	0.177028816	39	D	H	0.28966543	0.205820796
  366	Q	R	0.292637285	0.233099785	541	R	W	0.289647451	0.149474595
  45	E	K	0.292602703	0.135241306	963	S	R	0.289642486	0.119359764
  170	S	P	0.292487757	0.117055288	614	R	G	0.289631701	0.096593744
  522	--------	GVKKLNLY	0.292477218	0.205588046	903	R	K	0.289598509	0.276955136
  		(SEQ ID NO:
  		3455)
  184	S	T	0.292461578	0.171099938	700	K	E	0.289582689	0.146563937
  256	K	R	0.292459664	0.134546625	176	A	T	0.289565984	0.071489526
  898	K	R	0.292371281	0.233917307	862	V	L	0.28755723	0.122530143
  687	------	PTHILR (SEQ	0.292237604	0.252992689	376	A	D	0.287488687	0.149852687
  		ID NO: 3627)
  499	E	[stop]	0.292180944	0.205912614	717	G	A	0.287475979	0.138371481
  439	E	[stop]	0.291789527	0.178224776	871	R	G	0.287423469	0.12544588
  286	T	I	0.291597253	0.134630039	779	E	[stop]	0.287388451	0.214465092
  326	K	R	0.291167908	0.130858044	659	R	Q	0.287382153	0.188389105
  309	W	C	0.291117426	0.126634127	688	T	S	0.2872606	0.18090055
  141	L	V	0.291053469	0.125358393	450	A	G	0.287222025	0.226851871
  599	D	H	0.290990101	0.194898673	608	L	P	0.287206606	0.153956956
  714	R	G	0.289551118	0.131217053	74	T	A	0.28708898	0.151009591
  849	Q	E	0.289450204	0.14256548	101	Q	H	0.287075864	0.127870371
  861	V	L	0.289424991	0.184715842	168	L	M	0.287051161	0.164606192
  227	A	S	0.289407395	0.147147965	522	G	A	0.286889556	0.191392288
  337	Q	E	0.289400311	0.154536453	158	--	CN	0.286856801	0.104191954
  282	P	Q	0.289371748	0.241776764	822	D	Y	0.286792384	0.216414998
  147	-----	KGKPH (SEQ	0.289327222	0.167067239	31	LL	PV	0.286704233	0.167404084
  		ID NO: 3494)
  215	--------	GGNSCASG	0.28926976	0.113347286	753	------	IFENLS (SEQ	0.286664247	0.204891377
  		(SEQ ID NO:					ID NO: 3474)
  		3432)
  615	-	Q	0.288918789	0.138819471	894	----	SLLK (SEQ	0.286588033	0.088926565
  							ID NO: 3719)
  148	-------	GKPHTNY	0.288918789	0.145077971	443	S	R	0.286575868	0.16053834
  		(SEQ ID NO:
  		3438)
  70	L	V	0.288897546	0.141249384	813	G	S	0.286517663	0.166687094
  131	Q	H	0.28889109	0.089984222	545	I	T	0.28643634	0.175437623
  417	Y	[stop]	0.288830461	0.139069155	43	R	G	0.286322337	0.211707784
  917	E	Q	0.288684907	0.209421131	671	D	G	0.28629192	0.163952723
  681	K	R	0.288657171	0.188212382	501	S	T	0.286282753	0.120251174
  824	---	VLE	0.288568311	0.142383803	729	L	M	0.286200559	0.141100837
  757	L	M	0.288547614	0.138199941	264	L	F	0.28603772	0.148836446
  683	S	P	0.288449161	0.100064584	613	G	S	0.285821749	0.213295055
  879	N	D	0.288359669	0.112916417	806	S	P	0.285754508	0.139734573
  87	EF	AV	0.28833835	0.157423397	251	Q	R	0.285704309	0.129794167
  623	R	M	0.288312668	0.180378091	503	L	P	0.285623626	0.150765257
  360	D	G	0.288240177	0.1450193	544	K	N	0.285528499	0.105740594
  469	E	D	0.288213424	0.169330277	685	G	S	0.285482686	0.116956671
  488	D	H	0.288056714	0.224399768	66	L	P	0.285241304	0.178235911
  832	A	D	0.28797086	0.133987122	713	R	[stop]	0.281751627	0.150509506
  331	F	L	0.287898632	0.125465761	759	R	I	0.281715415	0.207490665
  880	D	N	0.287796432	0.265861692	103	A	D	0.281654023	0.156258821
  813	G	V	0.28764847	0.18793522	352	K	R	0.281644749	0.090972271
  125	S	R	0.287612867	0.078156909	23	G	D	0.281613067	0.110087313
  315	G	V	0.287582891	0.216366011	490	R	I	0.28158749	0.189684
  348	C	[stop]	0.285167016	0.232120541	534	Y	C	0.281578683	0.19797794
  615	V	L	0.285139566	0.138644746	728	N	K	0.281567938	0.122533743
  34	R	K	0.285068253	0.155629412	218	S	G	0.28156304	0.0827746
  606	G	D	0.284708065	0.131937418	131	Q	K	0.28143462	0.261996702
  564	G	R	0.284584869	0.153328649	117	D	Y	0.281261616	0.150312544
  767	R	G	0.284520477	0.167110905	809	C	S	0.281246687	0.119977311
  459	K	N	0.284319069	0.144116629	899	R	S	0.281103794	0.115069396
  100	A	G	0.284064196	0.232698011	192	A	P	0.281083951	0.125030936
  182	T	S	0.284017418	0.165066704	913	N	S	0.280977138	0.259159821
  552	A	P	0.28399207	0.192922882	232	C	S	0.28083211	0.170644437
  874	E	[stop]	0.283924403	0.212096559	928	I	L	0.280808974	0.249623753
  656	G	V	0.283837412	0.096364514	495	A	G	0.280579997	0.166279564
  527	N	D	0.283828964	0.095606466	917	-----	ETHAA (SEQ	0.280544768	0.259917773
  							ID NO: 3399)
  560	N	D	0.283827293	0.131100485	85	W-	LS	0.280472053	0.101385815
  518	W	[stop]	0.283768829	0.144873432	344	W	[stop]	0.280246002	0.139860723
  900	F	Y	0.283754684	0.18210141	493	P	H	0.280219202	0.225933372
  485	W	C	0.283722783	0.101623525	189	G	A	0.28010846	0.181165246
  528	L	M	0.283582823	0.241404553	565	E	G	0.28010846	0.126376781
  463	V	L	0.283409253	0.174572622	944	Q	R	0.279992746	0.221800854
  938	Q	R	0.283399277	0.159588016	674	G	A	0.27982066	0.112736684
  809	C	R	0.2832933	0.140866937	45	E	V	0.279758496	0.126165976
  765	G	V	0.283226034	0.181883423	281	P	A	0.27973122	0.169207983
  253	V	E	0.283192966	0.158310209	828	L	P	0.279653349	0.165044194
  745	A	D	0.283094632	0.139036808	460	A	D	0.27950426	0.185233285
  739	R	S	0.283000418	0.086394522	539	K	R	0.279423784	0.231876099
  262	A	D	0.282981572	0.21883829	62	S	G	0.279325036	0.105769252
  75	E	D	0.282861668	0.096240394	883	S	T	0.278909433	0.17133128
  122	L	V	0.28282995	0.142431105	166	---	LIL	0.27890183	0.114735325
  427	K	R	0.282689541	0.126741896	553	N	K	0.276534729	0.129122139
  472	K	E	0.282354225	0.243592384	500	N	K	0.276479484	0.075342066
  69	L	V	0.282311609	0.233097353	796	Y	[stop]	0.276459628	0.151040972
  128	A	D	0.282136746	0.144684711	313	K	E	0.276424062	0.141250225
  240	L	P	0.282112821	0.187484636	184	S	R	0.276360484	0.093462218
  840	N	D	0.28205862	0.169019904	770	M	V	0.276349013	0.177344184
  496	I	L	0.281766947	0.156440465	30	T	S	0.27626759	0.074607362
  445	D	N	0.27879438	0.120139275	887	G	C	0.276203171	0.205245818
  121	R	G	0.278752599	0.152495589	885	T	S	0.276162821	0.125136939
  66	LN	PV	0.278503247	0.058556198	372	K	E	0.2761455	0.186164615
  603	-------	LETGSLK	0.278503247	0.20379117	161	S	F	0.276099268	0.101256778
  		(SEQ ID NO:
  		3545)
  225	G	[stop]	0.278489806	0.182580993	280	LP	PV	0.2760948	0.15312325
  175	---	EAN	0.278488851	0.117512649	118	G	A	0.276069076	0.158472607
  274	A	S	0.278435433	0.213434648	945	T	S	0.275967844	0.217091948
  870	D	G	0.278347965	0.136371883	597	W	S	0.275959763	0.205648781
  683	S	T	0.278234202	0.119170388	700	K	[stop]	0.275943939	0.231744011
  792	P	H	0.277909356	0.196357382	654	L	M	0.275895098	0.222206287
  18	N	R	0.277904726	0.144376969	34	R	I	0.275728667	0.262529033
  484	K	R	0.277812806	0.156918996	650	K	N	0.275727906	0.092682765
  51	P	H	0.27780081	0.207949147	347	V	D	0.275634849	0.162043607
  549	A	D	0.277618034	0.184792104	701	Q	E	0.275445666	0.129639485
  285	H	Q	0.277595201	0.164383067	221	S	P	0.275424064	0.253543179
  772	E	[stop]	0.277569205	0.252009775	902	H	Y	0.275413846	0.238626124
  233	M	T	0.277522281	0.101460422	408	K	N	0.275278915	0.187758493
  677	-------	LSRFKDS	0.277439144	0.176461932	410	G	R	0.275207307	0.148329245
  		(SEQ ID NO:
  		3578)
  444	E	D	0.277438575	0.185715982	202	R	T	0.27519939	0.225294793
  287	K	R	0.277424076	0.122002352	190	Q	H	0.275101911	0.155497318
  86	E	Q	0.277422525	0.267475322	296	V	A	0.274868513	0.216028266
  650	K	R	0.277338051	0.1661601	176	A	V	0.274754076	0.101747221
  119	N	K	0.2772012	0.097660237	16	D	V	0.274707044	0.080710216
  419	E	D	0.27717758	0.091079949	338	A	G	0.274649181	0.21549192
  849	Q	H	0.277146577	0.10057266	908	K	[stop]	0.274631009	0.235774306
  745	A	P	0.277094424	0.180486538	745	A	T	0.274596368	0.139876086
  895	L	V	0.277059576	0.147621158	582	I	T	0.274539152	0.136455089
  200	V	R	0.276947529	0.109871945	73	Y	H	0.274522926	0.183155681
  491	G	A	0.276923451	0,236639042	525	------	KLNLYL	0.272179534	0.127115618
  							(SEQ ID NO:
  							3512)
  437	L	P	0.276817656	0.127643327	178	D	H	0.27217863	0.114858223
  794	K	E	0.276808052	0.108760175	186	G	S	0.272004663	0.206440397
  609	K	E	0.274518342	0.096584602	797	LS	PV	0.271846299	0.116235959
  148	-----	GKPHT (SEQ	0.274483854	0.138944547	434	H	L	0.271775834	0.108387354
  		ID NO: 3436)
  269	S	I	0.274483065	0.167999753	124	S	C	0.271634239	0.201362524
  600	L	P	0.274446407	0.156944314	687	----	PTHI (SEQ ID	0.271046382	0.217907583
  							NO: 3625)
  609	K	N	0.274296988	0.098675974	626	R	I	0.271037385	0.191496316
  548	E	G	0.274291628	0.174184065	717	G	V	0.271024109	0.162847575
  282	P	R	0.274223113	0.269615449	534	Y	[stop]	0.270681224	0.104188898
  743	Y	N	0.274041951	0.169744437	150	P	H	0.270599643	0.192362809
  273	LA	PV	0.273953381	0.083004597	552	A	S	0.270597368	0.181876059
  241	-----	TKYQD (SEQ	0.273953381	0.041697608	150	P	S	0.270581156	0.14794261
  		ID NO: 3752)
  752	LI	PV	0.273953381	0.179521275	270	A	S	0.270550408	0.145246028
  500	-----	NSILD (SEQ	0.273953381	0.096079618	563	S	Y	0.270533409	0.17681632
  		ID NO: 3598)
  88	FQ	DR	0.273953381	0.132934109	664	---	PAV	0.270462826	0.090794222
  548	E	K	0.273785339	0.140999456	97	S	I	0.270410385	0.155670382
  758	S	T	0.273170088	0.17814745	64	A	D	0.270367942	0.13574281
  884	W	S	0.27315778	0.127540825	143	Q	E	0.27021122	0.220203083
  258	E	D	0.273147573	0.172394328	686	N	I	0.270089028	0.228432562
  720	R	M	0.272984313	0.209562405	544	K	[stop]	0.270051777	0.124983342
  217	N	H	0.272871217	0.212149421	537	G	A	0.270050779	0.18424231
  0	M	R	0.272866831	0.105028991	902	H	L	0.269853978	0.238618549
  376	A	G	0.27284261	0.107816996	361	G	A	0.269774718	0.191146018
  221	S	C	0.272816553	0.204562414	963	S	C	0.269617744	0.20243244
  691	LR	PV	0.272779276	0.168092844	965	Y	H	0.26944455	0.246260675
  796	YL	DR	0.272779276	0.144849416	66	---	LNK	0.269318761	0.181427468
  439	----	EERR (SEQ	0.272779276	0.117493254	959	-----	ETWQS (SEQ	0.269318761	0.133778085
  		ID NO: 3381)					ID NO: 3402)
  383	S	N	0.272651878	0.203030872	509	-----	SKQYN (SEQ	0.269239232	0.199612231
  							ID NO: 3712)
  603	L	M	0.272615876	0.2046327	32	L	I	0.269033673	0.109933858
  183	Y	H	0.27230417	0.167987777	913	N	I	0.265873279	0.228181021
  858	R	K	0.272264159	0.162833579	775	Y	S	0.265844485	0.132207982
  209	K	N	0.269020729	0.109971766	678	S	R	0.265770435	0.147977027
  48	R	[stop]	0.268939151	0.082435645	602	S	R	0.265750704	0.118408744
  466	-	T	0.268825688	0.095723888	121	R	T	0.265718915	0.126781949
  45	E	Q	0.268733142	0.139266278	818	S	R	0.265623217	0.145609734
  843	E	Q	0.268599201	0.195661988	798	S	C	0.265584497	0.073889024
  643	V	L	0.268577714	0.156052892	864	------	DLSVEL	0.265506357	0.19885122
  							(SEQ ID NO:
  							3365)
  285	H	R	0.268299231	0.21489701	373	R	G	0.265364174	0.162678423
  317	D	G	0.268047511	0.116283826	803	Q	E	0.265269725	0.202509841
  195	F	L	0.268045884	0.108480308	628	D	E	0.265261641	0.142156395
  590	R	K	0.267781681	0.208536761	194	D	N	0.265249363	0.155857424
  180	L	V	0.267694655	0.240305187	336	R	I	0.2651284	0.181377392
  21	KA	TV	0.267470584	0.147038119	602	S	I	0.265065039	0.204267576
  210	P	H	0.267434518	0.190772597	34	R	S	0.265026085	0.223416007
  612	N	S	0.267419306	0.129882451	775	Y	N	0.264899495	0.150356822
  440	E	G	0.267419306	0.166870392	647	----	SNIK (SEQ ID	0.264896362	0.152108713
  							NO: 3725)
  651	P	L	0.267350724	0.179171164	369	A	G	0.264866639	0.127314344
  686	-------	NPTHILR	0.267281547	0.145940038	407	KKHGEDWG	RSTARTGA	0.26465494	0.11425501
  		(SEQ ID NO:				(SEQ ID NO:	(SEQ ID NO:
  		3595)				3269)	3688)
  56	Q	E	0.267209421	0.156465006	117	D	H	0.264598341	0.092643909
  656	G	D	0.267197717	0.143131022	149	K	R	0.26429667	0.254633892
  591	Q	E	0.267046259	0.172628923	624	R	S	0.264277774	0.09593797
  771	A	P	0.266971248	0.20146384	526	L	M	0.26419728	0.176624184
  667	I	N	0.266893998	0.140849994	671	D	N	0.264084519	0.212711081
  333	L	P	0.26683779	0.202160591	572	N	K	0.264075863	0.218490453
  168	L	V	0.266833554	0.09646076	949	T	S	0.263657544	0.110498861
  43	R	P	0.266528412	0.166392391	20	KKA	T-V	0.263583848	0.126615658
  76	M	T	0.26642278	0.06437874	56	Q	R	0.263561421	0.151855491
  85	WE	CC	0.266335966	0.095081027	492	K	N	0.263524564	0.121563708
  784	A	D	0.266225364	0.186318048	315	G	D	0.26350398	0.250984577
  179	E	G	0.266200643	0.159572948	440	E	[stop]	0.260572941	0.226197983
  282	P	T	0.266142294	0.234821238	245	D	Y	0.260411841	0.171518027
  505	I	V	0.266033676	0.153318009	838	T	A	0.260310871	0.127668195
  884	W	C	0.265892315	0.146379991	510	K	E	0.260303511	0.170827119
  705	Q	L	0.265873279	0.218762249	885	T	I	0.260229119	0.18213929
  625	T	S	0.263431268	0.11997699	606	G	C	0.260187776	0.249968408
  657	I	S	0.26332391	0.140695845	298	A	P	0.260175418	0.137767012
  688	T	R	0.26332192	0.129910161	31	L	R	0.260094537	0.205569477
  835	W	R	0.263224631	0.136063076	19	T	I	0.259989986	0.207028692
  903	R	S	0.263145681	0.157044964	886	K	R	0.259901164	0.087667222
  876	S	T	0.262876961	0.112192073	817	T	S	0.259831477	0.054519088
  468	K	R	0.262863102	0.120169191	901	S	T	0.259815097	0.082797155
  590	---	RQG	0.26279648	0.125412364	343	W	S	0.259761267	0.144643456
  912	L	R	0.262679132	0.194562045	25	T	R	0.259617038	0.188030957
  222	G	R	0.262575495	0.121179798	238	S	P	0.259597922	0.12796144
  379	P	A	0.262556362	0.200217288	343	W	R	0.259570669	0.092335686
  7	N	Y	0.262545332	0.249153444	317	D	Y	0.259540606	0.174340169
  514	C	R	0.262528328	0.153764358	347	------	VCNVICK	0.259425173	0.186479916
  							(SEQ ID NO:
  							3770)
  964	--	FY	0.262491519	0.18918584	606	G	S	0.259379927	0.201078104
  951	N	I	0.262433241	0.181173796	879	N	S	0.259300679	0.19356618
  738	A	S	0.262344275	0.213159289	784	A	S	0.259182688	0.192685039
  109	Q	K	0.262161279	0.235829587	48	R	I	0.259088713	0.132594855
  371	Y	C	0.262089785	0.121531872	112	L	M	0.25908476	0.122948809
  62	S	I	0.262062515	0.217469036	181	V	A	0.259030426	0.153412207
  967	K	N	0.261999761	0.11991933	567	V	M	0.258972858	0.206147057
  395	R	T	0.261975414	0.202071604	787	A	P	0.258909575	0.199316536
  546	K	E	0.261933935	0.196957538	741	---	LLY	0.258835623	0.170116186
  473	D	H	0.26183541	0.210514432	280	--	LP	0.258711013	0.142341042
  422		ERIDKKV	0.261766763	0.175889641	639	-------	ERREVLD	0.258711013	0.096645952
  		(SEQ ID NO:					(SEQ ID NO:
  		3393)					3395)
  661	E	D	0.261685468	0.21738252	11	RR	AS	0.258711013	0.198257452
  807	K	N	0.261631077	0.137745855	660	G	V	0.258707306	0.163939116
  495	A	P	0.261336035	0.145111761	519	-----	QKDGVK	0.255711118	0.090066635
  							(SEQ ID NO:
  							3641)
  474	E	V	0.261129255	0.1424745	977	V	E	0.255573788	0.223531947
  100	A	V	0.261042682	0.097040591	448	S	P	0.255534334	0.216106849
  660	G	A	0.260992911	0.257791059	872	----	LSEE (SEQ	0.255312236	0.130213196
  							ID NO: 3572)
  613	G	V	0.260991628	0.142830183	534	-Y	DS	0.255312236	0.080703663
  356	---	EKK	0.260606313	0.08939761	765	--	GK	0.255312236	0.10865158
  419	E	R	0.260606313	0.127113021	28	MK	C-	0.255312236	0.091611028
  62	S	N	0.258582734	0.206139171	826	EK	DR	0.255312236	0.103881802
  716	G	C	0.258579754	0.205579693	302	I	S	0.2552956	0.169641843
  185	L	M	0.258521471	0.171738368	866	S	I	0.255156321	0.209048192
  407	K	N	0.258498581	0.130697064	472	K	M	0.255025429	0.186702335
  973	W	C	0.258383156	0.162271324	165	R	S	0.25497678	0.100932181
  419	E	[stop]	0.258326013	0.179526252	242	K	R	0.254948866	0.230748057
  457	R	K	0.258323684	0.189885325	311	---	KLK	0.25494628	0.09906032
  876	S	R	0.258284608	0.118534232	200	V	E	0.254874846	0.123567532
  19	T	S	0.258270715	0.163493921	129	C	R	0.25474894	0.168215252
  680	F	S	0.258237866	0.129529513	284	P	A	0.254723328	0.141080203
  2	E	A	0.257800465	0.161538463	232	---	CMG	0.254645266	0.200305653
  20	K	D	0.257606921	0.080857215	946	N	S	0.2545847	0.199844301
  481	K	E	0.257527339	0.131433394	80	I	V	0.254434146	0.224490053
  227	A	P	0.257425537	0.162403215	327	G	V	0.25442364	0.168129037
  319	A	G	0.25734846	0.183688663	107	I	V	0.254364427	0.144921072
  773	R	T	0.257312824	0.076585471	777	R	I	0.254281708	0.219559132
  59	S	R	0.257311236	0.098683009	801	L	P	0.254280774	0.139428109
  522	G	D	0.257141461	0.205906219	417	Y	H	0.254230823	0.102936144
  164	E	D	0.257089377	0.152824439	251	Q	L	0.254085129	0.154282551
  705	QA	R-	0.257083631	0.186668119	856	Y	[stop]	0.254033585	0.087466157
  82	H	Y	0.256846745	0.145259346	753	I	F	0.25397349	0.160875608
  606	G	R	0.256772211	0.222683526	303	W	G	0.253842324	0.162875151
  281	P	L	0.256724807	0.103452649	852	Y	H	0.253666441	0.130229811
  471	D	Y	0.256649107	0.251689277	223	P	S	0.253640033	0.10193396
  231	A	S	0.256583564	0.187236499	472	K	[stop]	0.253606489	0.18360472
  433	K	N	0.256518065	0.138408672	471	D	N	0.250823008	0.230246417
  883	S	G	0.256375244	0.115658726	714	R	[stop]	0.250772621	0.098784657
  672	P	A	0.256302042	0.169194225	192	A	S	0.25063862	0.18266448
  681	KD	R-	0.256180855	0.206050883	668	A	D	0.250605134	0.186660163
  762	G	A	0.256159485	0.149790153	147	--	KG	0.250457437	0.166419391
  774	Q	R	0.256113556	0.176872341	464	IE	DR	0.250457437	0.129773988
  630	P	T	0.255980317	0.147464802	325	--	LK	0.250457437	0.197198993
  151	H	Q	0.255948941	0.118092357	812	C	R	0.250440238	0.175896886
  38	PDL	LT[stop]	0.255810824	0.132108929	215	G	C	0.250425413	0.161826099
  240	LT	PV	0.255810824	0.138991378	564	G	D	0.250350924	0.110254953
  851	T	S	0.25343316	0.097399235	787	A	D	0.250325364	0.160958271
  725	K	E	0.253359857	0.175271591	674	G	V	0.25029228	0.086627759
  115	V	L	0.253354021	0.093695173	182	T	A	0.250160953	0.131790182
  918	T	I	0.253156435	0.23080792	383	S	R	0.250148943	0.108851149
  630	P	L	0.252953716	0.223745102	497	E	G	0.250036476	0.073841396
  75	E	Q	0.252809731	0.120415311	154	Y	C	0.250036476	0.229055007
  480	L	M	0.252718021	0.192126204	827	K	R	0.250016633	0.209047833
  197	S	T	0.252713621	0.125864993	722	Y	[stop]	0.249927847	0.149439604
  779	E	Q	0.25259488	0.11277405	380	Y	H	0.249902562	0.080398395
  340	EV	DC	0.252472535	0.047624791	68	K	[stop]	0.249695921	0.134323821
  12	R	K	0.252469729	0.189301078	178	D	Y	0.24960373	0.233005696
  515	A	S	0.252433747	0.168422609	880	D	V	0.249521617	0.133706258
  615	----	VIEK (SEQ	0.252369421	0.112001396	543	K	R	0.249512007	0.164262829
  		ID NO: 3778)
  513	N	S	0.252353713	0.094778563	101	Q	E	0.249509933	0.220597507
  274	A	P	0.252335379	0.222801897	261	L	P	0.249467079	0.135680009
  474	E	Q	0.252314637	0.161495393	410	G	A	0.249451996	0.157770206
  898	K	E	0.252289386	0.197783073	916	---------	FETHAAEQA	0.249445316	0.231377364
  							(SEQ
  							ID NO: 3410)
  397	Q	K	0.252164481	0.217428232	467	L	M	0.249366626	0.154018589
  455	W	S	0.25204917	0.248519347	745	A	V	0.249363082	0.18169323
  135	P	S	0.252041319	0.143618662	773	R	K	0.249259705	0.143796066
  500	N	D	0.252036438	0.129905572	221	S	Y	0.249177365	0.225580403
  204	S	I	0.252028425	0.131493678	953	DK	CL	0.248980289	0.153230139
  235	A	T	0.251989659	0.158776047	29	KT	NC	0.247444507	0.126896702
  839	I	M	0.251899392	0.164461403	777	R	G	0.247073817	0.140696212
  473	D	N	0.251700557	0.215226558	720	R	T	0.246870637	0.139065914
  715	A	D	0.251688144	0.14707302	529	---	YLI	0.246804685	0.066320143
  352	K	E	0.251658395	0.165058904	977	V	M	0.24675063	0.232768749
  413	R	I	0.251517421	0.230382833	414	G	C	0.246666689	0.173156358
  272	G	R	0.251488679	0.185835986	487	G	D	0.246317089	0.205561043
  647	S	R	0.251423405	0.100129809	696	S	G	0.246296346	0.111834798
  333	L	M	0.251344003	0.196286065	515	A	G	0.246293045	0.17108612
  964	F	Y	0.25104576	0.166483614	438	--	EE	0.246243471	0.172505379
  474	E	K	0.250927827	0.172968831	730	A	S	0.246013083	0.141113967
  751	M	V	0.250846737	0.147715329	574	N	D	0.245981475	0.227302881
  213	------	QIGGNS	0.248980289	0.134226006	747	T	S	0.245965899	0.17316365
  		(SEQ ID NO:
  		3639)
  57	P	H	0.248900571	0.215896368	740	D	Y	0.245945789	0.167910919
  301	V	L	0.24886944	0.106508651	640	R	I	0.245900817	0.188813199
  586	A	P	0.248863678	0.211216154	3	I	F	0.245678	0.179390362
  909	F	Y	0.248749713	0.182356511	355	N	D	0.245670687	0.09594124
  626	R	T	0.248743703	0.208846467	371	Y	[stop]	0.245500092	0.105713424
  186	G	R	0.24871786	0.199871451	51	P	S	0.24544462	0.203086773
  645	D	N	0.248657263	0.126033155	28	M	L	0.245403036	0.189135882
  173	K	R	0.24855018	0.153000538	458	A	D	0.245377197	0.208634207
  519	Q	[stop]	0.248535487	0.209163595	572	N	I	0.24524576	0.164550203
  888	R	I	0.248471987	0.104169936	959	E	[stop]	0.245144817	0.219795779
  491	G	C	0.248444417	0.204717262	527	N	S	0.245098015	0.16437657
  527	N	K	0.248397784	0.121054149	321	P	S	0.245086017	0.160736605
  893	L	V	0.248370955	0.162725859	579	N	K	0.244981546	0.165374413
  379	P	H	0.248321642	0.237522233	707	A	P	0.244857358	0.22019856
  900	F	L	0.248316685	0.187112489	414	G	A	0.244717702	0.113316145
  974	-----	KPAV (SEQ	0.24830974	0.09950399	963	S	G	0.244450471	0.188301401
  		ID NO:
  		3518)[stop]
  409	H	R	0.248289463	0.198716638	108	D	H	0.244382837	0.099322593
  278	I	T	0.248133293	0.145997719	19	T	R	0.244301214	0.22638105
  230	-----	DACMG	0.248087937	0.141736439	457	R	S	0.244059876	0.203207391
  		(SEQ ID NO:
  		3342)
  412	------	DWGKVY	0.248000785	0.085936492	735	R	Q	0.243928198	0.170841115
  		(SEQ ID NO:
  		3370)
  548	E	V	0.244464905	0.11615159	280	L	P	0.243719915	0.122012762
  135	P	H	0.247697198	0.24068468	529	Y	C	0.241113191	0.148105236
  824	V	E	0.247676063	0.211426874	102	P	S	0.241100901	0.126616893
  250	H	N	0.247644364	0.173527273	568	P	R	0.241086845	0.174639843
  101	Q	[stop]	0.247598429	0.141658982	416	V	L	0.24098406	0.086334529
  364	F	S	0.247520151	0.139448351	834	G	S	0.240965197	0.161966438
  420	A	G	0.247498728	0.234162787	322	L	M	0.240965197	0.161073617
  627	Q	P	0.243601279	0.172067752	538	G	s	0.240933783	0.072861862
  571	--	VN	0.243561744	0.078796567	536	K	E	0.240888218	0.130971778
  25	T	A	0.243399906	0.118102255	676	P	s	0.240757682	0.111329254
  129	C	S	0.243399597	0.045331126	108	D	E	0.240718917	0.12602791
  522	G	S	0.243323907	0.089702225	217	N	K	0.240713475	0.15867648
  695	E	K	0.243320032	0.148139423	342	D	E	0.24062135	0.069616641
  603	L	V	0.243217969	0.148743728	471	D	H	0.240564636	0.181535186
  404	H	Q	0.242964457	0.173626579	218	S	N	0.240529528	0.151826239
  469	E	Q	0.242802772	0.126770274	191	R	I	0.240513696	0.229207246
  484	KWY	NSS	0.242735572	0.182387025	963	---	SFY	0.240421887	0.098315268
  797	L	V	0.2425558	0.204091719	77	K	N	0.240381155	0.116252284
  928	I	F	0.242416049	0.232458614	637	----	TFER (SEQ	0.240288787	0.148900082
  							ID NO: 3744)
  974	K	R	0.242320513	0.114367362	571	V	L	0.240279118	0.074639743
  687	P	L	0.242304633	0.20007901	346	M	T	0.240147015	0.108146398
  885	T	R	0.242245862	0.204992576	512	Y	[stop]	0.240104852	0.068415116
  768	T	S	0.242193729	0.178836886	430	G	C	0.240047705	0.20806366
  588	----	GKRQ (SEQ	0.242084293	0.124769338	599	D	G	0.239869359	0.206138755
  		ID NO: 3440)
  262	------	ANLKD1	0.242084293	0.137081914	462	F	s	0.23971457	0.144092402
  		(SEQ ID NO:
  		3325)
  246	I	C	0.242084293	0.107590717	724	S	R	0.239681347	0.127922837
  288	E	[stop]	0.242056668	0.219648186	61	T	S	0.239626948	0.164373644
  978	-[stop]	YV	0.242009218	0.097706533	525	K	[stop]	0.239380142	0.131802154
  110	R	[stop]	0.241965346	0.120709959	296	V	E	0.239355864	0.120748179
  741	L	M	0.241912289	0.193137515	968	K	Q	0.238999998	0.129755167
  72	D	Y	0.241758248	0.224435844	617	E	K	0.238964823	0.084548152
  653	N	Y	0.24166971	0.0887834	120	E	K	0.238945442	0.100801456
  324	R	[stop]	0.241651421	0.106997792	44	L	V	0.238860984	0.10949901
  293	Y	D	0.241440886	0.202068751	315	G	R	0.238751925	0.215543005
  695	E	A	0.241330438	0.115436697	87	E	[stop]	0.238731064	0.177299521
  798	--------	SKTLAQYT	0.241309883	0.196326087	204	S	C	0.236855446	0.164372504
  		(SEQ ID NO:
  		3714)
  866	S	G	0.241237257	0.109329768	82	H	Q	0.236837713	0.172606609
  818	S	G	0.238509249	0.201919192	861	-------	VVKDLSVE	0.236770505	0.195127344
  							(SEQ ID NO:
  							3837)
  189	G	V	0.238447609	0.179422249	493	P	L	0.236700832	0.181806123
  394	A	D	0.238439863	0.125867824	474	E	G	0.236695789	0.180206764
  861	-	V	0.238439176	0.202222792	302	I	F	0.236588615	0.136160472
  357	K	E	0.238434177	0.184905545	109	Q	R	0.236576305	0.166840659
  353	L	V	0.23831895	0.17206072	97	S	R	0.236508024	0.179878709
  488	D	V	0.2382354	0.188903119	40	L	V	0.236210141	0.21459356
  684	-----	LGNPT (SEQ	0.2382268	0.157487774	761	F	C	0.236145536	0.170046245
  		ID NO: 3549)
  376	A	V	0.238191318	0.142572457	50	K	N	0.236137845	0.22219675
  349	N	D	0.238174065	0.053089179	205	N	K	0.236073257	0.12180008
  331	F	S	0.238131141	0.093269792	399	G	D	0.236045787	0.181873656
  971	E	D	0.238076025	0.194709418	521	D	Y	0.235934057	0.180076567
  775	Y	F	0.238057448	0.214475137	665	A	D	0.235822456	0.220273467
  730	A	T	0.238038323	0.175731569	252	K	R	0.235675801	0.120466673
  631	---	ALF	0.237949975	0.190053084	646	S	R	0.235675637	0.183914638
  504	D	H	0.23794567	0.139048842	102	P	A	0.235653058	0.16760539
  94	G	D	0.237937578	0.15570335	810	S	N	0.235539825	0.164257896
  291	E	[stop]	0.237828954	0.19900832	936	R	S	0.235496123	0.188093786
  871	R	I	0.237759309	0.236033629	111	K	R	0.235492778	0.118354865
  761	F	Y	0.237669703	0.128380283	220	A	V	0.235467868	0.198253635
  910	----	VCLN (SEQ	0.237633429	0.152561858	855	---	RYK	0.235222552	0.156668306
  		ID NO: 3768)
  731	D	Y	0.237566392	0.167223625	354	I	N	0.235178848	0.098023234
  245	D	A	0.237553897	0.189220496	158	C	F	0.235135625	0.169427052
  979	L-E	VWS	0.237546222	0.150693183	689	H	R	0.235102048	0.220671524
  208	V	E	0.237546113	0.17752812	594	E--F	GRII (SEQ ID	0.235051862	0.132444365
  							NO: 3451)
  483	Q	R	0.23746372	0.159123209	154	Y	D	0.234980588	0.232501764
  634	V	M	0.237398857	0.152995502	870	D	V	0.234951394	0.118777361
  837	T	I	0.237183554	0.104666535	198	I	N	0.234906329	0.184047389
  479	E	Q	0.237085358	0.157162064	76	M	I	0.234796263	0.126238567
  555	F	V	0.237065318	0.182110462	434	H	N	0.234726089	0.143174214
  872	LS	PV	0.23698628	0.179042308	570	E	Q	0.232497705	0.099759258
  601	L	P	0.236954247	0.122470012	645	D	E	0.2323596	0.127143455
  127	F	L	0.236892252	0.129435749	54	I	N	0.23228755	0.182788712
  484	--KW	NSSL (SEQ	0.234680329	0.165662856	725	K	R	0.232253631	0.11253677
  		ID NO: 3599)
  49	K	[stop]	0.234415257	0.114263318	771	A	S	0.232158252	0.16845905
  896	L	P	0.234287413	0.192149813	896	L	V	0.232108864	0.141878039
  530	L	V	0.234192802	0.173965176	487	G	V	0.232053935	0.22651513
  643	V	A	0.234106948	0.176627185	655	I	V	0.231994505	0.148078533
  711	E	K	0.234002178	0.154011045	708	K	R	0.231988811	0.183732743
  918	-----	THAAEQ	0.23373891	0.117744474	699	E	D	0.231934703	0.178386576
  		(SEQ ID NO:
  		3747)
  473	D	E	0.233630727	0.181285916	446	A	P	0.231896096	0.131534649
  666	V	E	0.233615017	0.210063502	902	H	P	0.231793863	0.226418313
  610	-------	LANGRVIE	0.233598549	0.098900798	555	F	S	0.231772683	0.154329003
  		(SEQ ID NO:
  		3538)
  463	V	A	0.233582437	0.13705941	685	G	R	0.231646911	0.113490558
  771	A	V	0.233335501	0.144017771	430	G	A	0.231581897	0.168869877
  89	Q	H	0.233314663	0.120225936	423	R	G	0.231294589	0.188648387
  18	N	D	0.233234266	0.100130745	773	R	S	0.231238362	0.139470334
  547	P	A	0.233232691	0.192665943	148	---	GKP	0.231166477	0.084708483
  628	D	H	0.233191566	0.113338873	795	TY	PG	0.231166477	0.229360354
  290	I	V	0.233178351	0.147527858	598	N	S	0.230890539	0.114382772
  837	----	TTIN (SEQ ID	0.233038063	0.141130326	109	Q	[stop]	0.230738213	0.089332392
  		NO: 3761)
  909	--	FV	0.233038063	0.131142006	481	----	KLQK (SEQ	0.23071553	0.20441951
  							ID NO: 3513)
  260	R	G	0.232970656	0.120191772	592	-GR	DNQ	0.230655892	0.071944702
  707	-------	AKEVEQR	0.232896265	0.116012039	254	I	T	0.2306357	0.069580284
  		(SEQ ID NO:
  		3314)
  638	F	S	0.232893598	0.149395863	530	L	R	0.230571343	0.193066361
  671	D	A	0.232880356	0.163658679	365	W	[stop]	0.230333383	0.12753339
  443	S	T	0.232784832	0.170920909	131	Q	R	0.2302555	0.206903114
  392	K	N	0.232687633	0.108105318	244	Q	E	0.230190451	0.222512927
  500	N	I	0.232640715	0.1305158	900	F	I	0.230181139	0.149890666
  111	K	E	0.232613623	0.097737029	318	E	Q	0.230160478	0.212890421
  610	L	V	0.229644521	0.180175813	312	L	M	0.230110955	0.204915228
  847	E	G	0.229640073	0.111868196	106	N	S	0.230101564	0.155287559
  636	--	LT	0.229485665	0.192188426	968	K	R	0.230017803	0.168949701
  665	A	G	0.229408129	0.212381399	631	A	P	0.229723383	0.159718894
  82	H	R	0.229295108	0.108155794	864	D	G	0.226094276	0.177950676
  371	Y	D	0.229277426	0.117283148	140	K	R	0.226067524	0.114127554
  148	G	V	0.229238098	0.159823444	814	F	S	0.225959256	0.114511043
  443	S	I	0.229142738	0.169822985	215	G	D	0.225350951	0.086324983
  660	G	C	0.229029418	0.194710612	138	V	L	0.225143743	0.155359682
  181	V	D	0.228966959	0.164951106	192	A	T	0.22512485	0.144695235
  832	A	P	0.228767879	0.092204547	502	I	S	0.225038868	0.197567126
  152	T	A	0.228705386	0.182569685	494	F	V	0.224968248	0.143764694
  685	G	A	0.228675631	0.17392363	162	E	D	0.224950043	0.153078143
  112	L	P	0.22866263	0.221195984	788	Y	[stop]	0.22492674	0.129943744
  214	I	T	0.22857342	0.11423526	263	N	I	0.224722541	0.117014395
  610	L	M	0.22841473	0.205382368	918	-------	THAAEQA	0.224719714	0.202778103
  							(SEQ ID NO:
  							3748)
  110	R	G	0.228257249	0.086720324	272	G	A	0.224696933	0.211543463
  590	R	S	0.228041456	0.143022556	322	L	V	0.2246772	0.156881144
  596	I	M	0.227907909	0.117874099	132	C	R	0.224659007	0.146010501
  1	Q	P	0.227785203	0.168369144	657	I	F	0.224649177	0.161870244
  567	V	E	0.227660557	0.156302233	917	-	E	0.224592553	0.150266826
  32	L	V	0.227635279	0.12966479	704	------	IQAAKE	0.224567514	0.109443666
  							(SEQ ID NO:
  							3481)
  65	N	S	0.22749218	0.063907676	328	---	FPS	0.224567514	0.088644166
  291	E	G	0.227296993	0.128103388	455	W	R	0.224240948	0.159412878
  635	A	V	0.22713711	0.159876533	528	--	LY	0.224210461	0.204469226
  894	S	I	0.227093532	0.165363718	289	G	A	0.224158556	0.07475664
  675	C	R	0.227077437	0.19145584	477	RCE	SFS	0.224109734	0.175971589
  863	K	E	0.227027728	0.176903569	290	I	M	0.224106784	0.121750806
  130	S	N	0.226933191	0.162445952	699	EK	AV	0.223971566	0.120407858
  187	K	E	0.226883263	0.185467572	190	------	QRALDFY	0.223971566	0.118248938
  							(SEQ ID NO:
  							3646)
  330	S	G	0.226753105	0.138020012	287	K	[stop]	0.223966216	0.119362605
  224	V	A	0.226536103	0.153342124	33	V	A	0.223884337	0.200194354
  802	A	T	0.226368502	0.154358709	321	P	R	0.223833871	0.153353055
  148	G	S	0.226168476	0.097680006	149	K	[stop]	0.221989288	0.160692576
  732	D	E	0.226134547	0.109002487	230	---	DAC	0.221929991	0.119956442
  350	V	L	0.223803585	0.123552417	559	-I	TV	0.221929991	0.162385076
  598	N	D	0.223755594	0.127015451	125	S	T	0.221924231	0.192354491
  784	A	V	0.22374846	0.140061096	738	A	P	0.221764129	0.166374434
  540	L	P	0.223660834	0.130300184	389	K	L	0.221512528	0.096823472
  330	S	R	0.2236138	0.142019721	829	K	M	0.22130603	0.111760034
  162	E	Q	0.223613045	0.201165398	435	I	V	0.221227154	0.143247597
  128	A	V	0.223401934	0.126557909	626	R	S	0.221038435	0.198631408
  296	V	L	0.223401818	0.13392173	135	P	R	0.221017429	0.116069626
  634	V	E	0.223309652	0.118175475	203	E	Q	0.22076143	0.119826394
  356	E	Q	0.22323735	0.143945409	783	T	I	0.220740744	0.134860122
  289	G	V	0.223202197	0.145913012	672	P	S	0.220729114	0.141569742
  805	T	N	0.223188037	0.139245678	361	G	D	0.220639166	0.141910298
  599	D	Y	0.223008187	0.183323322	690	I	M	0.220631897	0.180897111
  246	I	M	0.222998811	0.092368092	552	A	G	0.220614882	0.110523427
  36	M	K	0.222893666	0.113406903	441	R	I	0.220543521	0.155159451
  476	C	[stop]	0.222743024	0.176188321	218	S	R	0.220420945	0.153071466
  464	I	V	0.222701858	0.18421718	917	------	ETHAAE	0.220288736	0.09840913
  							(SEQ ID NO:
  							3400)
  224	V	L	0.222626458	0.136476862	204	S	R	0.220214876	0.101819626
  42	E	G	0.22255062	0.189996134	255	K	E	0.220080844	0.12573371
  832	A	S	0.222538216	0.190249328	479	E	D	0.220079089	0.099777598
  734	V	I	0.222476682	0.141366416	438	E	G	0.219979549	0.120742867
  146	D	H	0.22246095	0.16577062	605	T	1	0.219976898	0.126979027
  755	AN	DS	0.222404547	0.10970681	109	Q	E	0.219959218	0.140761458
  581	I	V	0.222357666	0.17105795	744	Y	C	0.219956045	0.132833086
  698	K	[stop]	0.222296953	0.103211977	930	------	RSWLFL	0.219822658	0.120132898
  							(SEQ ID NO:
  							3689)
  507	G	D	0.22225927	0.153400026	172	H	Q	0.219757029	0.10461302
  246	I	V	0.222098073	0.120973819	329	P	A	0.219753668	0.110968401
  47	L	P	0.222066189	0.162841956	783	T	S	0.219504994	0.118049041
  301	VI	CL	0.222059585	0.122617461	610	L	P	0.219499239	0.160199117
  210	PL	DR	0.222059585	0.108090576	433	---	KHI	0.216309574	0.092546366
  174	------	PEANDE	0.222059585	0.182232379	375	E	[stop]	0.216261145	0.199757211
  		(SEQ ID NO:
  		3616)
  160	---	VSE	0.222059585	0.137662445	297	V	A		0 216143366	0.15509483
  68	K	E	0.222044865	0.16348242	148	-------	GKPHTNYF	0.216132461	0.211503255
  							(SEQ ID NO:
  							3439)
  38	P	A	0.219404694	0.107368636	645	D	V	0.21604012	0.117781298
  446	A	V	0.218887024	0.176662627	147	KG	R-	0.215998635	0.103939398
  41	R	K	0.218858764	0.128896181	292	A	S	0.215943856	0.157240024
  810	S	R	0.21870856	0.129689435	387	R	G	0.215798372	0.151215331
  83	V	L	0.218625171	0.138945755	157	R	T	0.215790548	0.152247144
  474	E	D	0.218570822	0.130400355	203	E	K	0.215703649	0.168783031
  712	Q	[stop]	0.218254094	0.091444311	123	T	S	0.21570133	0.105624839
  371	Y	H	0.218137961	0.189187449	383	S	G	0.215603433	0.137401501
  35	V	L	0.218110612	0.095949997	310	Q	[stop]	0.21551735	0.135329921
  687	P	R	0.21806458	0.159278352	592	G	A	0.215456343	0.13373272
  621	Y	N	0.218036238	0.089590425	562	K	R	0.215325036	0.122831356
  753	I	N	0.21792347	0.101271232	951	N	S	0.21531813	0.214926405
  337	Q	L	0.217694196	0.180223104	823	R	I	0.215273573	0.191310901
  366	Q	E	0.217564323	0.195945495	723	A	P	0.215193332	0.108699964
  156	G	R	0.217510036	0.186872459	713	R	T	0.215008884	0.104394548
  813	G	A	0.217404463	0.109971024	878	N	I	0.214931515	0.11752804
  911	C	W	0.217360044	0.181625646	145	N	H	0.214892161	0.185408691
  896	L	Q	0.217312492	0.09770592	338	A	T	0.21480521	0.15310635
  395	R	S	0.217267056	0.103436045	169	L	V	0.214751891	0.163877193
  506	S	R	0.217238346	0.104753923	30	T	P	0.214714414	0.144104489
  459	KA	NR	0.217171538	0.126085081	164	E	A	0.214693055	0.151750991
  605	T	S	0.217140582	0.104288213	734	V	F	0.214507965	0.184315198
  147	K	R	0.217113942	0.165662771	841	G	V	0.21449654	0.163419397
  358	K	R	0.217018444	0.148484962	848	G	D	0.214491489	0.166744246
  710	V	E	0.216906218	0.158321415	93	VGL	WA [stop]	0.21434042	0.171347302
  948	T	N	0.216794988	0.204294035	747	T	K	0.214238165	0.122971462
  62	S	T	0.216604466	0.167204921	688	T	K	0.214222271	0.126368648
  827	K	E	0.216603742	0.107241416	878	N	Y	0.214205323	0.111547616
  457	R	G	0.216513116	0.052626339	190	Q	E	0.214170887	0.122424442
  159	N	K	0.216507269	0.109954763	901	------	SHRPVQE	0.212684828	0.084903934
  							(SEQ ID NO:
  							3707)
  177	N	D	0.216431319	0.179290406	459	K	E	0.212680715	0.093525423
  921	-------	AEQAALN	0.216389396	0.149922966	228	L	V	0.212591965	0.092947468
  		(SEQ ID NO:
  		3308)
  633	--	FV	0.216309574	0.179645361	831	T	I	0.212576099	0.16705965
  523		VKKLN (SEQ	0.214126014	0.14801882	819	A	T	0.212522918	0.164976137
  		ID NO: 3782)
  792	---	PSK	0.214126014	0.088425611	645	D	G	0.21251225	0.121902674
  171	---	PHK	0.214126014	0.186440571	794	K	R	0.212502396	0.178916123
  918	--	TH	0.214126014	0.10224323	859	Q	P	0.212311083	0.170329714
  833	T	S	0.214086868	0.0993742	738	A	G	0.212248976	0.161293316
  72	D	E	0.214062412	0.115630034	409	H	Q	0.212187222	0.201696134
  560	N	K	0.213945541	0.173784949	192	-----	ALDFY (SEQ	0.212165997	0.132724298
  							ID NO: 3317)
  906	Q	L	0.213845132	0.187470303	782	------	LTAKLA	0.212165997	0.121732843
  							(SEQ ID NO:
  							3580)
  461	S	I	0.21384342	0.180386801	86	EEF	DCL	0.212165997	0.090389548
  622	N	I	0.213809938	0.161761781	251	Q	H	0.212109948	0.151365816
  768	T	I	0.213809607	0.08102538	197	S	R	0.211641987	0.087103971
  204	---	SNH	0.21345676	0.114570097	196	Y	C	0.211596178	0.195825393
  944	-	Q	0.213449244	0.157411492	125	S	I	0.211507893	0.117116373
  49	K	R	0.213334728	0.181645679	237	A	T	0.211485023	0.118730598
  411	E	[stop]	0.213222053	0.149931485	574	N	S	0.211257767	0.135650502
  719	S	A	0.213134782	0.140566151	73	Y	C	0.211200986	0.169366394
  731	D	E	0.213022905	0.120709041	380	Y	[stop]	0.21093329	0.132735624
  475	F	S	0.213010505	0.137035236	219	C	Y	0.210905605	0.190298454
  305	N	K	0.213008678	0.108878566	777	R	S	0.210879382	0.15535129
  30	TL	PC	0.212945774	0.075648365	799	------	KTLAQYT	0.210719207	0.130227708
  							(SEQ ID NO:
  							3530)
  611	A	G	0.212935031	0.195766935	79	A	T	0.210637972	0.047863719
  266	DI	AV	0.212926287	0.127744646	654	L	R	0.210450467	0.143325776
  730	----	ADDM (SEQ	0.212926287	0.097551919	479	E	K	0.210277517	0.147945245
  		ID NO: 3302)
  684	--	LG	0.212926287	0.093015719	595	F	I	0.208631842	0.129889087
  979	LE[stop]GSPG	VSSKDLK	0.212926287	0.091900005	765	G	R	0.208575469	0.10091353
  	(SEQ ID NO:	(SEQ ID NO:
  	3251)	3808)
  241	----	TKYQ (SEQ	0.212926287	0.1464038	506	S	G	0.208540925	0.155512988
  		ID NO: 3751)
  949	T	I	0.212862846	0.194719268	408	K	R	0.208534867	0.133392724
  709	E	G	0.212846074	0.116849712	171	P	A	0.208511912	0.145333852
  926	--	LN	0.212734596	0.151263965	953	--	DK	0.208375969	0.185478366
  587	F	E	0.210211385	0.204490333	518	W	C	0.208374964	0.121746678
  444	E	Q	0.210197326	0.171958409	34	R	G	0.208371871	0.100655798
  546	K	Q	0.210196739	0.176398222	663	----	IPAV (SEQ ID	0.208314284	0.125213293
  							NO: 3479)
  645	D	Y	0.210085231	0.190055155	737	T	S	0.208225559	0.129504354
  67	N	S	0.210019556	0.13100266	6	I	N	0.208110644	0.078448603
  403	L	P	0.209919624	0.075615563	677	L	M	0.208075234	0.142372791
  452	L	P	0.209882094	0.127675947	456	L	Q	0.208040599	0.142959764
  733	M	V	0.209851123	0.136163056	190	Q	R	0.207948331	0.189816674
  872	L	P	0.209831548	0.152338232	382	S	G	0.207889255	0.137324724
  882	S	R	0.209789855	0.108285285	953	D	H	0.207762178	0.180457041
  679	R	T	0.209762925	0.169692137	522	G	R	0.207711735	0.201735272
  553	-------	NRFYTVI	0.209733011	0.13607198	655	I	F	0.207554053	0.114186846
  		(SEQ ID NO:
  		3596)
  650	----	KPMN (SEQ	0.209706804	0.099600175	345	D	N	0.207459671	0.194429167
  		ID NO: 3523)
  802	AQ	DR	0.209706804	0.100831295	619	T	A	0.20742287	0.107807162
  415	K	R	0.209696722	0.172211853	273	L	M	0.207369167	0.150911133
  470	A	P	0.209480997	0.11945606	695	E	G	0.207324806	0.170023455
  389	K	R	0.209459216	0.190864781	662	N	S	0.207198335	0.146245893
  233	M	K	0.209263613	0.148910419	102	P	R	0.2071 03872	0.104479817
  846	V	A	0.209194154	0.132301095	212	E	G	0.207077093	0.167731322
  803	Q	R	0.209112961	0.157007924	118	G	V	0.20699607	0.113451465
  594	-EF	GRI	0.209067243	0.142920346	841	G	R	0.20698149	0.160303912
  418	D	Y	0.208952621	0.201914561	501	S	R	0.206963691	0.188972116
  424	I	N	0.208940616	0.184257414	402	L	M	0.206953352	0.103953797
  152	-----	TNYFG (SEQ	0.208921679	0.069015043	642	-------	EVLDSSN	0.206944663	0.088763805
  		ID NO: 3756)					(SEQ ID NO:
  							3406)
  184	-------	SLGKFGQ	0.208921679	0.145515626	448	S	C	0.205480956	0.165327281
  		(SEQ ID NO:
  		3717)
  944	----	QTNK (SEQ	0.208921679	0.115799997	341	V	L	0.205333121	0.121382241
  		ID NO: 3652)
  435	IK	DR	0.208921679	0.100379476	351	K	[stop]	0.205260708	0.137391414
  926	LN	PV	0.208921679	0.122257143	408	K	[stop]	0.205233141	0.101895161
  31	L	P	0.208720548	0.120146815	626	R	[stop]	0.204917321	0.133170214
  426	------	KKVEGLS	0.206944663	0.120828794	426	K	N	0.204813329	0.115277631
  		(SEQ ID NO:
  		3507)
  273	--	LA	0.206944663	0.200099204	217	N	D	0.204605492	0.15571936
  631	AL	DR	0.206944663	0.132545056	55	P	A	0.204494052	0.203454056
  75	E	V	0.206746722	0.108008381	979	L--E	VSSK (SEQ	0.204463305	0.104199954
  							ID NO: 3797)
  159	------	NVSEHER	0.206678079	0.108971025	789	EG	GD	0.204429605	0.094907378
  		(SEQ ID NO:
  		3606)
  974	-	K	0.206678079	0.087902725	174	P	H	0.204410022	0.192547659
  13	L	T	0.206678079	0.17404612	37	T	I	0.20435056	0.108024009
  135	P	L	0.206613655	0.11493052	230	D	Y	0.204310577	0.163888419
  576	D	N	0.206571359	0.197674836	369	A	D	0.204246596	0.143255593
  396	--	YQ	0.206474109	0.165665557	567	V	L	0.204221782	0.133245956
  426	K	R	0.206261752	0.175070461	356	E	G	0.204079788	0.096784994
  720	R	S	0.206187746	0.130762963	826	E	G	0.204045427	0.079692638
  731	D	H	0.206140141	0.18515674	234	------	GAVASF	0.203921342	0.148635343
  							(SEQ ID NO:
  							3423)
  792	-----	PSKTY (SEQ	0.206037621	0.119445689	791	-	LP	0.203921342	0.086381396
  		ID NO: 3623)
  470	------	ADKDEFC	0.206037621	0.160849031	550	F	Y	0.203856294	0.154808557
  		(SEQ ID NO:
  		3306)
  846	----	VEGQ (SEQ	0.205946011	0.115023996	139	Y	H	0.203748432	0.112669732
  		ID NO: 3773)
  730	-----	ADDMV	0.205946011	0.203904239	842	K	E	0.203739019	0.14619773
  		(SEQ ID NO:
  		3303)
  195	F	S	0.205931771	0.0997168	565	E	D	0.203689065	0.115937226
  763	R	G	0.205931024	0.177755816	667	IA	TV	0.203650432	0.146532587
  668	A	G	0.205831825	0.181720031	554	-----	RFYTV (SEQ	0.203650432	0.085651298
  							ID NO: 3666)
  123	T	I	0.205810457	0.169798366	481	-----	KLQKW	0.203650432	0.173739202
  							(SEQ ID NO:
  							3514)
  394	A	G	0.205790009	0.129212763	64	A	V	0.203579261	0.147026682
  776	T	N	0.205770287	0.088016724	429	E	K	0.203478388	0.197959656
  779	E	D	0.205703015	0.117547264	659	R	W	0.203469266	0.155374384
  787	A	G	0.205542455	0.113825299	644	L	M	0.201626647	0.191409491
  775	Y	[stop]	0.203457477	0.112309611	326	K	E	0.201516415	0.172628702
  420	A	P	0.203276202	0.137871454	584	P	T	0.201277532	0.157595812
  844	--	LK	0.20327417	0.108693201	216	G	A	0.201151425	0.135718161
  543	KK	DR	0.20327417	0.081409516	158	C	R	0.200895575	0.132515505
  483	QK	DR	0.203103924	0.108226373	557	T	P	0.20079665	0.175823626
  661	E---N	DHSRD (SEQ	0.203103924	0.080468187	615	-------	VIEKTLY	0.20079665	0.14533527
  		ID NO: 3355)					(SEQ ID NO:
  							3779)
  591	--------	QGREFIWN	0.203103924	0.127711804	121	R	I	0.200425228	0.146944719
  		(SEQ ID NO:
  		3637)
  434	-----	HIKLE (SEQ	0.203103924	0.128782985	67	N	K	0.200404848	0.19495599
  		ID NO: 3461)
  192	A	D	0.203101012	0.088663269	258	E	G	0.200396788	0.144009482
  979	LE	VW	0.203097285	0.114357374	232	--	CM	0.200312143	0.13867079
  905	V	E	0.2029568	0.158582123	526	--	LN	0.200312143	0.15960761
  648	N	K	0.202865781	0.076554962	202	-RE	SSS	0.200312143	0.113603268
  811	N	D	0.202736819	0.184175153	68	K	T	0.200238961	0.196349346
  573	F	Y	0.202703202	0.143842683	448	S	Y	0.200204468	0.144800694
  388	K	E	0.202623765	0.1173393	837	---	TTI	0.200162181	0.089943784
  265	K	[stop]	0.202622408	0.159704419	158	-----	CNVSE (SEQ	0.200162181	0.088327822
  							ID NO: 3339)
  511	Q	E	0.202512176	0.199826141	796	-------	YLSKTLA	0.200048174	0.1285851
  							(SEQ ID NO:
  							3852)
  375	E	Q	0.202480508	0.162732896	276	--	PK	0.200048174	0.079289415
  106	N	K	0.202431652	0.125127347	801	----	LAQY (SEQ	0.200048174	0.196038539
  							ID NO: 3540)
  52	E	G	0.202421366	0.17180627	651	-----	PMNLI (SEQ	0.200048174	0.135317157
  							ID NO: 3620)
  597	W	[stop]	0.202346989	0.135138719	756	-	N	0.200048174	0.172777109
  153	N	K	0.202320957	0.084739162	149	------	KPHTNY	0.200048174	0.109852809
  							(SEQ ID NO:
  							3521)
  471	D	E	0.202309983	0.069685161	494	--	FA	0.200048174	0.123840308
  486	Y	H	0.202105792	0.189019359	181	V	I	0.19996686	0.166465973
  732	D	V	0.202045584	0.172766987	616	I	M	0.19990025	0.183539616
  833	T	I	0.202003023	0.114654955	264	--	LK	0.198353725	0.107390522
  220	A	D	0.201986226	0.167650811	296	----	VVAQ (SEQ	0.198353725	0.116995821
  							ID NO: 3835)
  386	D	G	0.201893421	0.144223833	152	T	I	0.198333224	0.117839718
  271	N	K	0.201821721	0.136225013	720	R	G	0.198275202	0.180739318
  236	VA	-C	0.201781577	0.118494484	236	V	L	0.198162379	0.091047961
  661	E	Q	0.201717523	0.126595353	903	R	[stop]	0.197764314	0.184873287
  227	A	-	0.199865011	0.119483676	190	Q	[stop]	0.197676182	0.135507554
  866	S	R	0.199834101	0.105100812	19	TK	PG	0.197606812	0.087295898
  664	------	PAVIALT	0.199723054	0.116432821	554	R	[stop]	0.197270424	0.119115645
  		(SEQ ID NO:
  		3612)
  955	R	W	0.199719648	0.122422647	63	R	K	0.197266572	0.156106069
  507	G	A	0.199700659	0.133738835	671	D	Y	0.197186873	0.193857965
  925	----	ALNI (SEQ	0.199681554	0.112069534	380	YL	T[stop]	0.197159823	0.186882164
  		ID NO: 3320)
  419	---	EAW	0.199681554	0.151874009	210	P	R	0.197120998	0.088119535
  663	I	N	0.199667187	0.147345549	637	T	S	0.196993711	0.074085124
  845	K	R	0.199649448	0.119477749	657	I	M	0.196919314	0.094328263
  782	L	V	0.199620025	0.156520261	458	--	AK	0.196819897	0.136384351
  173	K	E	0.199587002	0.098249426	304	V	F	0.196773726	0.171052025
  615	-------	VIEKTLYN	0.199584873	0.182641156	263	N	K	0.196728929	0.082784462
  		(SEQ ID NO:
  		3780)
  630	P	A	0.199530215	0.103804567	601	L	V	0.196677335	0.163553469
  446	AQ	DR	0.199529716	0.10633379	545	I	N	0.196522854	0.15815205
  374	Q	[stop]	0.199329379	0.131990493	571	VN	AV	0.196419899	0.093569564
  778	M	K	0.199291554	0.158456568	284	-----	PHTKE (SEQ	0.196419899	0.146831822
  							ID NO: 3618)
  858	R	S	0.199265103	0.108121324	163	-HE	PTR	0.196323235	0.180126799
  579	N	I	0.19915895	0.103520322	57	P	L	0.196165872	0.129483671
  63	R	G	0.199095742	0.127135026	659	R	P	0.196165872	0.140190097
  646	S	I	0.199062518	0.104634011	784	A	P	0.196137855	0.183129066
  90	K	E	0.199052878	0.198240775	323	Q	H	0.196115938	0.150227482
  203	--	ES	0.19897765	0.14607778	763	R	W	0.195967691	0.113028792
  439	E	Q	0.198907882	0.179263601	257	N	Y	0.195936425	0.189617104
  621	Y	C	0.198885865	0.125823263	125	s	G	0.19588405	0.126337645
  310	Q	H	0.198723557	0.146313995	787	A	T	0.195855224	0.170500255
  60	N	K	0.198659421	0.192782927	213	Q	L	0.195810372	0.164285983
  299	Q	R	0.1986231	0.112149973	979	---	VSS	0.195756097	0.115771783
  279	T	s	0.198506775	0.126696973	440	E	Q	0.192625703	0.16228978
  278	I	N	0.198457202	0.188794837	698	K	N	0.192440231	0.067040488
  462	--	FV	0.198353725	0.132924725	757	L	Q	0.192392703	0.11735809
  466	G	D	0.195631404	0.128114426	446	----	AQSK (SEQ	0.192307738	0.188279486
  							ID NO: 3329)
  388	K	R	0.195529616	0.155892093	91	D	Y	0.192222499	0.161107527
  767	R	K	0.195477683	0.182282632	65	N	K	0.192152721	0.086051749
  673	E	V	0.195473785	0.111723182	228	L	Q	0.192019982	0.075226208
  864	D	Y	0.195306139	0.092331083	107	I	N	0.191587572	0.153969194
  885	T	K	0.195258477	0.131521124	307	N	S	0.191540821	0.186358955
  856	Y	C	0.195214677	0.129834532	944	QT	PV	0.191451442	0.133263263
  205	N	S	0.194826059	0.070507432	526	------	LNLYLI (SEQ	0.191451442	0.098341333
  							ID NO: 3565)
  696	S	R	0.194740876	0.106074027	750	-A	LS	0.191451442	0.07841082
  498	A	V	0.194435389	0.108630638	651	---	PMN	0.191451442	0.159749911
  281	P	H	0.194325757	0.164586878	370	-----	GYKRQ (SEQ	0.191451442	0.172523736
  							ID NO: 3456)
  106	N	D	0.194156411	0.113601316	654	L	V	0.191441378	0.100236525
  756	---	NLS	0.194120313	0.113317678	332	P	L	0.191427852	0.132400599
  591	----	QGRE (SEQ	0.194120313	0.089464524	724	S	G	0.191322798	0.152424888
  		ID NO: 3635)
  572	N	D	0.194049735	0.182872987	206	H	D	0.191266107	0.183831734
  762	G	S	0.193891502	0.138436771	594	E	D	0.191101272	0.114552929
  41	R	[stop]	0.193882715	0.149226534	525	K	E	0.190973602	0.101119046
  370	G	D	0.193873435	0.131402011	576	D	E	0.190942249	0.134849057
  58	I	T	0.193827338	0.18015548	663	I	V	0.190923863	0.098130963
  64	A	S	0.193814684	0.163559402	225	G	A	0.190920356	0.167486936
  203	E	G	0.193809853	0.182009134	227	A	V	0.190541259	0.158522801
  318	E	K	0.193618764	0.182298755	539	----	KLRF (SEQ	0.190525892	0.118424918
  							ID NO: 3515)
  867	V	L	0.193526313	0.149480344	336	-------	RQANEVD	0.190525892	0.095546149
  							(SEQ ID NO:
  							3676)
  343	W	[stop]	0.193259223	0.086409476	511	---	QYN	0.190525892	0.10542285
  920	----	AAEQ (SEQ	0.1932196	0.09807778	182	--	TY	0.190525892	0.095282059
  		ID NO: 3298)
  559	I	N	0.193172208	0.185545361	955	R	K	0.190477708	0.163763612
  577	D	E	0.193102893	0.104761592	936	------	RSQEYK	0.188141846	0.120467426
  							(SEQ ID NO:
  							3686)
  721	K	N	0.193081281	0.123219324	428	VE	AV	0.188141846	0.111936388
  767	R	S	0.19293341	0.180949858	419	----	EAWE (SEQ	0.188141846	0.161004571
  							ID NO: 3378)
  353	L	P	0.192916533	0.142447603	148	------	GKPFITN	0.188141846	0.126152225
  							(SEQ ID NO:
  							3437)
  662	N	D	0.192798707	0.113762689	972	------	VWICPA	0.188141846	0.100559027
  							(SEQ ID NO:
  							3838)
  87	E	G	0.192780117	0.1542337	328	F	S	0.188082476	0.152191585
  347	V	G	0.192656101	0.11936042	596	I	N	0.188043065	0.141822306
  669	L	V	0.190343627	0.076107876	482	L	V	0.187880246	0.186391629
  492	K	Q	0.190290589	0.150334427	582	I	V	0.18725447	0.136748728
  721	K	E	0.190242607	0.123347897	699	E	Q	0.187137878	0.176072109
  389	K	E	0.190239723	0.177951808	758	S	I	0.18709104	0.158068821
  619	T	I	0.190153498	0.116807589	113	1	N	0.187005943	0.142849404
  93	V	E	0.190153374	0.163133537	968	K	E	0.186636923	0.128956962
  336	R	G	0.190122687	0.099072113	168	-----	LLSPH (SEQ	0.186576707	0.08269231
  							ID NO: 3560)
  878	N	K	0.190097445	0.16631012	833	TGWM (SEQ	PAG[stop]	0.186576707	0.125195246
  						ID NO: 3289)
  847	--	EG	0.190063819	0.165413398	272	-------	GLAFPK	0.186576707	0.060722091
  							(SEQ ID NO:
  							3442)
  481	---	KLQ	0.190063819	0.144467422	529	-----	YLIIN (SEQ	0.186576707	0.104569212
  							ID NO: 3851)
  655	I	N	0.190024208	0.138898845	261	-------	LANLKD	0.186576707	0.081389931
  							(SEQ ID NO:
  							3539)
  696	S-	TG	0.189908515	0.068382259	884	W	[stop]	0.18656617	0.16960295
  55	P	R	0.189907461	0.115309052	719	S	F	0.186508523	0.176978743
  269	S	N	0.18989023	0.150359662	825	L	M	0.185209061	0.126954087
  210	P	L	0.189875815	0.142379934	727	K	M	0.185134776	0.155871835
  798	S	Y	0.18982788	0.189131471	28	M	K	0.1848853	0.176098567
  258	E	K	0.189676636	0.183203558	404	H	R	0.184633168	0.163423927
  190	Q	P	0.189645523	0.168321089	394	A	T	0.184555363	0.1424277
  377	L	V	0.189542806	0.136436344	581	I	F	0.184470581	0.083013305
  500	N	S	0.189535073	0.180860478	766	K	M	0.184394313	0.16735316
  295	N	S	0.18951855	0.108197323	547	P	L	0.184346525	0.155161861
  974	K	[stop]	0.189482309	0.139647592	275	F	S	0.184250266	0.085183481
  54	I	V	0.189429698	0.1555694	537	G	V	0.184185986	0.146420736
  736	N	D	0.189336313	0.075796871	873	S	N	0.184149692	0.143102895
  505	I	N	0.189099927	0.151637022	198	-I	CL	0.184139991	0.106675461
  396	Y	H	0.189044775	0.129353397	639	---	ERR	0.184139991	0.11669463
  117	D	V	0.188915066	0.132090825	287	-K	CL	0.184067988	0.105370778
  8	K	M	0.188755388	0.159809948	404	H	N	0.183958455	0.132891407
  699	E	K	0.188739566	0.092771182	710	-----	VEQRR (SEQ	0.183918384	0.104439918
  							ID NO: 3776)
  132	C	G	0.188700628	0.133537793	889	S	P	0.183788189	0.164091129
  338	A	V	0.188698117	0.151434141	144	V	L	0.183743996	0.065170935
  641	R	[stop]	0.188367145	0.11062471	165	R	K	0.183736362	0.17610787
  208	V	L	0.188333358	0.080207667	28	M	V	0.183560659	0.134087452
  207	P	T	0.188302368	0.15553127	611	A	T	0.183558778	0.136945744
  879	N	K	0.186386792	0.12079248	148	GK	DR	0.183483799	0.153480995
  712	Q	L	0.186379419	0.129128012	515	A	C	0.183483799	0.109594032
  583	L	P	0.186146799	0.156442099	367	N	S	0.183341948	0.159877593
  323	----	QRLK (SEQ	0.186069265	0.110701992	868	E	K	0.183187044	0.163165035
  		ID NO: 3648)
  358	----	KEDG (SEQ	0.18604741	0.119601341	306	L	Q	0.183120006	0.156397405
  		ID NO: 3492)
  835	--	WM	0.18604741	0.100790291	216	G	D	0.183066489	0.119789101
  839	-------	INGKELK	0.18604741	0.115878922	728	N	Y	0.183065668	0.166304554
  		(SEQ ID NO:
  		3477)
  463	V	E	0.186017541	0.06776571	879	N	I	0.183004606	0.128653405
  299	Q	H	0.185842115	0.085070655	126	G	V	0.182789208	0.179342988
  832	A	C	0.185822701	0.103905008	35	V	M	0.182763396	0.156289233
  127	F	Y	0.185786991	0.140080792	443	S	N	0.182633222	0.162446869
  159	N	S	0.185693031	0.145375399	951	N	D	0.182629417	0.175906154
  532	--	IN	0.185685948	0.088889817	410	G	S	0.182624091	0.128840332
  439	-----	EERRS (SEQ	0.185685948	0.095520154	382	SS	CL	0.180218478	0.105067529
  		ID NO: 3382)
  152	--	TN	0.185685948	0.085877547	369	AG	DS	0.180218478	0.132171137
  684	---	LGN	0.18563709	0.122810431	757	LS	PV	0.180218478	0.120148198
  718	Y	[stop]	0.185557954	0.073476523	674	--------	GCPLSRFK	0.180218478	0.119094301
  							(SEQ ID NO:
  							3425)
  585	L	P	0.185474446	0.130833458	418	--	DE	0.180218478	0.162709755
  85	W	R	0.185353654	0.134359698	702	-------	RTIQAAK	0.180179308	0.102882749
  							(SEQ ID NO:
  							3693)
  931	-----	SWLFL (SEQ	0.185304071	0.113870586	81	L	P	0.180116381	0.137095425
  		ID NO: 3735)
  543	----	KKIK (SEQ	0.185304071	0.066752877	939	---	EYK	0.18007812	0.13192478
  		ID NO: 3501)
  547	-------	PEAFEAN	0.185304071	0.089391329	31	L	Q	0.180015666	0.152602881
  		(SEQ ID NO:
  		3615)
  91	D	G	0.1853036	0.092089443	213	-----	QIGGN (SEQ	0.179890016	0.080439406
  							ID NO: 3638)
  766	K	R	0.185284272	0.110005204	379	--	PY	0.179789203	0.118280148
  461	-----	SFVIE (SEQ	0.185264915	0.156592075	331	F	Y	0.179617168	0.14637274
  		ID NO: 3698)
  950	-----	GNTDK (SEQ	0.185264915	0.154386625	540	L	M	0.179584486	0.167412262
  		ID NO: 3446)
  233	M	V	0.182567289	0.115088116	693	I	V	0.179569128	0.124539552
  96	M	L	0.182378018	0.128312349	776	T	S	0.179453432	0.075575874
  753	------	IFANLS (SEQ	0.182269944	0.088037483	264	L	V	0.179340275	0.144429387
  		ID NO: 3472)
  634	V	A	0.182243984	0.121794563	547	P	R	0.179333799	0.110886672
  556	Y	S	0.182208476	0.102238152	820	D	E	0.179273983	0.124243775
  972	-------	VWKPAV	0.182135365	0.122971859	604	E	K	0.17907609	0.153006263
  		(SEQ ID NO:
  		3839)[stop]
  716	G	D	0.182118038	0.088377906	651	P	S	0.17907294	0.16496086
  419	E	G	0.182093842	0.165354368	382	S	C	0.179061797	0.042397129
  145	N	K	0.181832601	0.074663212	680	F	Y	0.179026865	0.083849485
  652	M	R	0.181725898	0.15882275	552	A	V	0.178983921	0.137645246
  183	Y	[stop]	0.181723054	0.087766244	693	I	F	0.178916903	0.17080226
  229	S	R	0.18162155	0.118611624	151	HT	LS	0.178787645	0.11267363
  589	K	E	0.181594685	0.120760487	190	-----	QRALD (SEQ	0.178787645	0.150480322
  							ID NO: 3645)
  304	V	I	0.181591972	0.14363826	208	-----	VKPLE (SEQ	0.178787645	0.112763983
  							ID NO: 3783)
  873	S	C	0.181321853	0.144241543	194	D	V	0.178645393	0.146182868
  114	P	S	0.181260379	0.131437002	767	RT	Sc	0.176164273	0.119651092
  100	A	S	0.181149523	0.170663024	678	S	N	0.176147348	0.146692604
  413	W	[stop]	0.181066052	0.139390154	817	T	A	0.176123605	0.120992816
  166	L	M	0.180963828	0.128703075	635	A	G	0.176061926	0.119367224
  496	------	IEAENS (SEQ	0.180890191	0.096196015	212	E	A	0.175873239	0.11085302
  		ID NO: 3468)
  504	D	V	0.180843532	0.116307526	821	Y	[stop]	0.175384143	0.118184345
  199	H	Q	0.180819165	0.098967075	447	Q	R	0.175284629	0.123528707
  675	C	W	0.180770613	0.172891211	257	N	S	0.175186561	0.099304683
  94	G	S	0.180639091	0.140246364	618	K	R	0.175178956	0.153225543
  212	E	D	0.180617877	0.126552831	217	N	S	0.175170771	0.153898212
  557	T	N	0.180519556	0.15369828	852	Y	[stop]	0.175104531	0.090584521
  753	I	S	0.180492647	0.165598334	255	K	R	0.175069831	0.070668507
  872	L	V	0.180432435	0.164444609	430	---	GLS	0.175035484	0.093564105
  596	------	IWNDLL	0.180218478	0.160627748	827	----	KLKK (SEQ	0.175035484	0.069987475
  		(SEQ ID NO:					ID NO: 3510)
  		3487)
  163	H	R	0.178633884	0.108142143	796	---	YLS	0.175035484	0.092544675
  383	S	I	0.178486259	0.158810182	414	---------	GKVYDEAW	0.175035484	0.140128399
  							E (SEQ ID
  							NO: 3441)
  156	G	D	0.178426488	0.134868493	547	-----	PEAFE (SEQ	0.175035484	0.118947618
  							ID NO: 3614)
  234	G	E	0.178414368	0.12320748	186	------	GKFGQR	0.175035484	0.092907507
  							(SEQ ID NO:
  							3435)
  804	Y	[stop]	0.178116642	0.169884859	580	L	R	0.174993228	0.092760152
  582	I	N	0.177915368	0.151449157	422	E	K	0.174900558	0.171745203
  655	I	T	0.177824888	0.131979099	285	H	Y	0.174862549	0.137793142
  129	C	Y	0.177764169	0.131217004	737	T	I	0.174757975	0.115488534
  20	K	[stop]	0.177744686	0.162022223	455	W	G	0.174674459	0.156270727
  852	Y	C	0.177655192	0.126363222	401	L	P	0.174440338	0.064966394
  179	E	Q	0.177438027	0.163530401	953	-	DKR	0.174181069	0.090682808
  365	W	S	0.177330558	0.12784352	953	----	DKRA (SEQ	0.174181069	0.085814279
  							ID NO: 3359)
  245	D	E	0.177288135	0.128142583	360	D	N	0.174161173	0.117286104
  593	R	G	0.177150053	0.165372274	520	K	E	0.174117735	0.143263172
  838	T	S	0.177144418	0.166381063	255	K	M	0.171890748	0.139268571
  979	LE[stop]G	VSSR (SEQ	0.177037198	0.160568847	675	--	CP	0.171877476	0.064917248
  		ID NO: 3834)
  265	K	E	0.176890073	0.124809095	853	Y	C	0.171733581	0.087723362
  440	E	D	0.176868582	0.097257257	631	A	V	0.171731995	0.15053602
  107	I	M	0.176863119	0.14397234	668	A	V	0.171647872	0.129168631
  22	A	P	0.176753805	0.123959084	508	F	S	0.17126701	0.136692573
  292	A	G	0.176665583	0.159949136	925	AL	DR	0.17104041	0.083554381
  803	Q	[stop]	0.176624558	0.101059884	437	--	LE	0.17104041	0.06885585
  329	P	S	0.176586746	0.173503743	853	--	YN	0.17104041	0.123300185
  196	Y	[stop]	0.176517802	0.122355941	797	------	LSKTLA	0.17104041	0.064415402
  							(SEQ ID NO:
  							3574)
  758	S	N	0.176368261	0.089480066	815	---	TIT	0.17104041	0.104377719
  298	A	T	0.176357721	0.087659893	462	--FV	ERL[stop]	0.17104041	0.089353273
  333	L	V	0.176333899	0.163860363	471	--	DK	0.17104041	0.0730883
  518	W	R	0.176185261	0.104632883	418	-----	DEAWE (SEQ	0.170904662	0.126366449
  							ID NO: 3348)
  459	KA	-V	0.176164273	0.103778218	213	---	QIG	0.170882441	0.117196646
  192	AL	DR	0.176164273	0.079837153	703	----	TIQA (SEQ	0.170763645	0.147647998
  							ID NO: 3750)
  979	LE----[stop]G	VSSKDLQA	0.176164273	0.074531926	356	E	A	0.170659559	0.127216719
  		(SEQ ID NO:
  		3810)
  35	VMT	ETA	0.176164273	0.104758915	869	L	V	0.170596065	0.1158133
  145	N	D	0.174107257	0.119744646	106	NI	TV	0.170299453	0.164756763
  819	----	ADYD (SEQ	0.174068679	0.17309276	160	V	L	0.170273865	0.111449611
  		ID NO: 3307)
  561	K	[stop]	0.174057181	0.086009056	163	H	Q	0.170101095	0.104599592
  761	F	S	0.17403349	0.168753775	210	P	T	0.170021527	0.150133417
  563	S	P	0.173902999	0.138700996	748	QD	R-	0.169874659	0.074658631
  70	L	P	0.173882613	0.120818159	775	------	YTRMED	0.169874659	0.080414628
  							(SEQ ID NO:
  							3859)
  24	K	[stop]	0.173808747	0.113872328	513	N	I	0.169811112	0.150139289
  834	G	A	0.173722333	0.117168406	743	--	YY	0.169783049	0.088429509
  167	I	N	0.173700086	0.14772793	467	-------	LKEADKD	0.169783049	0.163043441
  							(SEQ ID NO:
  							3556)
  496	--------	IEAENSILD	0.173653508	0.110162475	859		QNVVK (SEQ	0.167565632	0.122604368
  		(SEQ ID NO:					ID NO: 3643)
  		3470)
  618	K	[stop]	0.173508668	0.101750483	719	S	P	0.167206156	0.083551442
  297	V	E	0.173261294	0.132967549	712	Q	R	0.167205037	0.147128575
  426	K	E	0.173245682	0.081642461	964	F	S	0.166884399	0.138397154
  182	T	K	0.173138422	0.156579716	359	E	G	0.16680448	0.139659272
  660	G	S	0.17299716	0.158169348	191	R	K	0.166577954	0.144007057
  805	T	S	0.172972548	0.12868971	339	N	D	0.166374831	0.157063101
  458	A	S	0.172827968	0.144714634	212	E	K	0.166305352	0.157035199
  731	D	V	0.172739834	0.130565896	413	WG	LS	0.166270685	0.125303472
  829	K	E	0.172710008	0.121812751	149	--	KP	0.166270685	0.076773688
  859	Q	[stop]	0.172627299	0.130823394	284	----	PHTK (SEQ	0.166270685	0.139854804
  							ID NO: 3617)
  305	--	NL	0.172611068	0.12831984	146	D	N	0.166006779	0.113823305
  178	-	DE	0.172611068	0.108355628	686	N	D	0.165853975	0.141480032
  652	M	V	0.172566944	0.106266804	492	K	R	0.16571672	0.088451245
  582	I	M	0.172413921	0.144870464	580	LI	PV	0.165563978	0.079217211
  335	E	G	0.172324707	0.120749484	661	---	ENI	0.165563978	0.126675099
  940	--	YK	0.172247171	0.104630004	829	K	R	0.165378823	0.103172827
  450	A	D	0.172235862	0.15659478	608	L	V	0.165024412	0.161094218
  187	K	T	0.172165735	0.159986695	451	---	ALT	0.164823895	0.158152194
  289	GI	AV	0.172163889	0.117287191	581	II	TV	0.164823895	0.074002626
  579	NL	DR	0.172163889	0.094383078	297	----	VAQI (SEQ	0.164823895	0.107420642
  							ID NO: 3765)
  843	E	G	0.172115298	0.163114025	783	-	T	0.164823895	0.135845679
  259	K	E	0.171933606	0.128545463	496	I	V	0.164665656	0.140996169
  663	-I	CL	0.169783049	0.106475808	979	LE[stop]G	VSSE (SEQ	0.164491714	0.145714149
  							ID NO: 3795)
  803	------	QYTSKT	0.169772888	0.094792337	932	----	WLFL (SEQ	0.164491714	0.083188044
  		(SEQ ID NO:					ID NO: 3841)
  		3655)
  808	------	TCSNCG	0.169772888	0.089412307	637	------	TFERRE	0.164491714	0.152633112
  		(SEQ ID NO:					(SEQ ID NO:
  		3739)					3745)
  845	K	E	0.169715078	0.127028772	325	---	LKG	0.164491714	0.125129505
  552	A	T	0.169382091	0.146396839	764	------	QGKRTFM	0.163440941	0.098647738
  							(SEQ ID NO:
  							3634)
  476	C	F	0.169278987	0.093974927	107	I	T	0.163178218	0.154967966
  711	E	D	0.169174495	0.118203075	633	FVAL (SEQ	LWP[stop]	0.163026367	0.076347451
  						ID NO: 3259)
  631	A	S	0.169116909	0.130583861	213	--	QI	0.163026367	0.09979216
  303	W	[stop]	0.169003266	0.078930757	186	-----	GKFGQ (SEQ	0.163026367	0.114909103
  							ID NO: 3434)
  561	K	I	0.168954178	0.166308652	592	G	D	0.162807696	0.109433096
  157	--	RC	0.168739459	0.094824256	257	N	K	0.162725471	0.091658038
  721	K	R	0.168620063	0.147491806	473	DE	YH	0.162404215	0.086992333
  614	R	[stop]	0.168568195	0.15863634	975	P	A	0.162340126	0.074611129
  611	A	D	0.168315642	0.157590847	833	T	A	0.162275301	0.096163195
  78	K	[stop]	0.168282214	0.125424128	871	R	S	0.162178581	0.080758991
  917	----	ETHA (SEQ	0.168207257	0.122439321	909	-----	FVCLN (SEQ	0.162125073	0.14885021
  		ID NO: 3398)					ID NO: 3421)
  756	NL	DR	0.168207257	0.079944251	341	--	VD	0.162125073	0.111287809
  678	S	G	0.168124453	0.111226188	57	PI	DS	0.162125073	0.110736083
  525	K	I	0.16804127	0.142310409	83	VY	AV	0.162125073	0.121259318
  653	N	K	0.167953422	0.124668308	643	---	VLD	0.162125073	0.148280778
  37	T	N	0.16794635	0.137106698	561	K	N	0.161973573	0.145314105
  174	P	S	0.167775884	0.122107474	349	N	K	0.161796683	0.105713204
  756	----	NLSR (SEQ	0.167679572	0.073550026	318	E	R	0.161659235	0.066441966
  		ID NO: 3594)
  168	------	LLSPHK	0.167679572	0.081935755	554	--	RF	0.161611946	0.149093192
  		(SEQ ID NO:
  		3561)
  160	-------	VSEHERLI	0.167679572	0.116191677	505	I	F	0.161489243	0.076235653
  		(SEQ ID NO:
  		3791)
  630	----	PALF (SEQ	0.164491714	0.073996533	102	P	T	0.161386248	0.119400583
  		ID NO: 3610)
  343	-----	WWDMV	0.164491714	0.076194534	514	CA	LS	0.16113532	0.083183292
  		(SEQ ID NO:
  		3846)
  642	--	EV	0.164491714	0.162646605	979	------	VSSKDLQ	0.161025471	0.108550491
  							(SEQ ID NO:
  							3809)
  419	-----	EAWER (SEQ	0.164491714	0.082157078	445	D	Y	0.161008394	0.118993907
  		ID NO: 3379)
  360	--	DG	0.164491714	0.073133393	143	Q	K	0.160693826	0.130109004
  408	K	E	0.16446662	0.067392631	547	P	S	0.160635883	0.144061844
  48	R	G	0.164301321	0.157884797	29	K	N	0.158279304	0.142748603
  613	G	D	0.164218988	0.127296459	372	K	R	0.158267712	0.11920003
  175	-----	EANDE (SEQ	0.164149182	0.111610409	275	F	L	0.158241303	0.120299703
  		ID NO: 3377)
  671	D	E	0.164120916	0.112217289	741	L	P	0.158158865	0.120228264
  794	-------	KTYLSKT	0.16411942	0.087804343	430	G	V	0.158115277	0.126566194
  		(SEQ ID NO:
  		3531)
  599	------	DLLSLE	0.16411942	0.120903184	921	---	AEQ	0.158108573	0.11103467
  		(SEQ ID NO:
  		3364)
  58	I-	LS	0.16411942	0.094001227	242	K	E	0.158032112	0.1512035
  826	E	D	0.163807302	0.112540279	148	GK	RQ	0.158026029	0.155853601
  889	S	[stop]	0.163771981	0.149267099	295	--	NV	0.157603522	0.100157866
  199	---H	PRLY (SEQ	0.163715064	0.07899198	876	----	SVNN (SEQ	0.157603522	0.131358152
  		ID NO: 3622)					ID NO: 3732)
  916	FET	VQA	0.163715064	0.085074401	215	G	A	0.157466168	0.125711629
  496	-------	IEAENSI	0.163715064	0.073631578	319	A	V	0.15742503	0.144655841
  		(SEQ ID NO:
  		3469)
  164	----	ERLI (SEQ ID	0.163715064	0.124419929	222	G	A	0.157400391	0.107390901
  		NO: 3394)
  345	D	G	0.16357556	0.12500461	523	V	D	0.157098281	0.069302906
  134	Q	[stop]	0.163522049	0.142382805	753	-------	IFANLSR	0.157085986	0.062378414
  							(SEQ ID NO:
  							3473)
  43	R	Q	0.160624353	0.132247177	177	N	S	0.157058654	0.117427271
  317	D	E	0.160609141	0.14140596	461	S	R	0.157014829	0.122688776
  807	K	[stop]	0.160484146	0.104229856	823	R	T	0.156977695	0.125466793
  572	N	S	0.160431799	0.062377966	427	K	M	0.156963925	0.118535881
  644	LD	PV	0.160242602	0.128569608	111	K	[stop]	0.156885345	0.101390983
  699	EK	DR	0.160242602	0.092172248	253	V	L	0.156787797	0.082680225
  850	I	V	0.160226988	0.152692033	91	D	V	0.156758895	0.14763673
  100	AQ	LS	0.160110772	0.101933413	71	T	I	0.156624998	0.127600056
  558	VI	CL	0.160110772	0.10892714	592	------	GREFIW	0.156575371	0.050528735
  							(SEQ ID NO:
  							3450)
  270	--	AN	0.160110772	0.124579798	847	-----	EGQIT (SEQ	0.156575371	0.108055014
  							ID NO: 3386)
  979	LE[stop]GS-	VSSKDLQAS	0.160110772	0.049257177	111	KL	S[stop]	0.156575371	0.112953961
  	PGIK (SEQ ID	NT (SEQ ID
  	NO:	NO: 3816)
  	3279)[stop]
  484	K---WYGD	NSSLSASF	0.160110772	0.077521171	979	L-E[stop]	VSSN (SEQ	0.156575371	0.054922359
  	(SEQ ID NO:	(SEQ ID NO:					ID NO: 3829)
  	3274)	3602)
  205	NH	LS	0.160110772	0.08695461	717	G	E	0.15414714	0.124750031
  281	P	C	0.160110772	0.141761431	667	I	V	0.154117319	0.147646705
  939	E	R	0.160110772	0.106121188	623	-----	RRTRQ (SEQ	0.153993707	0.122323206
  							ID NO: 3682)
  672	-	S	0.160110772	0.105653932	773	R	G	0.153915262	0.146586561
  894	-------	SLLKKRFS	0.160110772	0.071577892	433	--	KH	0.153881949	0.097541884
  		(SEQ ID NO:
  		3722)
  199	HV	T[stop]	0.160110772	0.129212095	35	V	G	0.153666817	0.124448628
  47	L	Q	0.159718064	0.101565653	211	L	V	0.153538313	0.134546484
  262	A	V	0.159650297	0.156994685	26	G	D	0.15349539	0.149545585
  788	------	YEGLPS	0.159522485	0.129386966	279	-----	TLPPQ (SEQ	0.15339361	0.125011235
  		(SEQ ID NO:					ID NO: 3754)
  		3848)
  529	Y	N	0.159442162	0.135286632	664	------	PAVIAL	0.15339361	0.13972264
  							(SEQ ID NO:
  							3611)
  604	E	V	0.159292857	0.097301034	377	----	LLPY (SEQ	0.15339361	0.12480719
  							ID NO: 3559)
  284	P	S	0.159001205	0.153355474	53	N	D	0.15332875	0.117758231
  750	A	D	0.158401706	0.125762435	140	K	N	0.153228737	0.097346381
  950	G	A	0.158324371	0.153957854	694	GE	DR	0.153190779	0.097274205
  688	T	I	0.158292674	0.119969439	741	----	LLYY (SEQ	0.153190779	0.13376095
  							ID NO: 3562)
  203	------	ESNHPV	0.156575371	0.141927058	592	-----	GREFI (SEQ	0.153190779	0.103123693
  		(SEQ ID NO:					ID NO: 3449)
  		3396)
  230	DA	LS	0.156575371	0.105363533	684	------	LGNPTHI	0.153147895	0.112048537
  							(SEQ ID NO:
  							3550)
  408	-----	KHGED (SEQ	0.156575371	0.140706352	532	---	INY	0.153147895	0.072663729
  		ID NO: 3497)
  606	-------	GSLKLAN	0.156575371	0.154364417	311	K	N	0.153086255	0.08609524
  		(SEQ ID NO:
  		3454)
  166	L	Q	0.156435151	0.079474192	678	-----	SRFKD (SEQ	0.152422378	0.09122337
  							ID NO: 3728)
  213	Q	H	0.156012357	0.091435578	969	LK	PV	0.152422378	0.0541377
  447	Q	E	0.155900092	0.095629939	419	EAWERIDKK	RPGRESTRR	0.152422378	0.081179935
  						V (SEQ ID	W (SEQ ID
  						NO: 3256)	NO: 3674)
  689	H	P	0.155877877	0.131928361	670	--	TD	0.152422378	0.096788119
  335	E	Q	0.155876225	0.110366115	383	---	SEE	0.152422378	0.066189551
  84	Y	D	0.155784728	0.135489779	880	---	DIS	0.15109455	0.085164607
  531	I	N	0.155410746	0.152604803	296	VV	DR	0.15109455	0.140218943
  103	A	S	0.155352263	0.149390311	293	YN	DS	0.15109455	0.094395956
  661	E	V	0.155230224	0.090301063	359	ED	AV	0.15109455	0.062026733
  865	-------	LSVELDR	0.15478543	0.145114034	210	PL	RQ	0.15109455	0.109823159
  		(SEQ ID NO:
  		3579)
  677	LS	PV	0.15478543	0.108120931	758	S-	TG	0.15109455	0.105413113
  570	E	G	0.154599098	0.10691093	232	CM	LS	0.15109455	0.096388212
  762	G	D	0.154432235	0.117428168	930	RSWLFL	EAGCS (SEQ	0.15109455	0.077157167
  						(SEQ ID NO:	ID NO:
  						3287)	3376)[stop]
  177	N	K	0.15431964	0.1416948	886	KG	C-	0.15109455	0.085064934
  484	K	N	0.154291635	0.117621744	594	EF	DC	0.15109455	0.055097165
  592	GRE--	DNQVG (SEQ	0.154254957	0.077027283	140	K	[stop]	0.150604639	0.124522684
  		ID NO: 3368)
  704	-----	IQAAK (SEQ	0.154254957	0.108682368	979	LE[stop]GS-	VSSKDI (SEQ	0.150527572	0.113935287
  		ID NO: 3480)					ID NO: 3803)
  285	-----	HTKEG (SEQ	0.154254957	0.106587271	979	L-E[stop]G	VSSKA (SEQ	0.150527572	0.106493096
  		ID NO: 3464)					ID NO: 3798)
  721	KY	TV	0.154254957	0.124126134	851	T	A	0.150513073	0.138774627
  650	-------	KPMNLIG	0.154254957	0.151047576	615	V	A	0.150425208	0.101961366
  		(SEQ ID NO:
  		3524)
  403	----	LHLE (SEQ	0.152422378	0.132942463	359	-	E	0.150399286	0.136024193
  		ID NO: 3551)
  389	KG	TV	0.152422378	0.11037889	508	------	FSKQYN	0.150399286	0.049469473
  							(SEQ ID NO:
  							3416)
  850	-----	ITYYN (SEQ	0.152422378	0.102611165	202	R--------	SSSLASGL	0.150399286	0.07744146
  		ID NO: 3484)					(SEQ ID NO:
  							3731)[stop]
  230	-------	DACMGAV	0.152422378	0.082337669	884	-----	WTKGR	0.150399286	0.084711675
  		(SEQ ID NO:					(SEQ ID NO:
  		3343)					3844)
  461	----	SFVI (SEQ ID	0.152422378	0.085894307	399	------	GDLLLH	0.150399286	0.08514719
  		NO: 3697)					(SEQ ID NO:
  							3426)
  673	E-	DR	0.152422378	0.059554386	39	D	G	0.150354378	0.13986784
  257	N	D	0.152411625	0.106853984	891	E	V	0.150263535	0.113865674
  590	R	G	0.152081011	0.117905973	450	A	P	0.150166455	0.146935336
  737	T	N	0.151886476	0.142783247	240	----	LTKY (SEQ	0.147451251	0.080958956
  							ID NO: 3581)
  790	G	E	0.151825437	0.098317165	942	KY	NC	0.147451251	0.116243971
  831	T	S	0.151806143	0.14386859	47	LR	C-	0.147451251	0.058888218
  906	QE	PV	0.151695593	0.100183043	807	KT	-C	0.147451251	0.120603495
  99	V	D	0.151565952	0.12300149	603	LE	PV	0.147451251	0.066385351
  959	---	ETW	0.151393972	0.086210639	873	---	SEE	0.147451251	0.078348652
  520	K	R	0.151365824	0.113621271	15	KD	R-	0.147451251	0.123855007
  852	Y	N	0.151328449	0.137543743	206	HP	DS	0.147451251	0.064383902
  444	E	G	0.151257656	0.118296919	599	DL	--	0.147451251	0.079608104
  147	---	KGK	0.15109455	0.054833005	979	L-E[stop]GS	VSSKDP	0.147451251	0.049212446
  							(SEQ ID NO:
  							3822)
  171	--	PH	0.15109455	0.08380172	979	LE[stop]GS-	VSSNDLQAS	0.147451251	0.067765787
  						PGIK (SEQ ID	NK (SEQ ID
  						NO:	NO: 3833)
  						3279)[stop]
  925	---	ALN	0.15109455	0.138412128	448	--	SK	0.147451251	0.090898875
  539	-----	KLRFK (SEQ	0.15109455	0.128926028	505	I-	LS	0.147451251	0.077683234
  		ID NO: 3516)
  334	-------	VERQANE	0.15109455	0.059721295	398	FG	SV	0.147451251	0.073631355
  		(SEQ ID NO:
  		3777)
  484	KW	TG	0.15109455	0.091510022	512	-Y	DS	0.147451251	0.05128316
  848	G-	AV	0.15109455	0.104352239	345	----	DMVC (SEQ	0.147451251	0.06441585
  							ID NO: 3366)
  236	------	VASFLT	0.15109455	0.088006138	177	ND--	FTG[stop]	0.147451251	0.085413531
  		(SEQ ID NO:
  		3767)
  429	E	D	0.149933575	0.107236607	36	MT	C-	0.147451251	0.118494367
  77	K	E	0.148931072	0.079170957	953	D-	AV	0.147451251	0.040719542
  259	-------	KRLANLKD	0.148805792	0.108390156	451	AL	DR	0.147451251	0.096339405
  		(SEQ ID NO:
  		3528)
  978	[stop]L	GI	0.148805792	0.119775179	631	A	C	0.147319263	0.109020371
  386	D-	AV	0.148805792	0.079572543	848	G	A	0.147279724	0.093306967
  748	QD	PV	0.148805792	0.094563395	239	F	S	0.147177048	0.142500129
  609	KL	DR	0.148805792	0.060702366	270	A	T	0.147117218	0.13621963
  699	EK	DC	0.148805792	0.122863259	352	K	N	0.147067273	0.12109567
  279	---	TLP	0.148805792	0.138832536	563	S	T	0.147049099	0.111696976
  24	K	M	0.148782741	0.14630409	612	N	K	0.146927237	0.108594483
  798	S	T	0.148583442	0.105674096	569	M	V	0.146754771	0.119310335
  349	N	S	0.148310626	0.138528822	855	R	G	0.144425593	0.123370913
  403	--	LH	0.148273333	0.102736	617	E	V	0.144206082	0.126166622
  967	------	KKLKEVW	0.148059201	0.11964291	918	--------	THAAEQAA	0.143857661	0.070236443
  		(SEQ ID NO:					(SEQ ID NO:
  		3504)					3749)
  157	RC	LS	0.14801524	0.133243315	733	----	MVRN (SEQ	0.143791778	0.090612696
  							ID NO: 3585)
  493	PF	TV	0.14801524	0.059147928	217	NS	TG	0.143791778	0.113745581
  188	------	FGQRALD	0.14801524	0.10137508	657	-----	IARGE (SEQ	0.143791778	0.039293361
  		(SEQ ID NO:					ID NO: 3466)
  		3412)
  898	KR	TG	0.14801524	0.120213578	533	N	S	0.14375365	0.085993529
  186	--	GK	0.14801524	0.114746024	185	-------	LGKFGQRA	0.14367777	0.094952199
  							(SEQ ID NO:
  							3548)
  328	F-	LS	0.14801524	0.071716609	616	-------	IEKTLYN	0.14367777	0.110151228
  							(SEQ ID NO:
  							3471)
  204	------	SNHPVKP	0.14801524	0.094645672	668	------	ALTDPE	0.14367777	0.113895553
  		(SEQ ID NO:					(SEQ ID NO:
  		3724)					3323)
  314	--	IG	0.14801524	0.075655093	259	----	KRLA (SEQ	0.14367777	0.070148108
  							ID NO: 3527)
  422	ER	AV	0.14801524	0.044733928	175	E-	DR	0.14367777	0.049065425
  64	AN	DS	0.14801524	0.108571015	610	------	LANGRV	0.14367777	0.105216814
  							(SEQ ID NO:
  							3537)
  855	--	RY	0.14801524	0.108772293	507	-------	GFSKQYN	0.14367777	0.101689858
  							(SEQ ID NO:
  							3430)
  504	D	E	0.147876758	0.098656217	487	---	GDL	0.14367777	0.046711447
  342	D	H	0.147844774	0.140125334	731	DD	CL	0.14367777	0.067816779
  86	EE	DR	0.147451251	0.143531987	265	KD	R-	0.14367777	0.130304386
  940	-Y	SV	0.14673352	0.076906931	386	---	DRK	0.14367777	0.092432212
  794	KT	NC	0.14673352	0.093083088	790	-----	GLPSK (SEQ	0.14367777	0.104428158
  							ID NO: 3444)
  487	----	GDLR (SEQ	0.14673352	0.141269601	147	--------	KGKPHTNY	0.140217655	0.060731949
  		ID NO: 3427)					(SEQ ID NO:
  							3496)
  717	--	GY	0.14673352	0.129086357	979	LE[stop]GS-	VSSKDV	0.140217655	0.126849347
  							(SEQ ID NO:
  							3824)
  468	----	KEAD (SEQ	0.14673352	0.112176586	342	-	D	0.140217655	0.083180031
  		ID NO: 3490)
  102	P	L	0.146729077	0.094784801	701	------	QRTIQA	0.140217655	0.094973524
  							(SEQ ID NO:
  							3650)
  462	F	V	0.146714745	0.123539268	588	G	R	0.140077599	0.123307802
  291	E	Q	0.146533408	0.078647294	248	L	V	0.139838145	0.132091481
  657	------	IDRGEN	0.146511494	0.145489762	641	R	G	0.139811399	0.120984089
  		(SEQ ID NO:
  		3467)
  32	L	F	0.146467882	0.099225719	375	E	G	0.13977585	0.117490416
  619	T	N	0.146372017	0.145146105	179	E	K	0.139614148	0.122113279
  355	N	K	0.146341962	0.141209887	285	---	HTK	0.139514563	0.076217964
  132	C	S	0.146274101	0.131138669	166	--	LI	0.139514563	0.075733937
  831	T	A	0.146217161	0.113775751	786	----	LAYE (SEQ	0.139514563	0.068877295
  							ID NO: 3541)
  868	E	V	0.145780526	0.143894902	274	AF	TV	0.139413376	0.092095094
  231	A	P	0.14576396	0.105172115	578	--	PN	0.139413376	0.112737023
  944	-----	QTNKT (SEQ	0.14564914	0.125394667	775	-----	YTRME (SEQ	0.13869596	0.096841774
  		ID NO: 3653)					ID NO: 3858)
  236	-----	VASFL (SEQ	0.14564914	0.09085897	838	TING (SEQ	PSTA (SEQ	0.13869596	0.135948561
  		ID NO: 3766)				ID NO: 3290)	ID NO: 3624)
  709	--	EV	0.14564914	0.119119066	75	E	K	0.138622423	0.112055782
  865	L	P	0.145527367	0.10928669	556	Y	C	0.138477684	0.131330328
  510	----	KQYN (SEQ	0.145296444	0.112653295	98	R	[stop]	0.138179687	0.102036322
  		ID NO: 3525)
  959	--	ET	0.145296444	0.114339851	460	A	T	0.137813435	0.108501414
  414	G	V	0.1451247	0.140131131	111	K	N	0.137723187	0.11828435
  465	E	G	0.144909944	0.124547249	566	I	F	0.137434779	0.130961132
  300	I	T	0.144877384	0.129206612	438	------	EEERRS	0.137192189	0.064149715
  							(SEQ ID NO:
  							3380)
  215	G	S	0.144824715	0.07809376	58	I	M	0.13705694	0.089110339
  288	E	G	0.144744415	0.110082872	913	NCGFET	EAAVQA	0.134611486	0.113195929
  						(SEQ ID NO:	(SEQ ID NO:
  						3282)	3372)
  16	D	N	0.144678092	0.139073977	11	-R	AS	0.134611486	0.123271552
  774	QY	PV	0.14367777	0.076535556	978	[stop]LE[stop]	YVSSKDLQA	0.134611486	0.087096491
  						GS-PG (SEQ	(SEQ ID NO:
  						ID NO: 3251)	3864)
  910	--	VC	0.14367777	0.024273265	247	------	ILEHQK	0.134611486	0.104206673
  							(SEQ ID NO:
  							3476)
  484	KW	DR	0.14367777	0.094175463	517	I	T	0.134524102	0.104605605
  20	--	CL	0.14367777	0.08704024	18	N	Y	0.134422379	0.132333464
  847	--------	EGQITYYN	0.14367777	0.054370233	804	----	YTSK (SEQ	0.134383084	0.102298299
  		(SEQ ID NO:					ID NO: 3860)
  		3389)
  114	P	L	0.143623976	0.107371623	872	-------	LSEESVN	0.134383084	0.104954479
  							(SEQ ID NO:
  							3573)
  294	N	S	0.143486731	0.084830242	743	Y	H	0.134286698	0.08203884
  473	D	G	0.143465301	0.122194432	250	H	Q	0.134238241	0.111012466
  376	A	T	0.1434567	0.101440197	268	A	P	0.134027791	0.098451313
  637	T	A	0.143296115	0.114711319	978	[stop]LE[stop]	YVSSKDLQ	0.134010909	0.133274253
  						GSPG (SEQ	(SEQ ID NO:
  						ID NO: 3251)	3863)
  365	W	C	0.143131818	0.093254266	664	--	PA	0.134010909	0.124393367
  559	I	S	0.142993499	0.107801059	979	LE[stop]G-	VSSND (SEQ	0.133919467	0.126494561
  							ID NO: 3830)
  671	D	S	0.142731931	0.123439168	241	T	N	0.133870518	0.110803484
  487	-----	GDLRGK	0.14265438	0.086040474	153	N	S	0.133623126	0.12555263
  		(SEQ ID NO:
  		3428)
  211	LEQIG (SEQ	RNRSA (SEQ	0.14265438	0.100691421	196	Y	H	0.133619017	0.107174466
  	ID NO: 3280)	ID NO: 3670)
  26	GP	CL	0.14265438	0.067388407	744	Y-	LS	0.133358224	0.114892564
  421	--	WE	0.14265438	0.084239003	633	F	S	0.133277029	0.122435158
  211	----	LEQI (SEQ ID	0.14265438	0.118588014	619	T	S	0.133139525	0.08963831
  		NO: 3543)
  767	R	[stop]	0.141592128	0.123403074	742	L	P	0.133131448	0.09127341
  290	I	N	0.141531787	0.136370873	809	C	[stop]	0.133028515	0.072072201
  774	Q	[stop]	0.141517184	0.125118121	86	E	D	0.132733699	0.128073996
  341	V	E	0.14127686	0.094518287	473	D	V	0.132562245	0.055193421
  176	A	S	0.140653486	0.112098857	568	--	PM	0.130626359	0.119168349
  562	K	N	0.140512419	0.126501373	362	K	R	0.130604026	0.105840846
  317	D	H	0.140493859	0.124148887	359	E	V	0.130475561	0.064946527
  941	------	KKYQTN	0.140217655	0.077001548	426	----	KKVE (SEQ	0.130424348	0.109290243
  		(SEQ ID NO:					ID NO: 3506)
  		3508)
  826	E	K	0.136937076	0.066669616	300	IV	DR	0.130424348	0.08495594
  955	R	T	0.136388186	0.086919652	893	--	LS	0.130424348	0.106896252
  400	-----	DLLLH (SEQ	0.136321349	0.064628042	256	KN	TV	0.130424348	0.057621352
  		ID NO: 3361)
  163	--------	HERLILL	0.136321349	0.117792482	767	----	RTFM (SEQ	0.130424348	0.06446722
  		(SEQ ID NO:					ID NO: 3691)
  		3460)
  950	-	G	0.136321349	0.089773613	324	R	G	0.13036573	0.130162815
  353	-------	LINEKKE	0.136321349	0.11384298	460	A	P	0.129809906	0.111386576
  		(SEQ ID NO:
  		3554)
  469	--------	EADKDEFC	0.136321349	0.136235916	744	Y	S	0.129801283	0.120155085
  		(SEQ ID NO:
  		3373)
  298	------	AQIVIW	0.136321349	0.124259801	297	V	L	0.1296923	0.098130283
  		(SEQ ID NO:
  		3328)
  967	---	KKL	0.136321349	0.087024226	979	LE	VP	0.129554025	0.068280994
  834	G	D	0.136317736	0.131556677	595	-------	FIWNDLL	0.129554025	0.083916268
  							(SEQ ID NO:
  							3414)
  675	C	S	0.135933989	0.124817499	909	F	C	0.129452838	0.12013501
  295	N	D	0.135903192	0.116385268	39	D	N	0.128914064	0.121593627
  489	L	P	0.135710175	0.113005835	263	N	D	0.128846416	0.111193487
  316	R	W	0.135665116	0.08159144	403	-------	LHLEKKH	0.128586666	0.071668629
  							(SEQ ID NO:
  							3553)
  782	L	P	0.135444097	0.094158481	979	LE[stop]GS-G	VSSKDLV	0.128586666	0.121567211
  							(SEQ ID NO:
  							3821)
  252	K	I	0.135215444	0.118419704	876	------	SVNNDI	0.128586666	0.054233667
  							(SEQ ID NO:
  							3733)
  703	--	TI	0.135116856	0.093813019	228	------	LSDACMG	0.128586666	0.126842965
  							(SEQ ID NO:
  							3571)
  671	---	DPE	0.135116856	0.117221994	701	----	QRTI (SEQ ID	0.128586666	0.098093616
  							NO: 3649)
  763	R	Q	0.135073853	0.130952104	549	-------	AFEANRFY	0.127406426	0.084837264
  							(SEQ ID NO:
  							3310)
  815	T	S	0.135026549	0.096980291	979	LE[stop]GSPG	VSSKDLQE	0.127187739	0.092227907
  						I (SEQ ID NO:	(SEQ ID NO:
  						3278)	3817)
  141	L	M	0.134960075	0.098794232	445	D	E	0.127007554	0.122060316
  789	E	K	0.134893603	0.120008321	82	H	N	0.126805938	0.104486705
  36	M	L	0.13488937	0.122340012	676	P	L	0.126754121	0.080812602
  278	I	F	0.134789571	0.111040576	951	----	NTDK (SEQ	0.126641231	0.099218396
  							ID NO: 3604)
  358	K	I	0.132508402	0.120198091	979	LE[stop]GS-	VSSKDLQAS	0.126641231	0.095848514
  						PGIK (SEQ ID	NN (SEQ ID
  						NO:	NO: 3815)
  						3279)[stop]
  476	-	C	0.132326289	0.087739647	204	----	SNHP (SEQ	0.126641231	0.07625836
  							ID NO: 3723)
  953	DK	E-	0.132326289	0.066036843	426	KK	DR	0.126641231	0.097925475
  770	------	MAERQY	0.132326289	0.083381966	923	QAA	PV-	0.126641231	0.093158654
  		(SEQ ID NO:
  		3584)
  887	-------	GRSGEAL	0.132326289	0.072961347	101	QP	ET	0.126641231	0.062121806
  		(SEQ ID NO:
  		3453)
  630	P	S	0.132221835	0.08064538	942	K-Y	NCL	0.126641231	0.088910569
  290	I	T	0.132066117	0.101441805	826	EK	AV	0.126641231	0.091897908
  81	L	Q	0.132063026	0.114766305	292	-----	AYNNV (SEQ	0.126641231	0.106376872
  							ID NO: 3338)
  809	C	F	0.131888449	0.093326725	879	------	NDISSWT	0.126641231	0.078787272
  							(SEQ ID NO:
  							3590)
  497	------	EAENSIL	0.131863052	0.100142921	181	VTYSLGKFG	-	0.126641231	0.089695218
  		(SEQ ID NO:				Q (SEQ ID	SHTAWASSD
  		3374)				NO: 3296)	(SEQ ID NO:
  							3709)
  717	-----	GYSRK (SEQ	0.131863052	0.112950153	137	YV	DR	0.126641231	0.109693213
  		ID NO: 3458)
  386	----	DRKK (SEQ	0.131863052	0.08146183	548	----	EAFE (SEQ	0.126641231	0.095888318
  		ID NO: 3369)					ID NO: 3375)
  68	KL	TV	0.131863052	0.070945883	670	------	TDPEGCP	0.12652671	0.087582312
  							(SEQ ID NO:
  							3743)
  700	KQ	DR	0.131863052	0.063471315	344	--	WD	0.12652671	0.059784458
  831	TAT	PPP	0.131863052	0.067816715	589	K	[stop]	0.126002643	0.117169902
  157	-----	RCNVS (SEQ	0.131863052	0.080937513	670	T	I	0.125333365	0.115123087
  		ID NO: 3659)
  953	------	DKRAFV	0.131771442	0.07848717	843	E	K	0.125307936	0.1170313
  		(SEQ ID NO:
  		3360)
  978	[stop]L	GF	0.131771442	0.061548024	209	---	KPL	0.125145098	0.058688797
  979	LE[stop]G	VSCK (SEQ	0.131568591	0.101292375	256	-----	KNEKR (SEQ	0.125145098	0.118773295
  		ID NO: 3788)					ID NO: 3517)
  855	R	S	0.131540317	0.054730727	627	-------	QDEPALF	0.125145098	0.11944079
  							(SEQ ID NO:
  							3633)
  128	A	T	0.13150991	0.131075942	637	TF	S-	0.125145098	0.075022945
  225	G	R	0.131348437	0.12857841	846	------	VEGQIT	0.125145098	0.095200634
  							(SEQ ID NO:
  							3774)
  874	E	D	0.131154993	0.12741404	112	LI	PV	0.125145098	0.061303825
  54	I	T	0.130796445	0.072189843	592	GRE-	DNQV (SEQ	0.125145098	0.061215515
  							ID NO: 3367)
  797	--------	LSKTLAQYT	0.128586666	0.060991971	273	-------	LAFPKIT	0.125145098	0.062360109
  		(SEQ ID NO:					(SEQ ID NO:
  		3575)					3535)
  14	VK	AG	0.128586666	0.085310723	773	----	RQYT (SEQ	0.125145098	0.098790624
  							ID NO: 3680)
  423	RI	LS	0.128586666	0.084850033	274	AF	DS	0.125145098	0.089301627
  583	--	LP	0.128586666	0.051620503	686	N-	TV	0.125145098	0.106327975
  979	LE[stop]GS-	VSSNDLQAS	0.128586666	0.102476858	549	-	A	0.125145098	0.111251903
  	PGIK (SEQ ID	N (SEQ ID
  	NO: 3279)	NO: 3832)
  979	LE[stop]GS-	FSSKDLQAS	0.128586666	0.093654912	615	---	VIE	0.125145098	0.115519537
  	PGIK (SEQ ID	NK (SEQ ID
  	NO:	NO: 3420)
  	3279)[stop]
  533	--	NY	0.128586666	0.127517343	486	Y	[stop]	0.12498861	0.117668911
  563	----	SGEI (SEQ ID	0.128586666	0.112169649	479	E	G	0.124803485	0.119823525
  		NO: 3702)
  979	L-E[stop]GS	VSSKDH	0.128586666	0.096285329	225	G	E	0.124549307	0.110077498
  		(SEQ ID NO:
  		3802)
  755	----	ANLS (SEQ	0.12851771	0.091942401	123	T	N	0.123826195	0.091669684
  		ID NO: 3326)
  461	S	N	0.128271168	0.11452282	436	K	E	0.123328926	0.10928445
  864	D	E	0.128210448	0.108842691	139	Y	[stop]	0.123256307	0.11429924
  84	Y	C	0.128022871	0.110536014	669	-	L	0.119637812	0.05675251
  720	----	RKYA (SEQ	0.127406426	0.102905352	845	------	KVEGQI	0.119637812	0.06612892
  		ID NO: 3669)					(SEQ ID NO:
  							3532)
  416	VYDEAWE	CTMRPG	0.127406426	0.059900059	400	------	DLLLHL	0.119637812	0.07276695
  	(SEQ ID NO:	(SEQ ID NO:					(SEQ ID NO:
  	3297)	3340)-					3362)
  808	----	TCSN (SEQ	0.127406426	0.082184056	757	L	R	0.119502434	0.108713549
  		ID NO: 3738)
  791	------	LPSKTY	0.127406426	0.108127962	578	P	L	0.119430629	0.116829607
  		(SEQ ID NO:
  		3568)
  162	------	EHERLI (SEQ	0.127406426	0.099109571	634	VA	LS	0.119372647	0.100712827
  		ID NO: 3390)
  858	------	RQNVVKDL	0.126641231	0.065591267	510	K--	SHL	0.119372647	0.080479619
  		(SEQ ID NO:
  		3679)
  231	A	C	0.126641231	0.070173983	979	LE[stop]G	ASSK (SEQ	0.119372647	0.074447954
  							ID NO: 3332)
  898	KRF	NCL	0.126641231	0.049641927	798	-S	TA	0.119372647	0.036802807
  789	EG	AV	0.126641231	0.10544887	653	NL	DR	0.119372647	0.061028998
  640	RR	TG	0.126641231	0.104632778	854	-N	LS	0.119372647	0.074161693
  303	-----	WVNLN	0.126641231	0.064376538	420	A	S	0.119261972	0.115184751
  		(SEQ ID NO:
  		3845)
  640	R-	TV	0.126641231	0.051697037	519	---	QKD	0.119051026	0.108753459
  890	GE	DR	0.126641231	0.058497447	600	LLS	PV-	0.119011185	0.056536344
  513	-------	NCAFIWQK	0.126641231	0.110534935	271	-------	NGLAFPK	0.119011185	0.073725244
  		(SEQ ID NO:					(SEQ ID NO:
  		3589)					3592)
  36	MT	TV	0.126641231	0.096682191	51	P	L	0.118978183	0.099712186
  979	--	AV	0.126641231	0.031136061	403	-----	LHLEK (SEQ	0.118963684	0.11518549
  							ID NO: 3552)
  607	---	SLK	0.126641231	0.117782054	457	-----	RAKAS (SEQ	0.118963684	0.088377062
  							ID NO: 3656)
  979	LE[stop]G	FSSK (SEQ	0.126627253	0.064240928	776	----	TRME (SEQ	0.118963684	0.083809802
  		ID NO: 3418)					ID NO: 3759)
  29	KT	LS	0.126627253	0.070400509	320	KPLQRL	SHCRD (SEQ	0.118677331	0.073630679
  						(SEQ ID NO:	ID NO:
  						3270)	3704)[stop]
  510	KQ-Y	SHLQ (SEQ	0.126602218	0.092982894	685	GNPT (SEQ	ATLH (SEQ	0.118677331	0.086334956
  		ID NO: 3705)				ID NO: 3263)	ID NO: 3334)
  960	---	TWQ	0.12652671	0.053263565	178	----	DELV (SEQ	0.118677331	0.101525884
  							ID NO: 3352)
  665	---	AVI	0.12652671	0.057438099	160	-----	VSEHE (SEQ	0.113504256	0.099167463
  							ID NO: 3789)
  675	-	C	0.12652671	0.103567494	745	-----	AVTQD (SEQ	0.113504256	0.111375922
  							ID NO: 3336)
  451	-------	ALTDWLR	0.12652671	0.081452296	570	E	K	0.1130503	0.100973674
  		(SEQ ID NO:
  		3324)
  805	-----	TSKTC (SEQ	0.12652671	0.07786947	368	L	P	0.111983406	0.095724154
  		ID NO: 3760)
  890	GE	VAKPLLQQ	0.12652671	0.093632788	275	F	Y	0.111191948	0.100665217
  		(SEQ ID NO:
  		3764)
  885	--	TK	0.12652671	0.12280066	521	D	E	0.111133748	0.10058089
  831	T	N	0.123113024	0.105004336	562	K	E	0.110566391	0.097349138
  147	------	KGKPHTN	0.123112897	0.091739528	136	L	Q	0.110244812	0.107286129
  		(SEQ ID NO:
  		3495)
  256	---	KNE	0.122844147	0.106923843	411	E	G	0.110174632	0.097582202
  179	EL	A-	0.122844147	0.091584443	381	LS	PV	0.110164473	0.095898615
  406	-----	EKKHG (SEQ	0.122844147	0.089153499	616	I	V	0.109853606	0.094001833
  		ID NO: 3392)
  295	------	NVVAQ (SEQ	0.122844147	0.103819809	843	E	R	0.109803145	0.097494217
  		ID NO: 3607)
  658	D	E	0.122389699	0.080353294	676	P	H	0.109607681	0.091744681
  206	H	Q	0.122384978	0.08971464	484	KWYG (SEQ	NSSL (SEQ	0.109535927	0.106819917
  						ID NO: 3273)	ID NO: 3600)
  689	H	Q	0.122256431	0.089420446	511	QY	PV	0.109451554	0.106726398
  306	LN	PV	0.121921649	0.07283705	979	LE[stop]GSP	VSSKDV	0.108902792	0.077647274
  							(SEQ ID NO:
  							3824)
  620	LY	PV	0.121921649	0.084823364	420	A	V	0.108649806	0.097722159
  910	--	SG	0.121685511	0.114110877	53	N	K	0.108567111	0.086753227
  508	--------	FSKQYNCA	0.121235544	0.060533533	114	P	A	0.108538006	0.106859466
  		(SEQ ID NO:
  		3417)
  314	I	F	0.120726616	0.074980055	637	-------	TFERREV	0.108360722	0.063051456
  							(SEQ ID NO:
  							3746)
  746	VT	C-	0.120516649	0.087097894	286	TK	DR	0.108360722	0.053025872
  910	VC	CL	0.119637812	0.085877084	249	EH	AV	0.108360722	0.095653705
  621	------	YNRRTR	0.119637812	0.065553526	67	NK	DR	0.108360722	0.039884349
  		(SEQ ID NO:
  		3853)
  467	------	LKEAD (SEQ	0.119637812	0.109940477	944	-------	QTNKTTG	0.108360722	0.078648908
  		ID NO: 3555)					(SEQ ID NO:
  							3654)
  827	-	KL	0.119637812	0.054530509	513	------	NCAFIW	0.108360722	0.045078115
  							(SEQ ID NO:
  							3588)
  374	---	QEA	0.119637812	0.063378708	429	----	EGLS (SEQ	0.108360722	0.046808088
  							ID NO: 3384)
  145	---	NDK	0.119637812	0.051846935	615	VI	AV	0.108360722	0.089957198
  979	LE[stop]GSPG	FSSKDLQ	0.119637812	0.067517262	927	----	NIAR (SEQ	0.108360722	0.096224338
  	(SEQ ID NO:	(SEQ ID NO:					ID NO: 3593)
  	3251)	3419)
  338	---	ANE	0.119637812	0.103007188	56	Q	V	0.108360722	0.076115958
  389	KG	R-	0.119637812	0.050940425	852	YY	C-	0.108360722	0.054744482
  587	------	FGKRQG	0.118677331	0.110043529	816	IT	LS	0.108360722	0.074232993
  		(SEQ ID NO:
  		3411)
  783	------	TAKLAY	0.118677331	0.076704941	210	P	S	0.108088041	0.085752595
  		(SEQ ID NO:
  		3736)
  542	--	FK	0.118677331	0.098685141	251	---	QKV	0.107840626	0.092439
  733	------	MVRNTAR	0.118677331	0.078476963	351	----	KKLI (SEQ	0.107840626	0.05939446
  		(SEQ ID NO:					ID NO: 3502)
  		3586)
  396	----	YQFG (SEQ	0.118677331	0.08225792	962	------	QSFYRKK	0.107840626	0.060903469
  		ID NO: 3855)					(SEQ ID NO:
  							3651)
  837	-----	TTING (SEQ	0.118677331	0.059978646	594	EFI	DCL	0.107840626	0.078577001
  		ID NO: 3762)
  729	L	P	0.118360335	0.091091038	600	---	LLS	0.107840626	0.107212137
  194	D	E	0.117679069	0.090466918	979	LE[stop]GS-	ASSKDLQAS	0.107840626	0.073484536
  						PGIK (SEQ ID	N (SEQ ID
  						NO: 3279)	NO: 3333)
  582	ILP	SC-	0.11732562	0.090313521	606	---	GSL	0.107840626	0.104907627
  901	---	SHR	0.11712133	0.108439325	604	---	ETG	0.107840626	0.105428162
  67	N	D	0.116939695	0.113264127	473	-------	DEFCRCE	0.107840626	0.072973962
  							(SEQ ID NO:
  							3351)
  309	W	R	0.116671977	0.111491729	798	------	SKTLAQ	0.107840626	0.085530107
  							(SEQ ID NO:
  							3713)
  74	T	S	0.11653877	0.0855649	607	-----	SLKLA (SEQ	0.107840626	0.087611083
  							ID NO: 3178)
  838	T	N	0.116394614	0.094955966	705	Q-	ET	0.107840626	0.102652999
  137	Y	[stop]	0.116334699	0.088258455	215	GG	CL	0.105199237	0.057087854
  591	Q	[stop]	0.116290785	0.093561727	886	KG	TV	0.105199237	0.077099458
  686	N	K	0.116232458	0.062605741	198	-I	TV	0.105199237	0.087584827
  445	-----	DAQSK (SEQ	0.115532631	0.10378499	878	NN	DS	0.105199237	0.079694461
  		ID NO: 3344)
  134	Q	P	0.114967131	0.11371497	76	MK	IC	0.105199237	0.090203405
  698	-	KE	0.114412847	0.098843087	227	ALSDA (SEQ	SPERR (SEQ	0.105199237	0.101107303
  						ID NO: 3252)	ID NO: 3727)
  701	QR	PV	0.114412847	0.104102361	134	Q-P	HCL	0.105199237	0.057452451
  281	---	PPQ	0.114412847	0.077542482	794	K-T	NCL	0.105199237	0.055344005
  708	K	[stop]	0.113715295	0.106986973	532	-----	INYFK (SEQ	0.105199237	0.091675146
  							ID NO: 3478)
  696	SYK	LQR	0.113676993	0.07036758	558	VI	AV	0.105199237	0.093989814
  703	--	TIQ	0.113676993	0.062517799	610	--	LA	0.105199237	0.085523633
  596	I	F	0.113504467	0.107709004	82	-H	DS	0.105199237	0.045790293
  197	------	SIHVTRE	0.108360722	0.081689422	780	DW	AV	0.105199237	0.092887336
  		(SEQ ID NO:
  		3710)
  510	KQYNCA	SHLQNS	0.108360722	0.044585998	708	-------------	KEVEQR	0.105052225	0.060231645
  	(SEQ ID NO:	(SEQ ID NO:					(SEQ ID NO:
  	3271)	3706)					3493)
  953	D	C	0.108360722	0.098828046	548	EAFE (SEQ	RPSR (SEQ	0.105052225	0.087924295
  						ID NO: 3255)	ID NO: 3675)
  63	RA	SC	0.108360722	0.091093584	251	-----	QKVIK (SEQ	0.105052225	0.044504449
  							ID NO: 3642)
  597	-----	WNDLL (SEQ	0.108360722	0.065802495
  		ID NO: 3842)			497	EA	AV	0.105052225	0.084527693
  208	VK	CL	0.108360722	0.044537036	841	-------	GKELKVE	0.105052225	0.091417746
  							(SEQ ID NO:
  							3433)
  468	-------	KEADKDE	0.108360722	0.074432186	575	F-	LS	0.105052225	0.076582865
  		(SEQ ID NO:
  		3491)
  84	-Y	DS	0.108360722	0.088490546	910	-----	VCLNC (SEQ	0.105052225	0.090851749
  							ID NO: 3769)
  496	--	IE	0.108360722	0.07371372	570	-----	EVNFN (SEQ	0.104207678	0.100821855
  							ID NO: 3407)
  672	P---E	SGCV (SEQ	0.108360722	0.07159837	661	--	EN	0.104134797	0.102286534
  		ID NO:
  		3701)[stop]
  910	VC	AV	0.108360722	0.062775349	500	---	NSI	0.104134797	0.058937244
  868	EL	DR	0.108360722	0.050620256	420	-------	AWERIDK	0.104134797	0.06870659
  							(SEQ ID NO:
  							3337)
  235	--	AV	0.108360722	0.094955272	285	-------	HTKEGIE	0.10063092	0.059060467
  							(SEQ ID NO:
  							3465)
  332	PL	RQ	0.108360722	0.062876398	347	---	VCN	0.10063092	0.070834064
  461	-------	SFVIEGLK	0.108360722	0.064022496	671	-	D	0.10063092	0.070617109
  		(SEQ ID NO:
  		3699)
  562	KSGEI (SEQ	SPAR (SEQ	0.108360722	0.067954904	103	AP	DS	0.10063092	0.044259819
  	ID NO: 3272)	ID NO: 3726)-
  556	------	YTVINKK	0.108360722	0.070852948	584	---	PLA	0.10063092	0.096095285
  		(SEQ ID NO:
  		3861)
  121	RLT	SC-	0.108360722	0.070897115	685	GN	DS	0.10063092	0.057986016
  868	EL	NW	0.108360722	0.108128749	837	-------	TTINGKE	0.10063092	0.070942034
  							(SEQ ID NO:
  							3763)
  745	----	AVTQ (SEQ	0.108360722	0.088762315	509	----	SKQY (SEQ	0.10063092	0.078527136
  		ID NO: 3335)					ID NO: 3711)
  674	------	GCPLSR	0.107840626	0.089241733	914	-C	LS	0.10063092	0.094652044
  		(SEQ ID NO:
  		3424)
  185	-------	LGKFGQR	0.107840626	0.068363178	932	---	WLF	0.10063092	0.060195605
  		(SEQ ID NO:
  		3547)
  344	WD	LS	0.107840626	0.066070011	979	LE[stop]G	VSRK (SEQ	0.10063092	0.052097814
  							ID NO: 3794)
  274	-	AF	0.107840626	0.075101467	194	------	DFYSIH (SEQ	0.10063092	0.073983623
  							ID NO: 3354)
  577	D	G	0.1075508	0.10472372	596	----	IWND (SEQ	0.10063092	0.075782386
  							ID NO: 3486)
  700	K	M	0.107451835	0.099853237	32	L	S	0.099998377	0.098160777
  641	--	RE	0.106527066	0.104478931	822	D	E	0.099951571	0.083423411
  599	----	DLLS (SEQ	0.106527066	0.100649327	957	F	S	0.099918571	0.054364404
  		ID NO: 3363)
  564	GE	DR	0.106527066	0.090487961	902	----	HRPV (SEQ	0.099764722	0.080515888
  							ID NO: 3462)
  836	MT	IC	0.106527066	0.100530022	474	-----	EFCRC (SEQ	0.099764722	0.089224756
  							ID NO: 3383)
  853	-----	YNRYK (SEQ	0.106527066	0.088862545	242	---	KYQ	0.099764722	0.054563676
  		ID NO: 3854)
  586	----	AFGK (SEQ	0.106527066	0.08642655	342	D	C	0.099764722	0.075335971
  		ID NO: 3311)
  275	-F	SV	0.106527066	0.099879454	413	--	WG	0.099764722	0.079591734
  429	--	EG	0.106527066	0.066947062	149	-------	KPHTNYF	0.099764722	0.070518497
  							(SEQ ID NO:
  							3522)
  612	N	T	0.106459427	0.08415093	510	KQY	SHL	0.099764722	0.087972807
  611	---	ANG	0.105912094	0.09807063	775	----	YTRM (SEQ	0.097097924	0.054287911
  							ID NO: 3857)
  563	-----	SGEIV (SEQ	0.105912094	0.10402865	607	--	SL	0.097097924	0.071187897
  		ID NO: 3703)
  203	E-	DR	0.10545658	0.048953383	897	-K	TE	0.097097924	0.05492748
  872	--	LS	0.10545658	0.08227801	118	GN	DS	0.097097924	0.083309653
  291	EA	-C	0.10545658	0.078263499	425	D	V	0.096834118	0.093228512
  894	S-	TG	0.10545658	0.077864616	704	--	IQ	0.096824625	0.053400496
  851	-T	LS	0.10545658	0.071676834	207	----	PVKPLE	0.096824625	0.074740089
  							(SEQ ID NO:
  							3630)
  251	--	QK	0.105199237	0.101057895	154	--	YF	0.096824625	0.067984555
  194	-----	DFYSI (SEQ	0.105199237	0.05958457	668	----	ALTD (SEQ	0.096824625	0.088221952
  		ID NO: 3353)					ID NO: 3322)
  236	---	VAS	0.105199237	0.084024149	386	--	DR	0.096824625	0.067625309
  899	RF	SC	0.105199237	0.046835281	388	----	KKGK (SEQ	0.096824625	0.060426936
  							ID NO: 3498)
  533	----	NYFK (SEQ	0.104134797	0.074535749	880	----	DISS (SEQ ID	0.096824625	0.089590245
  		ID NO: 3609)					NO: 3358)
  747	---	TQD	0.104134797	0.072847901	783	--------	TAKLAYEG	0.096824625	0.064829377
  							(SEQ ID NO:
  							3737)
  371	--	YK	0.104134797	0.087850723	643	--------	VLDSSNIK	0.096824625	0.089286037
  							(SEQ ID NO:
  							3785)
  625	TR	-Q	0.104134797	0.077810682	157	---	RCN	0.096824625	0.095145301
  195	--	FY	0.104134797	0.074775738	576	-------	DDPNLII	0.096824625	0.040738988
  							(SEQ ID NO:
  							3346)
  464	--	IE	0.103802674	0.096071807	296	-----	VVAQI (SEQ	0.096824625	0.081486595
  							ID NO: 3836)
  451	A	T	0.103708002	0.093659384	559	-I	CL	0.096824625	0.07248553
  245	DII	ETV	0.10291048	0.070762893	979	LE-[stop]	VSIK (SEQ ID	0.096824625	0.050151323
  							NO: 3792)
  504	----	DISG (SEQ ID	0.10291048	0.066659076	767	------	RTFMAE	0.096824625	0.057097889
  		NO: 3356)					(SEQ ID NO:
  							3692)
  323	-Q	IH	0.10291048	0.071312882	820	-------	DYDRVLE	0.091736446	0.087280678
  							(SEQ ID NO:
  							3371)
  638	-----	FERRE (SEQ	0.10291048	0.096842919	415	KVY	NC-	0.091736446	0.087802292
  		ID NO: 3409)
  593	-------	REFIWNDLL	0.10291048	0.079136445	674	GCPL (SEQ	DAH[stop]	0.091736446	0.089744971
  		(SEQ ID NO:				ID NO: 3260)
  		3663)
  730	------	ADDMVR	0.10291048	0.102673345	705	QA	-C	0.091736446	0.071260814
  		(SEQ ID NO:
  		3304)
  827	KL	TV	0.10291048	0.094773598	307	-N	TD	0.091736446	0.071147866
  138	VY	C-	0.10291048	0.091363063	370	G-	AV	0.091736446	0.051182414
  310	QK	DR	0.10291048	0.068590108	954	KRA	T-V	0.091736446	0.081861067
  524	KKL	RN [stop]	0.102360708	0.063041226	326	KGFPS (SEQ	RASLA (SEQ	0.091644836	0.054125593
  						ID NO: 3267)	ID NO: 3657)
  940	-----	YKKYQ (SEQ	0.102324952	0.078047936	289	GI	LS	0.091644836	0.069499341
  		ID NO: 3850)
  918	---	THA	0.102324952	0.066375654	142	-E	CL	0.091644836	0.064151435
  979	LE[stop]GSPG	VSSNDLQ	0.102324952	0.073267994	10	RR	TG	0.091644836	0.090788699
  	(SEQ ID NO:	(SEQ ID NO:
  	3251)	3831)
  4	K	Q	0.101594625	0.098660596	193	LDFYSIH	RTSTAST	0.091277438	0.058446074
  						(SEQ ID NO:	(SEQ ID NO:
  						3276)	3694)
  589	-----	KRQGR (SEQ	0.101233118	0.096410486	979	LE[stop]GS-	VSIKDLQAS	0.091277438	0.055852497
  		ID NO: 3529)				PGIK (SEQ ID	NK (SEQ ID
  						NO:	NO: 3793)
  						3279)[stop]
  211	-----	LEQIG (SEQ	0.101233118	0.097193308	590	-----	RQGRE (SEQ	0.091277438	0.07404543
  		ID NO: 3544)					ID NO: 3678)
  649	I	N	0.101148579	0.091521137	308	---	LWQ	0.091277438	0.063930973
  220	------	ASGPVG	0.099764722	0.05025267	311	--------	KLKIGRDEA	0.091277438	0.090951045
  		(SEQ ID NO:					(SEQ ID NO:
  		3330)					3509)
  787	AYEG (SEQ	PTRD (SEQ	0.099764722	0.069079749	585	------	LAFGKR	0.091277438	0.057801256
  	ID NO: 3253)	ID NO: 3629)					(SEQ ID NO:
  							3534)
  888	-----	RSGEA (SEQ	0.099764722	0.094243718	466	-------	GLKEADK	0.091277438	0.064806465
  		ID NO: 3685)					(SEQ ID NO:
  							3443)
  504	------	DISGFS (SEQ	0.099764722	0.091750112	414	--	GK	0.089604136	0.067494445
  		ID NO: 3357)
  323	QR	RD	0.099764722	0.040967673	979	LE[stop]GSPG	ISSKDLQ	0.089062173	0.071078934
  						(SEQ ID NO:	(SEQ ID NO:
  						3251)	3482)
  647	SN	DS	0.099764722	0.071118435	300	----	IVIW (SEQ ID	0.089062173	0.052509601
  							NO: 3485)
  740	DLLY (SEQ	SAV-	0.099753827	0.050146089	209	KP	TV	0.089062173	0.046404323
  	ID NO: 3254)
  38	-	A	0.099114744	0.090540757	851	-T	CL	0.089062173	0.047830666
  261	LA	PV	0.099083678	0.060781559	466	GL	LS	0.089062173	0.060367604
  255	----	KKNE (SEQ	0.098543421	0.07624083	202	RE--	SSSL (SEQ ID	0.089062173	0.059904595
  		ID NO: 3505)					NO: 3730)
  280	----	LPPQ (SEQ	0.098543421	0.069822078	291	EA	DC	0.089062173	0.078319771
  		ID NO: 3567)
  308	LW	PV	0.097993366	0.087176639	871	RL	LS	0.089062173	0.055570451
  753	---	IFA	0.097806547	0.045793305	874	EE	DR	0.089062173	0.077193595
  205	N	I	0.097706358	0.075812724	868	ELDR (SEQ	NWT-	0.089062173	0.059312334
  						ID NO: 3257)
  142	E	Q	0.097553503	0.074603349	301	VI	AV	0.089062173	0.083633904
  717	-------	GYSRKYAS	0.097097924	0.054767341	208	----	VKPLEQI	0.089062173	0.046334388
  		(SEQ ID NO:					(SEQ ID NO:
  		3459)					3784)
  979	LE[stop]GSPG	VSSKDLH	0.097097924	0.068112769	305	-N	TT	0.089062173	0.072049193
  	(SEQ ID NO:	(SEQ ID NO:
  	3251)	3806)
  527	NLYL (SEQ	TCT[stop]	0.097097924	0.089930288	978	[stop]L	GP	0.089062173	0.071277586
  	ID NO: 3283)
  230	D	T	0.097097924	0.061172404	866	S-	TG	0.089062173	0.056446779
  595	----	FIWN (SEQ	0.097097924	0.075559339	628	DE	LS	0.089062173	0.070268313
  		ID NO: 3413)
  526	LN	PV	0.097097924	0.065035268	651	-P	TA	0.089062173	0.05500823
  928	IA	TV	0.096824625	0.059262285	276	---	PKI	0.089062173	0.06318371
  694	---	GES	0.096824625	0.04858003	299	-	V	0.089062173	0.08531757
  190	---	QRA	0.096824625	0.080026424	346	--	MV	0.089062173	0.060831249
  601	-------	LSLETGS	0.096824625	0.078527715	742	LY	PV	0.089062173	0.087665343
  		(SEQ ID NO:
  		3576)
  150	--	PH	0.096482996	0.069152449	743	YY	ET	0.089062173	0.059923968
  307	---	NLW	0.096482996	0.053647152	751	ML	RQ	0.089062173	0.045208162
  808	---	TCS	0.096381808	0.086676449	894	-S	RQ	0.089062173	0.071980752
  687	-------	PTHILRI	0.095815136	0.067505643	433	KH	TV	0.089062173	0.061328218
  		(SEQ ID NO:
  		3628)
  469	---	EAD	0.095416799	0.081758814	899	RF	LS	0.089062173	0.083069213
  181	VTYS (SEQ	SHTA (SEQ	0.095412022	0.081952005	582	---	ILP	0.089062173	0.053169618
  	ID NO: 3295)	ID NO: 3708)
  814	F	C	0.095092296	0.090308339	979	LE[stop]GS-	VSSKDLHAS	0.087252372	0.071793737
  						PGIK (SEQ ID	N (SEQ ID
  						NO:)	NO: 3807)
  389	K	[stop]	0.094408724	0.074513611	735	------	RNTARD	0.087252372	0.052948743
  							(SEQ ID NO:
  							3672)
  663	I	C	0.094255793	0.075689829	227	------------	ALSDACM	0.087252372	0.073258454
  							(SEQ ID NO:
  							3321)
  979	L	I	0.092483102	0.077877212	151	HTNYFGRCN	TPTTSADAT	0.087252372	0.05854259
  						V (SEQ ID	C (SEQ ID
  						NO: 3264)	NO: 3758)
  290	I-	LS	0.092483102	0.055600721	875	------	ESVNND	0.087252372	0.069839022
  							(SEQ ID NO:
  							3397)
  202	R-------E	SSSLASGL	0.092483102	0.051559995	151	-H	CL	0.087252372	0.072166234
  		(SEQ ID NO:
  		3731)[stop]
  130	S	I	0.092259428	0.091849472	517	-----	IWQKD (SEQ	0.087252372	0.059389612
  							ID NO: 3488)
  237	A	V	0.092157582	0.073154252	294	NN	ET	0.087252372	0.054113615
  550	F-	LS	0.091736446	0.078399586	979	LE[stop]GS-	VSSEDLQAS	0.087252372	0.053550045
  						PGIK (SEQ ID	NK (SEQ ID
  						NO:	NO: 3796)
  						3279)[stop]
  352	---	KLI	0.091736446	0.062601185	280	LP	C-	0.087252372	0.046361662
  257	------	NEKRLA	0.091736446	0.074344692	973	WK	CL	0.087252372	0.043130788
  		(SEQ ID NO:
  		3591)
  978	[stop]LE	QVS	0.091736446	0.070305933	859	-	Q	0.087252372	0.049734005
  878	NN	ET	0.091736446	0.057372719	383	-----	SEEDR (SEQ	0.087252372	0.079531899
  							ID NO: 3695)
  484	-KWYGD	NSSLSA	0.091736446	0.051261975	193	--------	LDFYSIHVT	0.087252372	0.075700876
  	(SEQ ID NO:	(SEQ ID NO:					(SEQ ID NO:
  	3274)	3601)					3542)
  796	--	YL	0.08954136	0.077067905	731	----	DDMV (SEQ	0.087252372	0.055852115
  							ID NO: 3345)
  872	---	LSE	0.089427419	0.072631533	586	---	AFG	0.087252372	0.059593552
  388	-----	KKGKK (SEQ	0.089427419	0.050485092	11	RR	GD	0.087252372	0.07840862
  		ID NO: 3499)
  211	LEQIGG	RNRSAA	0.089427419	0.058037112	979	LE[stop]G	VPSK (SEQ	0.086010969	0.05573546
  	(SEQ ID NO:	(SEQ ID NO:					ID NO: 3787)
  	3281)	3671)
  193	LDFYSIHV	RTSTAST	0.089427419	0.06189365	671	D	V	0.084756133	0.072837893
  	(SEQ ID NO:	(SEQ ID NO:
  	3277)	3694)[stop]
  769	FMAERQY	LWPRGST	0.089427419	0.048645432	462	---	FVI	0.083590457	0.068208408
  	(SEQ ID NO:	(SEQ ID NO:
  	3258)	3582)
  558	---	VIN	0.089427419	0.08506841	619	TLYNRRTR	PCTTGEPD	0.083590457	0.071170573
  						(SEQ ID NO:	(SEQ ID NO:
  						3292)	3613)
  973	---	WKP	0.089427419	0.059845159	337	QA	PV	0.083590457	0.078536227
  285	----	HTKE (SEQ	0.089427419	0.058488636	418	----	DEAW (SEQ	0.083590457	0.038813523
  		ID NO: 3463)					ID NO: 3347)
  353	--	LI	0.089427419	0.055053978	426	--	KK	0.083590457	0.07413354
  950	----	GNTD (SEQ	0.089427419	0.068410765	208	VK	AV	0.083590457	0.037512118
  		ID NO: 3445)
  642	-----	EVLDS (SEQ	0.089427352	0.04064403	519	--	QK	0.083590457	0.082570582
  		ID NO: 3405)
  586	AF	ET	0.089427352	0.026351335	122	LT	D[stop]	0.083590457	0.076976074
  147	KG	C-	0.089427352	0.03353623	659	RG	PV	0.083590457	0.0659041
  473	-----	DEFCR (SEQ	0.089427352	0.087380064	160	-------	VSEHERL	0.083590457	0.081613302
  		ID NO: 3350)					(SEQ ID NO:
  							3790)
  62	SR	CL	0.089427352	0.085389222	278	IT	TA	0.083590457	0.047460329
  946	N	C	0.089427352	0.086906423	242	KY	CL	0.083590457	0.045794039
  341	-----	VDWWD	0.089427352	0.088291312	518	WQ	GR	0.08340916	0.072293259
  		(SEQ ID NO:
  		3772)
  546	---	KPE	0.089427352	0.070048864	513	----	NCAF (SEQ	0.08340916	0.058923148
  							ID NO: 3587)
  979	LE[stop]G--	VSSKDLQAC	0.089062173	0.059857989	31	L	C	0.082126328	0.081561344
  	SPGI (SEQ ID	L (SEQ ID
  	NO: 3278)	NO: 3811)
  944	---	QTN	0.089062173	0.066135158	868	E	G	0.081974564	0.070868354
  170	SP	RQ	0.089062173	0.059574685
  771	-----	AERQY (SEQ	0.089062173	0.079594468	681	-----	KDSLG (SEQ	0.080796062	0.070617083
  		ID NO: 3309)					ID NO: 3489)
  808	TC	DS	0.089062173	0.069853908	552	--	AN	0.080796062	0.080329675
  347	--	VC	0.089062173	0.085265549	168	---	LLS	0.080796062	0.076933587
  554	RF	SC	0.089062173	0.05713278	418	--------	DEAWERID	0.080796062	0.062400841
  							(SEQ ID NO:
  							3349)
  419	EA	LS	0.089062173	0.062902243	356	-----	EKKED (SEQ	0.080428937	0.076250147
  							ID NO: 3391)
  184	------	SLGKFG	0.089062173	0.066443269	904	--	PV	0.077521024	0.061782081
  		(SEQ ID NO:
  		3716)
  524	K-K	ETE	0.089062173	0.078642197	8	KIR	ETG	0.075979618	0.06718831
  544	KI	NC	0.089062173	0.051439626	963	----	SFYR (SEQ	0.075979618	0.064323698
  							ID NO: 3700
  417	------	YDEAWE	0.089062173	0.084599468	34	RV	SC	0.075979618	0.063118319
  		(SEQ ID NO:
  		3847)
  911	CL	DR	0.089062173	0.07167912	369	------	AGYKRQ	0.075979618	0.050848396
  							(SEQ ID NO:
  							3313)
  735	--------	RNTARDLLY	0.089062173	0.058412514	242	KY	TV	0.075979618	0.056127246
  		(SEQ ID NO:
  		3673)
  305	N	D	0.089057834	0.075458081	297	VAQIV (SEQ	WPRS (SEQ	0.075979618	0.07433917
  						ID NO: 3293)	ID NO:
  							3843)[stop]
  886	KGR	RAD	0.08869535	0.056741957	672	-P	LS	0.075979618	0.056690099
  235	A	P	0.088591922	0.085721293	650	KP	TV	0.075979618	0.062837656
  494	-------	FAIEAEN	0.088487772	0.046582849	454	DW	AV	0.075979618	0.049282705
  		(SEQ ID NO:
  		3408)
  957	F	Y	0.088355066	0.088244344	312	LK	PV	0.075979618	0.074673373
  670	-----	TDPEG (SEQ	0.087352311	0.070989739	636	LT	PV	0.075651042	0.051037357
  		ID NO: 3742)
  388	--	KK	0.087352311	0.077174067	325	-----	LKGFP (SEQ	0.075651042	0.068819815
  							ID NO: 3557)
  294	--	NN	0.087352311	0.079627552	669	L	E	0.075651042	0.075396635
  748	------	QDAMLI	0.087352311	0.070738039	79	A	V	0.074780904	0.074608034
  		(SEQ ID NO:
  		3632)
  978	[stop]LE[stop]	SVSSK (SEQ	0.087252372	0.078631278	887		GRSGEA	0.073542892	0.072424639
  	G	ID NO: 3734)					(SEQ ID NO:
  							3452)
  743	------	YYAVTQ	0.087252372	0.074424467	404	EIL	DR	0.073542892	0.054184233
  		(SEQ ID NO:
  		3865)
  90	KDP	NCL	0.087252372	0.062483354	190	Q-R	HVA	0.073542892	0.04828771
  459	---	KAS	0.087252372	0.077679223	811	NC	DS	0.073542892	0.073088889
  319	--------	AKPLQRLK	0.087252372	0.077741662	824	----	VLEK (SEQ	0.073542892	0.055393108
  		(SEQ ID NO:					ID NO: 3786)
  		3316)
  844	-------	LKVEGQI	0.087252372	0.078010123	63	RA	TV	0.073542892	0.069467367
  		(SEQ ID NO:
  		3558)
  964	-----	FYRKK (SEQ	0.087252372	0.061717189	350	VK	AV	0.072378636	0.048322939
  		ID NO: 3422)
  510	-----	KQYNC (SEQ	0.087252372	0.072460113	690	ILRI (SEQ ID	PEN-	0.072378636	0.05860973
  		ID NO: 3526)				NO: 3265)
  211	LE	C-	0.087252372	0.072615166	384	EED	D-C	0.072378636	0.064425519
  154	---	YFG	0.087252372	0.050562832	349	-------	NVKKLIN	0.071251281	0.055420168
  							(SEQ ID NO:
  							3605)
  428	-	V	0.087252372	0.070602271	427	KVE	NCL	0.071251281	0.037488341
  328	-------	FPSFPLV	0.087252372	0.050986167	537	GGKLRFK	AASCGSR	0.071251281	0.047685675
  		(SEQ ID NO:				(SEQ ID NO:	(SEQ ID NO:
  		3415)				3261)	3301)
  334	---	VER	0.087252372	0.083245674	486	-----	YGDLR (SEQ	0.071251281	0.057530417
  							ID NO: 3849)
  635	---	ALT	0.087252372	0.058640453	586	-------	AFGKRQG	0.071251281	0.055531439
  							(SEQ ID NO:
  							3312)
  87	EF	DC	0.087252372	0.084662756	850	----	ITYY (SEQ	0.071251281	0.070061657
  							ID NO: 34843)
  763	----	RQGK (SEQ	0.087252372	0.06272177	929	---	ARS	0.071251281	0.070844259
  		ID NO: 3677)
  525	----	KLNL (SEQ	0.087252372	0.087055601	617	EK	AV	0.071251281	0.056273969
  		ID NO: 3511)
  482	LQK	PLM	0.087252372	0.0864173	977	V[stop]	AV	0.071036023	0.057250091
  228	--	LS	0.087252372	0.071648918	522	---	GVK	0.071036023	0.066325629
  149	----	KPHT (SEQ	0.087252372	0.063809398	903	RP	LS	0.070891186	0.042147704
  		ID NO: 3520)
  14	VKDSNTK	SRTATQR	0.087252372	0.086609324	689	HI	P-	0.070270828	0.063050321
  	(SEQ ID NO:	(SEQ ID NO:
  	3294)	3729)
  567	VP	C-	0.087252372	0.05902513	663	-	I	0.070270828	0.06150934
  275	--	FP	0.080428937	0.059363481	649	IK	RQ	0.070270828	0.060647973
  308	------	LWQKLK	0.080428937	0.078547724	258	--	EK	0.070270828	0.058125711
  		(SEQ ID NO:
  		3583)
  15	KDSNTKK	RTATQRR	0.080428937	0.072523813	152	TN	DS	0.070270828	0.059660679
  	(SEQ ID NO:	(SEQ ID NO:
  	3266)	3690)
  979	LE[stop]GSPG	VSSKDLQG	0.080428937	0.070440346	351	-----	KKLINE	0.070270828	0.061736597
  	I (SEQ ID NO:	(SEQ ID NO:					(SEQ ID NO:
  	3278)	3818)					3503)
  425	---	DKK	0.080428937	0.056582403	763	--	RQ	0.070270828	0.05541295
  288	EGI	RAS	0.080428937	0.054809688	666	VI	DS	0.070270828	0.069953364
  849	QI	R-	0.080428937	0.058314054	186	GK	RQ	0.066783091	0.059043838
  526	-----	LNLYL (SEQ	0.080428937	0.073029285	242	-------	KYQDHLE	0.066783091	0.058248788
  		ID NO: 3564)					(SEQ ID NO:
  							3533)
  546	----	KPEA (SEQ	0.080428937	0.06983999	190	-------	QRALDFYS	0.066783091	0.060436783
  		ID NO: 3519)
  792	--	PS	0.080428937	0.067496853	484	--KWYGDL	NSSLSASF	0.061911903	0.060235262
  						(SEQ ID NO:	(SEQ ID NO:
  						3275)	3603)
  706	--------	AAKEVEQR	0.080428937	0.075434091	416	VY	CT	0.061911903	0.058375882
  		(SEQ ID NO:
  		3300)
  710	----	VEQR (SEQ	0.080165897	0.064037522	900	FS	SV	0.060850202	0.045333847
  		ID NO: 3775)
  949	-T	LS	0.080165897	0.057028434	550	FE	CL	0.060850202	0.050669807
  224	V	C	0.080165897	0.062705318	169	LS	-P	0.059253838	0.055169203
  202	-----	RESNH (SEQ	0.08002463	0.069004172	487	GD	CL	0.058561444	0.050771143
  		ID NO: 3664)
  380	YLS	-T[stop]	0.079267535	0.078743084	800	------	TLAQYT	0.058239485	0.054115265
  							(SEQ ID NO:
  							3753)
  617	---	EKT	0.079267535	0.066283102	863	KD	RI	0.058239485	0.041340026
  237	AS	TA	0.079267535	0.061120875	407	KKHGE (SEQ	RSTAR (SEQ	0.058239485	0.049050481
  						ID NO: 3268)	ID NO: 3687)
  416	VYD	C-T	0.07889536	0.067603097	593	------	REFIW (SEQ	0.058239485	0.057097188
  							ID NO: 3662)
  554	--------	RFYTVINKK	0.078495111	0.06923226	979	LE[stop]G-SP	VSSKVLQ	0.050653241	0.049828056
  		(SEQ ID NO:					(SEQ ID NO:
  		3667)					3827)
  619	TLYN (SEQ	PC-T	0.078181072	0.043873495	42	ER	A-	0.050653241	0.043693463
  	ID NO: 3291)
  487	------	GDLRGKP	0.072378636	0.071208648	897	--	KK	0.050653241	0.046680114
  		(SEQ ID NO:
  		3429)
  644	L	[stop]	0.072378636	0.060246346	294	NN	DS	0.049177787	0.048944158
  544	KI	TV	0.072378636	0.05442277	186	GKFGQRAL	ASSDREPWT	0.049177787	0.048777834
  						DFY (SEQ ID	ST (SEQ ID
  						NO: 3262)	NO:	3331)
  933	----	LFLR (SEQ	0.072378636	0.06374014	696	SYK	-LQ	0.049177787	0.048584657
  		ID NO: 3546)
  276	PKITLP (SEQ	LRSPCL	0.072378636	0.070970251	552	AN	DS	0.049177787	0.044744659
  	ID NO: 3284)	(SEQ ID NO:
  		3570)
  808	-------	TCSNCGFT	0.072378636	0.065622369	979	LE[stop]G-	VSSKYLQAS	0.049086177	0.048688856
  		(SEQ ID NO:				SPGIK (SEQ	NK (SEQ ID
  		3740)				ID NO:	NO: 3828)
  						3279)[stop]
  978	[stop]LE[stop]	YVSSKDL	0.072378636	0.066035046	413	--------	WGKVYDEA	0.048681821	0.046101055
  	GS-	(SEQ ID NO:					(SEQ ID NO:
  		3862)					3840)
  919	HA	PV	0.072378636	0.058676376	920	-----	AAEQA (SEQ	0.048224673	0.046055533
  							ID NO: 3299)
  378	--------	LPYLSSE	0.072378636	0.071574474
  		(SEQ ID NO:
  		3569)
  858	RQ	LS	0.072378636	0.04290216
  152	--------	TNYFGRCN	0.072378636	0.054244402
  		(SEQ ID NO:
  		3757)
  859	------	QNVVKD	0.072378636	0.069366552
  		(SEQ ID NO:
  		3644)
  226	KA	LS	0.071324732	0.06748566
  849	------	QITYYN	0.071251281	0.061753986
  		(SEQ ID NO:
  		3640)
  376	----	ALLP (SEQ	0.071251281	0.046839434
  		ID NO: 3318)
  660	---	GEN	0.071251281	0.063597301
  		(SEQ ID NO:
  		3647)
  615	VI	DS	0.066783091	0.065544343
  295		NVVAQI	0.066783091	0.066726619
  		(SEQ ID NO:
  		3608)
  549	AFE	PTR	0.066783091	0.063274062
  924	-AL	PSG	0.066783091	0.057049314
  979	LE[stop]	VSR	0.06547263	0.059545386
  284	P	L	0.06489326	0.063807972
  620	--	LY	0.06268489	0.052769076
  668	-A	LS	0.06268489	0.057930418
  651	----	PMNL (SEQ	0.06268489	0.054376534
  		ID NO: 3619)
  723	--SK	PPLL (SEQ ID	0.061911903	0.057719078
  		NO: 3621)
  788	YEG	TRD	0.061911903	0.061258021
  572	NF	DS	0.061911903	0.059419672
  943	----	YQTN (SEQ	0.061911903	0.05179175
  		ID NO: 3856)
  979	LE[stop]GS-P	VSSKDVQ	0.061911903	0.05324798
  		(SEQ ID NO:
  		3825)
  49	KK	RS	0.061911903	0.057783548
  745	-A	LS	0.061911903	0.055420231
  262	-AN	ETD	0.061911903	0.056977155
  726	----	AKNL (SEQ	0.061911903	0.05965082
  		ID NO: 3315)
  583	----	LPLA (SEQ	0.061911903	0.053222838
  		ID NO: 3566)
  585	--	LA	0.061911903	0.047677961
  347	--------	VCNVKKLI	0.061911903	0.060561898
  		(SEQ ID NO:
  		3771)
  735	RN	Q-	0.061911903	0.057911259
  176	AN	TD	0.061911903	0.042711394
  979	LE[stop]GSPG	VSSKDFQ	0.047884408	0.043419619
  	(SEQ ID NO:	(SEQ	ID NO:
  	3251)	3801)
  423	RIDKKV	---NRQ	0.046868759	0.045505043
  	(SEQ ID NO:
  	3286)
  162	EH	AV	0.043166861	0.040108447
  741	LLY	CC-	0.041101883	0.039741701
  443	SEDAQS	RGRPI (SEQ	0.041101883	0.03770041
  	(SEQ ID NO:	ID NO:
  	3288)	3668)[stop]
  767	RT	TA	0.041101883	0.040956261

• In Table 6, [stop] respresent a stop codon, so that amino acids that follow are additional amino acids after a stop codon. (−) holds the position for the insertion shown in the adjacent “Alteration” column. Pos.: Position Ref.: Reference; Alt.: Alternation; Med. Enrich.: Median Enrichment.
Example 5 Cleavage Activity of Selected CasX Protein Variants and Variant Protein:sgRNA Pairs
• The effect of select CasX protein variants on CasX protein activity, using a reference sgRNA scaffold (SEQ ID NO: 5) and E6 and/or E7 spacers is shown in Table 7 below and FIGS. 10 and 11.
• In brief. EGFP HEK293T reporter cells were seeded into 96-well plates and transfected according to the manufacturer's protocol with lipofectamine 3000 (Life Technologies) and 100-200 ng plasmid DNA encoding the variant CasX protein. P2A-puromycin fusion and the reference sgRNA. The next day cells were selected with 1.5 μg/ml puromycin for 2 days and analyzed by fluorescence-activated cell sorting 7 days after selection to allow for clearance of EGFP protein from the cells EGFP disruption via editing was traced using an Attune N×T Flow Cytometer and high-throughput autosampler.

• TABLE 7
  Effect of CasX Protein Variants. These mutations are relative to SEQ ID NO: 2.

  Normalized
  Editing	Standard		SEQ ID
  Activity	Deviation	Mutation Descriptor	NO

  3.56	0.479918161	L379R + C477K + A708K + [P793] + T620P	3301
  3.44	0.065473567	M771A	3302
  3.25	0.243066966	L379R + A708K + [P793] + D732N	3303
  3.2	0.065443719	W782Q	3304
  3.08	0.06581193	M771Q	3305
  3.06	0.098482124	R458I + A739V	3306
  2.99	0.249667198	L379R + A708K + [P793] + M771N	3307
  2.98	0.226829483	L379R + A708K + [P793] + A739T	3308
  2.98	0.230093698	L379R + C477K + A708K + [P793] + D489S	3309
  2.95	0.225022742	L379R + C477K + A708K + [P793] + D732N	3310
  2.95	0.048047426	V711k	3311
  2.85	0.244869555	L379R + C477K + A708K + [P793] + Y797L	3312
  2.84	0.16661152	L379R + A708K + [P793]	3313
  2.82	0.219742241	L379R + C477K + A708K + [P793]+ M771N	3314
  2.75	0.215673641	A708K + [P793] + E386S	3315
  2.71	0.10301172	L379R + C477K + A708K + [P793]	3316
  2.62	0.066259269	L792D	3317
  2.61	0.069056066	G791F	3318
  2.56	0.138158681	A708K + [P793] + A739V	3319
  2.52	0.110846334	L379R + A708K + [P793] + A739V	3320
  2.5	0.070762901	C477K + A708K + [P793]	3321
  2.47	0.180431811	L249I, M771N	3322
  2.46	0.050035486	V747K	3323
  2.42	0.14702229	L379R + C477K + A708K + [P793] + M779N	3324
  2.36	0.045498608	F755M	3325
  2.3	0.179759799	L379R + A708K + [P793] + G791M	3326
  2.29	0.16573206	E386R + F399L + [P793]	3327
  2.24	0.000278715	A708K + [P793]	3328
  2.23	0.243365847	L404K	3329
  2.16	0.019745961	E552A	3330
  2.13	0.002238075	A708K	3331
  2.08	0.316339196	M779N	3332
  2.08	0.062500445	P793G	3333
  2.07	0.117354932	L379R + C477K + A708K + [P793] + A739V	3334
  2.03	0.057771128	L792K	3335
  2.01	0.186905281	L379R + A708K + [P793] + M779N	3336
  2.01	0.080358848	{circumflex over ( )}AS797	3337
  1.95	0.218366091	C477H	3338
  1.95	0.040076499	Y857R	3339
  1.94	0.032799694	L742W	3340
  1.94	0.038256856	I658V	3341
  1.93	0.055533894	C477K + A708K + [P793] + A739V	3342
  1.9	0.028572575	S932M	3343
  1.84	0.115143156	T620P	3344
  1.81	0.18802403	E385P	3345
  1.81	0.049828835	A708Q	3346
  1.76	0.043121298	L307K	3347
  1.7	0.03352434	L379R + A708K + [P793] + D489S	3348
  1.7	0.170748704	C477Q	3349
  1.65	0.051918988	Q804A	3350
  1.64	0.169459451	F399L	3351
  1.64	0.07984393	L379R + A708K + [P793] + Y797L	3352
  1.64	0.168799771	L379R + C477K + A708K + [P793] + G791M	3353
  1.63	0.035361733	D733T	3354
  1.63	0.062042898	P793Q	3355
  1.6	0.000928887	A739V	3356
  1.59	0.208295832	E386S	3357
  1.58	0.00189514	F536S	3358
  1.57	0.204148363	D387K	3359
  1.55	0.198137682	E386N	3360
  1.52	0.000291529	C477K	3361
  1.51	0.00032232	C477R	3362
  1.49	0.095600844	A739T	3363
  1.46	0.051799824	S219R	3364
  1.41	0.000272809	K416E & A708K	3365
  1.4	4.65E−05	L379R	3366
  1.38	0.043395969	E385K	3367
  1.36	0.000269797	G695H	3368
  1.35	0.02584186	L379R + C477K + A708K + [P793] + A739T	3369
  1.35	0.158192737	E292R	3370
  1.34	0.184524879	L792K	3371
  1.31	0.064556939	K25R	3372
  1.31	0.08768015	K975R	3373
  1.31	0.062237773	V959M	3374
  1.29	0.092916832	D489S	3375
  1.29	0.137197584	K808S	3376
  1.28	0.181775511	N952T	3377
  1.27	0.031730102	K975Q	3378
  1.25	0.030353503	S890R	3379
  1.23	0.350374014	[P793]	3380
  1.21	8.61E−05	A788W	3381
  1.21	0.057483618	Q338R + A339E	3382
  1.21	0.116491085	I7F	3383
  1.21	0.061416272	QT945KI	3384
  1.21	0.091585825	K682E	3385
  1.19	0.000423928	E385A	3386
  1.19	0.053255444	P793S	3387
  1.18	0.043774095	E385Q	3388
  1.18	0.124987984	D732N	3389
  1.17	0.101573595	E292K	3390
  1.16	0.000245107	S794R + Y797L	3391
  1.15	0.160445636	G791M	3392
  1.14	0.098217225	I303K	3393
  1.12	0.000275601	{circumflex over ( )}AS793	3394
  1.11	0.037923895	S603G	3395
  1.08	6.48E−05	Y797L	3396
  1.08	0.034990079	A377K	3397
  1.08	0.059730153	K955R	3398
  1.04	0.000376903	T886K	3399
  1.03	0.036131932	Q338R + A339K	3400
  1.03	0.031397109	P283Q	3401
  1.01	0.000158685	D600N	3402
  1.01	0.095937558	S867R	3403
  1.01	0.079977243	E466H	3404
  1	0.086320071	E53K	3405
  0.98	0.123364563	L792E	3406
  0.97	5.98E−05	Q338R	3407
  0.96	0.059312097	H152D	3408
  0.95	0.122246867	V254G	3409
  0.94	0.072611815	TT949PP	3410
  0.93	0.091846036	I279F	3411
  0.93	0.031803852	L897M	3412
  0.92	0.000288973	K390R	3413
  0.91	0.000565042	K390R	3414
  0.89	0.001316868	L792G	3415
  0.89	0.000623156	A739V	3416
  0.89	0.033874895	R624G	3417
  0.88	0.103894502	C349E	3418
  0.86	0.11267313	E498K	3419
  0.85	0.079415017	R388Q	3420
  0.84	0.000115651	I55F	3421
  0.84	0.000383356	E712Q	3422
  0.83	0.025220431	E475K	3423
  0.81	0.000172705	{circumflex over ( )}AS796	3424
  0.8	0.111675911	Q628E	3425
  0.79	0.000114918	C479A	3426
  0.79	0.001115871	Q338E	3427
  0.78	0.000744903	K25Q	3428
  0.76	0.000269223	{circumflex over ( )}AS795	3429
  0.74	0.000437653	L481Q	3430
  0.73	0.0001773	E552K	3431
  0.72	0.000298273	T153I	3432
  0.69	0.000273628	N880D	3433
  0.68	0.000192096	G791M	3434
  0.67	0.000295463	C233S	3435
  0.67	0.000123996	Q367K + I425S	3436
  0.67	0.000188025	L685I	3437
  0.66	0.000169478	K942Q	3438
  0.66	0.000374718	N47D	3439
  0.66	0.138212411	V635M	3440
  0.64	0.067027049	G27D	3441
  0.63	0.000195863	C479L	3442
  0.63	0.000439659	[P793] + P793AS	3443
  0.62	0.000211625	T72S	3444
  0.62	0.000217614	S270W	3445
  0.61	0.00019414	A751S	3446
  0.6	0.066962306	Q102R	3447
  0.57	0.052391074	M734K	3448
  0.53	0.000621789	{circumflex over ( )}AS795	3449
  0.53	0.145184217	F189Y	3450
  0.5	0.038258832	W885R	3451
  0.48	0.000505099	A636D	3452
  0.47	0.030480379	K416E	3453
  0.46	0.428767546	R693I	3454
  0.45	0.593145404	m29R	3455
  0.45	0.144374311	T946P	3456
  0.44	0.000253022	{circumflex over ( )}L889	3457
  0.42	0.000171566	E121D	3458
  0.37	0.042821047	P224K	3459
  0.37	0.683382544	K767R	3460
  0.36	0.026543344	E480K	3461
  0.34	0.000998618	I546V	3462
  0.27	0.164274898	K188E	3463
  0.22	0.00106697	Y789T	3464
  0.21	0.000512104	F495S	3465
  0.18	0.023184407	m29E	3466
  0.18	0.096249035	A238T	3467
  0.17	0.000141352	d231N	3468
  0.17	9.49E−05	I199F	3469
  0.17	0.031218317	N737S	3470
  0.16	3.87E−05	{circumflex over ( )}G661A	3471
  0.12	4.08E−05	K460N	3472
  0.08	0.000897639	k210R	3473
  0.08	3.47E−05	G492P	3474
  0.07	0.000266253	R591I	3475
  0.04	6.41E−05	{circumflex over ( )}T696	3476
  0.03	0.022802297	S507G + G508R	3477
  0.02	0.028138538	Y723N	3478
  −0.01	0.000529731	{circumflex over ( )}P696	3479
  −0.01	0.038340599	g226R	3480
  −0.02	0.052026759	W974G	3481
  −0.04	0.000176981	{circumflex over ( )}M773	3482
  −0.04	0.07902452	H435R	3483
  −0.06	0.069143378	A724S	3484
  −0.06	0.060317972	T704K	3485
  −0.06	0.017155351	Y966N	3486
  −0.08	0.036299549	H164R	3487
  −0.15	0.032952207	F556I, D646A, G695D, A751S, A820P	3488
  −0.17	0.04149111	D659H	3489
  −0.21	0.064777446	T806V	3490
  −0.24	0.001280151	Y789D	3491
  −0.31	0.05332531	C479A	3492
  −0.35	0.066448437	L212P	3493

• [] indicate deletions, and (″) indicate insertions at the specified positions of SEQ ID NO: 2. E6 and E7 spacers were used, and the data are the average of N=6 replicates. Stdev=Standard Deviation. Editing activity was normalized to that of the reference CasX protein of SEQ ID NO: 2.
• Selected CasX protein variants from the DME screen and CasX protein variants comprising combinations of mutations were assayed for their ability to disrupt via cleavage and in/del formation GFP reporter expression. CasX protein variants were assayed with two targets, with 6 replicates. FIG. 10 shows the fold improvement in activity over the reference CasX protein of SEQ ID NO: 2 of select variants carrying single mutations, assayed with the reference sgRNA scaffold of SEQ ID NO: 5.
• FIG. 11 shows that combining single mutations, such as those shown in FIG. 10, can produce CasX protein variants, that can improve editing efficiency by greater than two fold. The most improved CasX protein variants, which combine 3 or 4 individual mutations, exhibit activity comparable to Staphylococcus aureus Cas9 (Sa.Cas9) Which has been used in the clinic (Maeder et al. 2019, Nature Medicine 25(2):229-233).
• FIGS. 12A-12B shows that CasX protein variants, when combined with select sgRNA variants, can achieve even greater improvements in editing efficiency. For example, a protein variant comprising L379K and A708K substitutions, and a P793 deletion of SEQ ID NO: 2, when combined with the truncated stem loop T10C sgRNA variant more than doubles the fraction of disrupted cells.
Example 6 CasX Protein Variants Can Affect PAM Specificity
• The purpose of the experiment was to demonstrate the ability of CasX variant 2 (SEQ ID NO:2), and scaffold variant 2 (SEQ ID NO:5), to edit target gene sequences at ATCN, CTCN, and TTCN PAMs in a GFP gene. ATCN, CTCV, and TTCN spacers in the GFP gene were chosen based on PAM availability without prior knowledge of potential activity.
• To facilitate assessment of editing outcomes, HEK293T-GFP reporter cell line was first generated by knocking into 11EK293T cells a transgene cassette that constitutively expresses GFP. The modified cells were expanded by serial passage every 3-5 days and maintained in Fibroblast (FB) medium, consisting of Dulbecco's Modified Eagle Medium (DMEM, Corning Cellgro, #10-013-CV) supplemented with 10% fetal bovine serum (FBS; Seradigm, #1500-500), and 100 Units/mL penicillin and 100 mg/mL streptomycin (100x-Pen-Strep; GIBCO #15140-122), and can additionally include sodium pyruvate (100×, Thennofisher #11360070), non-essential amino acids (100× Thennofisher #11140050), HEPES buffer (100× Thermofisher #15630080), and 2-mercaptoethanol (1000× Thermofisher #21985023). The cells were incubated at 37° C. and 5% CO2, After 1-2 weeks, GFP+cells were bulk sorted into FB medium. The reporter lines were expanded by serial passage every 3-5 days and maintained in FB medium in an incubator at 37° C. and 5% CO2. Clonal cell lines were generated by a limiting dilution method.
• HEK293T-GFP reporter cells, constructed using cell line generation methods described above were used for this experiment. Cells were seeded at 20-40 k cells/well in a 96 well plate in 100 μL of FB medium and cultured in a 37° C. incubator with 5% CO2. The following day, cells were transfected at ˜75% confluence using lipofectamine 3000 and manufacturer recommended protocols. Plasmid DNA encoding CasX and guide construct (e.g., see table for sequences) were used to transfect cells at 100-400 ng/well, using 3 wells per construct as replicates. A non-targeting plasmid construct was used as a negative control. Cells were selected for successful transfection with puromycin at 0.3-3 μg/ml for 24-48 hours followed by recovery in FB medium. Edited cells were analyzed by flow cytometry 5 days after transduction. Briefly, cells were sequentially gated for live cells, single cells, and fraction of GFP-negative
• Results: The graph in FIG. 15 shows the results of flow cytometry analysis of Cas-mediated editing at the GFP locus in HEK293T-GFP cells 5 days post-transfection. Each data point is an average measurement of 3 replicates for an individual spacer. Reference CasX reference protein (SEQ ID NO: 2) and gRNA (SEQ ID NO: 5) RNP complexes showed a clear preference for TTC PAM (FIG. 15). This served as a baseline for CasX protein and sgRNA variants that altered specificity for the PAM sequence. FIG. 16 shows that select CasX protein variants can edit both non-canonical and canonical PAM sequences more efficiently than the reference CasX protein of SEQ ID NO: 2 when assayed with various PAM and spacer sequences in HEK293 cells. The construct with non-targeting spacer resulted in no editing (data not shown). This example demonstrates that, under the conditions of the assay, CasX with appropriate guides can edit at target sequences with ATCN, CTCN and TTCN PAMs in HEK293T-GFP reporter cells, and that improved CasX variants increase editing activity at both canonical and non-canonical PAMs.
Example 7 Reference Planctomycetes CasX RNPs are Highly Specific
• Reference CasX RNP complexes were assayed for their ability to cleave target sequences with 1-4 mutations, with results shown in FIGS. 17A-17F. Reference Planctolmycetes CasX RNPs were found to be highly specific and exhibited fewer off-target effects than SpyCas9 and SauCas9.
Example 8 Creation, Expression and Purification of CasX Constructs Growth and Expression
• Expression constructs for the CasX of Table 8 were constructed from gene fragments (Twist Biosciences) that were codon optimized for E.coli. The assembled construct contains a TEV-cleavable, C-terminal TwinStrep tag and was cloned into a pBR322-derivative plasmid backbone containing an ampicillin resistance gene. The sequences of Table 8 arc configured as: SV40 NLS-CasX-SV40 NLS-TEV cleavage site—TwinStrep tag. Expression constructs were transformed into chemically-competent BL21*(DE3) E. coli and a starter culture was grown overnight in LB broth supplemented with carbenicillin at 37° C., 180 RPM, in UltraYield Flasks (Thomson Instrument Company). The following day, this culture was used to seed expression cultures at a 1:100 v/v ratio (starter culture:expression culture). Expression cultures were inoculated into Terrific Broth (Novagen) supplemented with carbenicillin and grown in UltraYield flasks at 37° C., 180 RPM. Once the cultures reached an OD of 0.5, they were chilled to 16° C. while shaking over 2 hours and IPTG (isopropyl β-D-1-thiogalactopyranoside) was added to a final concentration of 1 mM, from a 1 M stock. The cultures were induced at 16° C., 180 RPM for 20 hours before being harvested by centrifugation at 4,000×g for 15 minutes. 4° C. The cell paste was weighed and resuspended in lysis buffer (50 mMHEPES-NaOH, 250 mM NaCl, 5 mM MgCl₂, 1 mM TCEP, 1 mM benzamidine-HCL, 1 mM PMSF, 0.5% CHAPS, 10% glycerol, pH 8) at a ratio of 5 mL of lysis buffer per gram of cell paste. Once resuspended, the sample was frozen at −80° C. until purification.

• TABLE 8
  Sequences of CasX constructs

  	DNA	Protein
  	[SEQ ID	[SEQ
  Construct	NO]	ID NO]	Amino Acid Sequence
  WT CasX	3494	3498	MAPKKKRKVSQEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPD
  sequence			LRERLENLRKKPENIPQPISNTSRANLNKLLTDYTEMKKAILHVYWEEF
  of SEQ			QKDPVGLMSRVAQPAPKNIDQRKLIPVKDGNERLTSSGFACSQCCQPLY
  ID NO: 2			VYKLEQVNDKGKPHTNYFGRCNVSEHERLILLSPHKPEANDELVTYSLG
  fused to			KFGQRALDFYSIHVTRESNHPVKPLEQIGGNSCASGPVGKALSDACMGA
  an N			VASFLTKYQDIILEHQKVIKKNEKRLANLKDIASANGLAFPKITLPPQP
  terminal			HTKEGIEAYNNVVAQIVIWVNLNLWQKLKIGRDEAKPLQRLKGFPSFPL
  NLS			VERQAENVDWWDMVCNVKKLINEKKEDGKVFWQNLAGYKRQEALLPYLS
  			SEEDRKKGKKFARYQFGDLLLHLEKKHGEDWGKVYDEAWERIDKKVEGL
  			SKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCEL
  			KLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY
  			LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDP
  			NLIILPLAFGKRQGREFIWWDLLSLETGSLKLANGRVIEKTLYNRRTRQ
  			DEPALFVALTFERREVLDSSNIKPMNLIGIDRGENIPAVIALTDPEGCP
  			LSRFKDSLGNPTHILRIGESYKEKQRTIQAAKEVEQRRAGGYSRKYASK
  			AKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQ
  			YTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDR
  			VLEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRL
  			SEESVNNDISSWTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAD
  			EQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVETWQSFYRKKLK
  			EVWKPAVAPKKKRKVSENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSHP
  			QFEKGRGSGC
  CasX 119	3495	3499	MAPKKKRKVSQEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPD
  			LRERLENLRKKPENIPQPISNTSRANLNKLLTDYTEMKKAILHVYWEEF
  			QKDPVGLMSRVAQPAPKNIDQRKLIPVKDGNERLTSSGFACSQCCQPLY
  			VYKLEQVNDKGKPHTNYFGRCNVSEHERLILLSPHKPEANDELVTYSLG
  			KFGQRALDFYSIHVTRESNHPVKPLEQIGGNSCASGPVGKALSDACMGA
  			VASFLTKYQDIILEHQKVIKKNEKRLANLKDIASANGLAFPKITLPPQP
  			HTKEGIEAYNNVVAQIVIWVNLNLWQKLKIGRDEAKPLQRLKGFPSFPL
  			VERQAENVDWWDMVCNVKKLINEKKEDGKVFWQNLAGYKRQEALLPYLS
  			SEEDRKKGKKFARYQFGDLLLHLEKKHGEDWGKVYDEAWERIDKKVEGL
  			SKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCEL
  			KLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY
  			LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDP
  			NLIILPLAFGKRQGREFIWWDLLSLETGSLKLANGRVIEKTLYNRRTRQ
  			DEPALFVALTFERREVLDSSNIKPMNLIGIDRGENIPAVIALTDPEGCP
  			LSRFKDSLGNPTHILRIGESYKEKQRTIQAAKEVEQRRAGGYSRKYASK
  			AKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQ
  			YTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV
  			LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLS
  			EESVNNDISSWTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHADE
  			QAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVETWQSFYRKKLKE
  			VWKPAVPPAPKKKRKVSENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSH
  			PQFEKGRGSGC
  CasX
  438	3496	3500	MAPKKKRKVSQEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPD
  			LRERLENLRKKPENIPQPISNTSRANLNKLLTDYTEMKKAILHVYWEEF
  			QKDPVGLMSRVAQPAPKNIDQRKLIPVKDGNERLTSSGFACSQCCQPLY
  			VYKLEQVNDKGKPHTNYFGRCNVSEHERLILLSPHKPEANDELVTYSLG
  			KFGQRALDFYSIHVTRESNHPVKPLEQIGGNSCASGPVGKALSDACMGA
  			VASFLTKYQDIILEHQKVIKKNEKRLANLKDIASANGLAFPKITLPPQP
  			HTKEGIEAYNNVVAQIVIWVNLNLWQKLKIGRDEAKPLQRLKGFPSFPL
  			VERQAENVDWWDMVCNVKKLINEKKEDGKVFWQNLAGYKRQEALLPYLS
  			SEEDRKKGKKFARYQFGDLLLHLEKKHGEDWGKVYDEAWERIDKKVEGL
  			SKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCEL
  			KLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY
  			LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDP
  			NLIILPLAFGKRQGREFIWWDLLSLETGSLKLANGRVIEKTLYNRRTRQ
  			DEPALFVALTFERREVLDSSNIKPMNLIGIDRGENIPAVIALTDPEGCP
  			LSRFKDSLGNPTHILRIGESYKEKQRTIQAAKEVEQRRAGGYSRKYASK
  			AKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQ
  			YTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV
  			LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLS
  			EESVNNDISSWTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHADE
  			QAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVETWQSFYRKKLKE
  			VWKPAVPPAPKKKRKVSENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSH
  			PQFEKGRGSGC
  CasX
  457	3497	3501	MAPKKKRKVSQEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPD
  			LRERLENLRKKPENIPQPISNTSRANLNKLLTDYTEMKKAILHVYWEEF
  			QKDPVGLMSRVAQPAPKNIDQRKLIPVKDGNERLTSSGFACSQCCQPLY
  			VYKLEQVNDKGKPHTNYFGRCNVSEHERLILLSPHKPEANDELVTYSLG
  			KFGQRALDFYSIHVTRESNHPVKPLEQIGGNSCASGPVGKALSDACMGA
  			VASFLTKYQDIILEHQKVIKKNEKRLANLKDIASANGLAFPKITLPPQP
  			HTKEGIEAYNNVVAQIVIWVNLNLWQKLKIGRDEAKPLQRLKGFPSFPL
  			VERQAENVDWWDMVCNVKKLINEKKEDGKVFWQNLAGYKRQEALLPYLS
  			SEEDRKKGKKFARYQFGDLLLHLEKKHGEDWGKVYDEAWERIDKKVEGL
  			SKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCEL
  			KLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY
  			LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDP
  			NLIILPLAFGKRQGREFIWWDLLSLETGSLKLANGRVIEKTLYNRRTRQ
  			DEPALFVALTFERREVLDSSNIKPMNLIGIDRGENIPAVIALTDPEGCP
  			LSRFKDSLGNPTHILRIGESYKEKQRTIQAAKEVEQRRAGGYSRKYASK
  			AKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRGFGRQGKRTFMAERQ
  			YTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV
  			LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLS
  			EESVNNDISSWTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHADE
  			QAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVETWQSFYRKKLKE
  			VWKPAVPPAPKKKRKVSENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSH
  			PQFEKGRGSGC

Purification
• Frozen samples were thawed overnight at 4° C. with gentle rocking. The viscosity of the resulting lysate was reduced by sonication and lysis was completed by homogenization in three passes at 17 k PSI using an Emulsitlex C3 homogeniser (Avestin). Lysate was clarified by centrifugation at 50,000×g. 4° C., for 30 minutes and the supernatant was collected. The clarified supernatant was applied to a Heparin 6 Fast Flow column (GE Life Sciences) using an AKTA Pure 25M FPLC system (GE Life Sciences). The column was washed with 5 CV of Heparin Buffer A (50 mM HEPES-NaOH, 250 mM NaCl, 5 mM MgCl₂, 1 mM TCEP, 10% glycerol, pH 8), then with 3 CV of Heparin Buffer B (Buffer A with the NaCl concentration adjusted to 500 mM). Protein was eluted with 1.75 CV of Heparin Buffer C (Buffer A with the NaCl concentration adjusted to 1 M). The heparin eluate was applied to a StrepTactin HP column (GE Life Sciences) by AKTA FPLC. The column was washed with 10 CV of Strep Buffer (50 mM HEPES-NaOH, 500 mM NaCl, 5 inM MgCl2, 1 mM TCEP, 10% glycerol, pH 8). Protein was eluted from the column using 2 CV of Strep Buffer with 2.5 mM Desthiobiotin added and collected in 0.8 CV fractions. CasX-containing fractions were pooled, concentrated at 4° C. using a 50 kDa cut-off spin concentrator (Millipore Sigma), and purified by size exclusion chromatography on a Superdex 200 pg column (GE Life Sciences) operated by AKTA FPLC. The column was equilibrated with SEC Buffer (25 mM sodium phosphate, 300 mM NaCl, 1 mM TCF.P, 10% glycerol. pH 7.25). CasX-containing fractions that eluted at the appropriate molecular weight were pooled, concentrated at 4° C., using a 50 kDa cut-off spin concentrator, aliquoted, and snap-frozen in liquid nitrogen before being stored at −80° C.
Results
• Following the growth and purification sections above, the following results were obtained.
• WT CasX derived from Planciomycetes (SEQ ID NO:2): Samples from throughout the purification procedure were resolved by SDS-PAGE and visualized by colloidal Cooniassie staining, as shown in FIGS. 24 and 26. Results from the gel filtration are shown in FIG. 25.
• The average yield was 0.75 mg of purified CasX protein per liter of culture at 75% purity, as evaluated by colloidal Coomassie staining.
• CasX Variant 119: Following the same expression and purification scheme for WT CasX, the following results were obtained for CasX variant 119. Samples from throughout the purification procedure were resolved by SDS-PAGE and visualized by colloidal Coomassie staining, as shown in FIG. 28. Results from the gel filtration are shown in FIG. 27. The average yield was 11.7 mg of purified CasX protein per liter of culture at 95% purity, as evaluated by colloidol Coomassie staining.
• CasX Variant 438: Following the same expression and purification scheme for WT CasX, the following results were obtained for CasX variant 438, Samples from throughout the purification procedure were resolved by SDS-PAGE and visualized by colloidal Coomassie staining, as shown in FIGS. 29 and 31. Results from the gel filtration are shown in FIG. 30. The average yield was 13.1 mg of purified CasX protein per liter of culture at 97.5% purity, as evaluated by colloidal Coomassie staining.
• CasX Variant 457: Following the same expression and purification scheme for WT CasX, the following results were obtained for CasX variant 457. Samples from throughout the purification procedure were resolved by SDS-PAGE and visualized by colloidal Coomassie staining, as shown in FIGS. 32 and 34. Results from the gel filtration are shown in FIG. 33. The average yield was 9.76 mg of purified CasX protein per liter of culture at 91.6% purity as evaluated by colloidal Coomassie staining.
• Overall, the results support that CasX variants can be produced and recovered at high levels of purity sufficient for experimental assays and evaluation.
Example 9 Design and Generation of CasX 119, 438 and 457
• In order to generate the CasX 119, 438, and 457 constructs (sequences in Table 9), the codon-optimized CasX 37 construct (based on the WT CasX Stx2 construct of Example 8, encoding Planctomycetes CasX SEQ ID NO: 2, with a A708K substitution and a [P793] deletion with fused NLS, and linked guide and non-targeting sequences) was cloned into a mammalian expression plasmid (pStX; see FIG. 35) using standard cloning methods. To build CasX 119, the CasX 37 construct DNA was PCR amplified in two reactions using Q5 DNA polymerase (New England BioLabs Cat #M0491L) according to the manufacturer's protocol, using primers oIC539 and oIC88 as well as oIC87 and oIC540 respectively (see FIG. 36). To build CasX 457, the CasX 365 construct DNA was PCR amplified in four reactions using Q5 DNA polymerase (New England BioLabs Cat #M04911,) according to the manufacturer's protocol, using primers oIC539 and oIC212, oIC211 and oIC376, oIC375 and oIC551, and oIC550 and oIC540 respectively. To build CasX 438, the CasX 119 construct DNA was PCR amplified in four reactions using Q5 DNA polymerase (New England BioLabs Cat #M0491L) according to the manufacturer's protocol, using primers oIC539 and oIC689, oIC688 and oIC376, oIC375 and oIC551, and oIC550 and oIC540 respectively. The resulting PCR amplification products were then purified using Zymoclean DNA clean and concentrator (Zymo Research Cat #4014) according to the manufacturer's protocol. The pStX backbone was digested using XbaI and SpeI in order to remove the 2931 base pair fragment of DNA between the two sites in plasmid pStx34. The digested backbone fragment was purified by gel extraction from a 1% agarose gel (Gold Bio Cat #A-201-500) using Zymoclean Gel DNA Recovery Kit (Zymo Research Cat #D4002) according to the manufacturer's protocol. The insert and backbone fragments were then pieced together using Gibson assembly (New England BioLabs Cat #E2621S) following the manufacturer's protocol. Assembled products in the pStx34 were transformed into chemically-competent Turbo Competent E. coli bacterial cells, plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. pStX34 includes an EF-1α promoter for the protein as well as a selection marker for both puromycin and carbenicillin. Sequences encoding the targeting sequences that target the gene of interest were designed based on CasX PAM locations. Targeting sequence DNA was ordered as single-stranded DNA (ssDNA) oligos (Integrated DNA Technologies) consisting of the targeting sequence and the reverse complement of this sequence. These two oligos were annealed together and cloned into pStX individually or in bulk by Golden Gate assembly using T4 DNA Ligase (New England BioLabs Cat #M0202L) and an appropriate restriction enzyme for the plasmid. Golden Gate products were transformed into chemically or electro-competent cells such as NEB Turbo competent E. coli (NEB Cat #C2984I), plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) and following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct ligation. SaCas9 and SpyCas9 control plasmids were prepared similarly to pStX plasmids described above, with the protein and guide regions of pStX exchanged for the respective protein and guide. Targeting sequences for SaCas9 and SpyCas9 were either obtained from the literature or were rationally designed according to established methods. The expression and recovery of the CasX proteins was performed as described in Example 8, however in that Example, the DNA sequences were codon optimized for expression in E. coli.

• TABLE 9
  Sequences of CasX 119, 438 and 457

  Construct	DNA [SEQ ID NO]	Protein [SEQ ID NO]
  CasX 119	3502	3505
  CasX 457	3503	3506
  CasX 438	3504	3507

Example 10 Design and Generation of CasX Constructs 278-280, 285-288, 290, 291, 293, 300, 492, and 493
• In order to generate the CasX 278-280, 285-288, 290, 291, 293, 300, 492, and 493 constructs (sequences in Table 10), the N- and C-termini of the codon-optimized CasX 119 construct (based on the CasX Stx37 construct of Example 9, encoding Planciomycetes CasX SEQ ID NO: 2, with a A708K substitution and a [P793] deletion with fused NLS, and linked guide and non-targeting sequences) in a mammalian expression vector were manipulated to delete or add NLS sequences (sequences in Table 11). Constructs 278, 279, and 280 were manipulations of the N- and C-termini using only an SV40 NLS sequence. Construct 280 had no NLS on the N-terminus and added two SV40 NLS′ on the C-terminus with a triple proline linker in between the two SV40 NLS sequences. Constructs 278, 279, and 280 were made by amplifying pStx34.119.174.NT with Q5 DNA polymerase (New England BioLabs Cat #M0491L) according to the manufacturer's protocol, using primers oIC527 and oiC528, oIC730 and oIC522, and oIC730 and oIC530 for the first fragments each and using oIC529 and oIC520, olC519 and oIC731, and oIC529 and oIC73 I to create the second fragments each. These fragments were purified by gel extraction from a 1% agarose gel (Gold Bio Cat #A-201-500) using Zymoclean Gel DNA Recovery Kit (Zymo Research Cat #D4002) according to the manufacturer's protocol. The respective fragments were cloned together using Gibson assembly (New England BioLabs Cat #E2621S) following the manufacturer's protocol. Assembled products in the pStx34 were transformed into chemically-competent Turbo Competent E. coli bacterial cells, plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat 214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Sequences encoding the targeting sequences that target the gene of interest were designed based on CasX PAM locations. Targeting sequence DNA was ordered as single-stranded DNA (ssDNA) oligos (Integrated DNA Technologies) consisting of the targeting sequence and the reverse complement of this sequence. These two oligos were annealed together and cloned into pStX individually or in bulk by Golden Gate assembly using T4 DNA Ligase (New England BioLabs Cat #M0202L) and an appropriate restriction enzyme for the plasmid. Golden Gate products were transformed into chemically- or electro-competent cells such as NEB Turbo competent E. coli (NEB Cat #C29841), plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzv Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) and following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct ligation.
• In order to generate constructs 285-288, 290, 291. 293, and 300, a nested PCR method was used for cloning. The backbone vector and PCR template used was construct pStx34 279.119.174.NT, having the CasX 119, guide 174, and non-targeting spacer (see Examples 8 and 9 and Tables therein for sequences). Construct 278 has the configuration SV40NLS-CasX119. Construct 279 has the configuration CasX119-SV40NLS. Construct 280 has the configuration CasX119-SV40NLS-PPP linker-SV40NLS. Construct 285 has the configuration CasX119-SV40NLS-PPP linker-SynthNLS3. Construct 286 has the configuration CasX119-SV40NLS-PPP linker-SynthNLS4. Construct 287 has the configuration CasX119-SV40NLS-PPP linker-SynthNLS5. Construct 288 has the configuration CasX119-SV40NLS-PPP linker-SynthNLS6. Constrict 290 has the configuration CasX119-SV40NLS-PPP linker-EGL-13 NLS. Construct 291 has the configuration CasX119-SV40NLS-PPP linker-c-Myc NLS. Construct 293 has the configuration CasX119-SV40NLS-PPP linker-Nucleolar RNA Helicase II NLS. Construct 300 has the configuration CasX119-SV40NLS-PPP linker-Influenza A protein NLS. Construct 492 has the configuration SV40NLS-CasX119-SV40NLS-PPP linker-SV40NLS. Construct 493 has the configuration SV40NLS-CasX119-SV40NLS-PPP linker-c-Myc NLS. Each variant had a set of three PCBs; two of which were nested, were purified by gel extraction, digested, and then ligated into the digested and purified backbone. Assembled products in the pStx34 were transthrmed into chemically-competent Turbo Competent E. coli bacterial cells, plated on LB-Agar plates (LB: Teknova Cat #9315, Agar: Quartz)/Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen. Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Sequences encoding the targeting sequences that target the gene of interest were designed based on CasX PAM locations. Targeting sequence DNA was ordered as single-stranded DNA (ssDNA) oligos (Integrated DNA Technologies) consisting of the targeting sequence and the reverse complement of this sequence. These two oligos were annealed together and cloned into the resulting pStX individually or in bulk by Golden Gate assembly using T4 DNA Ligase (New England BioLabs Cat #M0202L) and an appropriate restriction enzyme for the plasmid. Golden Gate products were transformed into chemically- or electro-competent cells such as NEB Turbo competent E. coli (NEB Cat #C29841), plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #L27104) and following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct ligation.
• In order to generate constructs 492 and 493, constructs 280 and 291 were digested using XbaI and BamII (NEB #R0145S and NEB #R3136S) according to the manufacturer's protocol. Next, they were purified by gel extraction from a 1% agarose gel (Gold Bio Cat #A-201-500) using Zymoclean Gel DNA Recovery Kit (Zymo Research Cat #D4002) according to the manufacturer's protocol. Finally, they were ligated using T4 DNA ligase (NEB #M0202S) according to the manufacturer's protocol into the digested and purified pStx34.119.174.NT using XbaI and BamHI and Zymoclean Gel DNA Recovery Kit. Assembled products in the pStx34 were transformed into chemically-competent Turbo Competent E. coli bacterial cells, plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Sequences encoding the targeting spacer sequences that target the gene of interest were designed based on CasX PAM locations. Targeting sequence DNA was ordered as single-stranded DNA (ssDNA) oligos (Integrated DNA Technologies) consisting of the targeting spacer sequence and the reverse complement of this sequence. These two oligos were annealed together and cloned into each pStX individually or in bulk by Golden Gate assembly using T4 DNA Ligase (New England BioLabs Cat #M0202L) and an appropriate restriction enzyme for the respective plasmids. Golden Gate products were transformed into chemically- or electro-competent cells such as NEB Turbo competent E. coli (NEB Cat #C2984I), plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) and following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct ligation. The plasmids would be used to produce and recover CasX protein utilizing the general methodologies of Examples 8 and 9.

• TABLE 10
  CasX 278-280, 285-288, 290, 291, 293, 300, 492,
  and 493 constructs and corresponding SEQ ID NOs

  	Construct	SEQ ID NO
  	278	3508
  	279	2509
  	280	3510
  	285	3511
  	286	3512
  	287	3513
  	288	3514
  	290	3515
  	291	3516
  	293	3517
  	300	3518
  	492	3519
  	493	3520

• TABLE 11
  Nuclear localization sequence list

  		SEQ		SEQ
  		ID		ID	Amino Acid
  CasX	NLS	NO	DNA Sequence	NO	Sequence
  278, 279, 280,	SV40	3521	CCAAAGAAGAAGCGG	352	PKKKRKV
  492, 493			AAGGTC
  285	SynthNLS3	3522	CACAAGAAGAAACAT	383	HKKKHPDASVNFS
  			CCAGACGCATCAGTCA		EFSK
  			ACTTTAGCGAGTTCAG
  			TAAA
  286	SynthNLS4	3523	CAGCGCCCTGGGCCTT	394	QRPGPYDRPQRPG
  			ACGATAGGCCGCAAA		PYDRP
  			GACCCGGACCGTATGA
  			TCGCCCT
  287	SynthNLS5	3524	CTCAGCCCGAGTCTTA	385	LSPSLSPLLSPS
  			GTCCACTGCTTTCCCC		LSPL
  			GTCCCTGTCTCCACTG
  288	SynthNLS6	3525	CGGGGCAAGGGTGGC	386	RGKGGKGLGK
  			AAGGGGCTTGGCAAG		GGAKRHRK
  			GGGGGGGCAAAGAGG
  			CACAGGAAG
  290	EGL-13	3526	AGCCGCCGCAGAAAA	379	SRRRKANPTKL
  			GCCAATCCTACAAAAC		SENAKKLAKE
  			TGTCAGAAAATGCGA		VEN
  			AAAAACTTGCTAAGG
  			AGGTGGAAAAC
  291	c-Myc	3527	CCTGCCGCAAAGCGA	354	PAAKRVKLD
  			GTGAAATTGGAC
  293	Nucleolar	3528	AAGCGGTCCTTCAGTA	375	KRSFSKAF
  	RNA		AGGCCTTT
  	Helicase
  	II
  300	Influenza	3529	AAACGGGGAATAAAC	373	KRGINDRNFW
  	A protein		GACCGGAACTTCTGGC		RGENERKTR
  			GCGGGGAAAACGAGC
  			GCAAAACCCGA

Example 11 Design and Generation of CasX Constructs 387, 395,5 485-491, and 494
• In order to generate CasX 395, CasX 485, CasX 486, CasX 487, the codon optimized CasX 119 (based on the CasX 37 construct of Example 9, encoding Planctomycetes CasX SEQ II) NO: 2, with a A708K substitution and a [P793] deletion with fused NLS, and linked guide and non-targeting sequences), CasX 435, CasX 438, and CasX 484 (each based on CasX 119 construct of Example 9 encoding Planctomycetes CasX SEQ ID NO: 2, with a L379R substitution, a A708K substitution, and a [P793] deletion with fused NLS. and linked guide and non-targeting sequences) were cloned respectively into a 4kb staging vector comprising a KanR marker, colE1 ori, and CasX with fused NLS (pStx1) using standard cloning methods. Gibson primers were designed to amplify the CasX SEQ ID NO: 1 Helical I domain from amino acid 192-331 in its own vector to replace this corresponding region (aa 193-332) on CasX 119, CasX 435, CasX 438, and CasX 484 in pStx1 respectively. The Helical I domain from CasX SEQ ID NO: 1 was amplified with primers oIC768 and oIC784 using Q5 DNA polymerase (New England BioLabs Cat #M0491L) according to the manufacturer's protocol. The destination vector containing the desired CasX variant was amplified with primers oIC765 and oIC764 using Q5 DNA polymerase (New England BioLabs Cat #M0491L) according to the manufacturer's protocol. The two fragments were purified by gel extraction from a 1% agarose gel (Gold Bio Cat #A-201-500) using Zymoclean Gel DNA Recovery Kit (Zymo Research Cat #D4002) according to the manufacturer's protocol. The insert and backbone fragments were then pieced together using Gibson assembly (New England BioLabs Cat #E2621S) following the manufacturer's protocol. Assembled products in the pStxl staging vector were transformed into chemically-competent Turbo Competent E. coli bacterial cells, plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing kanamycin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Correct clones were then cut and pasted into a mammalian expression plasmid (pStX; see FIG. 36) using standard cloning methods. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Sequences encoding the targeting spacer sequences that target the gene of interest were designed based on CasX PAM locations. Targeting spacer sequence DNA was ordered as single-stranded DNA (ssDNA) oligos (Integrated DNA Technologies) consisting of the targeting sequence and the reverse complement of this sequence. These two oligos were annealed together and cloned into pStX individually or in bulk by Golden Gate assembly using T4 DNA Ligase (New England BioLabs Cat #M02020 and an appropriate restriction enzyme for the plasmid. Golden Gate products were transformed into chemically or electro-competent cells such as NEB Turbo competent E. coli (NEB Cat #C2984I), plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct ligation.
• In order to generate CasX 488, CasX 489, CasX 490, and CasX 491 (sequences in Table 12), the codon optimized CasX 119 (based on the CasX 37 construct of Example 9, encoding Planctomycetes CasX SEQ ID NO: 2, with a A708K substitution and a [P793] deletion with fused NLS, and linked guide and non-targeting sequences). CasX 435, CasX 438, and CasX 484 (each based on CasX119 construct of Example 9 encoding Planctomycetes CasX SEQ ID NO: 2, with a L379R substitution, a A708K substitution, and a [P793] deletion with fused NLS, and linked guide and non-targeting sequences) were cloned respectively into a 4 kb staging vector that was made up of a KanR marker, colE1 ori, and STX with fused NLS (pStx1) using standard cloning methods. Gibson primers were designed to amplify the CasX Stx1 NTSB domain from amino acid 101-191 and Helical I domain from amino acid 192-331 in its own vector to replace this similar region (aa 103-332) on CasX 119. CasX 435, CasX 438, and CasX 484 in pStx1 respectively. The NTSB and Helical I domain from CasX SEQ ID NO: 1 were amplified with primers oIC766 and oIC784 using Q5 DNA polymerase (New England BioLabs Cat #M04911.) according to the manufacturer's protocol. The destination vector containing the desired CasX variant was amplified with primers oIC762 and oIC765 using Q5 DNA polymerase (New England BioLabs Cat #M0491L) according to the manufacturer's protocol. The two fragments were purified by gel extraction from a 1% agarose gel (Gold Bio Cat #A-201-500) using Zymoclean Gel DNA Recovery Kit (Zymo Research Cat #D4002) according to the manufacturer's protocol. The insert and backbone fragments were then pieced together using Gibson assembly (New England BioLabs Cat #E2621S) following the manufacturer's protocol. Assembled products in the pStx1 staging vector were transformed into chemically-competent Turbo Competent E. coli bacterial cells, plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing kanamycin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Correct clones were then cut and pasted into a mammalian expression plasmid (pStX; see FIG. 36) using standard cloning methods. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Sequences encoding the targeting spacer sequences that target the gene of interest were designed based on CasX PAM locations. Targeting spacer sequence DNA was ordered as single-stranded DNA (ssDNA) oligos (Integrated DNA Technologies) consisting of the targeting sequence and the reverse complement of this sequence. These two oligos were annealed together and cloned into pStX individually or in bulk by Golden Gate assembly using T4 DNA Ligase (New England BioLabs Cat #M0202L) and an appropriate restriction enzyme for the plasmid. Golden Gate products were transformed into chemically or electro-competent cells such as NEB Turbo competent E. coli (NEB Cat #C2984I), plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) and following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct ligation.
• In order to generate CasX 387 and CasX 494 (sequences in Table 12), the codon optimized CasX 119 (based on the CasX 37 construct of Example 9, encoding Planctomycetes CasX SEQ ID NO: 2, with a A708K substitution and a [P793] deletion with fused NLS, and linked guide and non-targeting sequences) and CasX 484 (based on CasX119 construct of Example 9 encoding Planctomycetes CasX SEQ ID NO: 2, with a L379R substitution, a A708K substitution, and a [P793] deletion with fused NLS, and linked guide and non-targeting sequences) were cloned respectively into a 4 kb staging vector that was made up of a KanR marker, colE1 ori, and STX with fused NIS (pStx1) using standard cloning methods. Gibson primers were designed to amplify the CasX Stx1 NTSB domain from amino acid 101-191 in its own vector to replace this similar region (an 103-192) on CasX 119 and CasX 484 in pStx1 respectively. The NTSB domain from CasX Stx1 was amplified with primers oIC766 and oIC767 using Q5 DNA polymerase (New England BioLabs Cat #M0491L) according to the manufacturer's protocol. The destination vector containing the desired CasX variant was amplified with primers oIC763 and oIC762 using Q5 DNA polymerase (New England BioLabs Cat #M04910 according to the manufacturer's protocol. The two fragments were purified by gel extraction from a 1% agarose gel (Gold Bio Cat #A-201-500) using Zymoclean Gel DNA Recovery Kit (Zvmo Research Cat #D4002) according to the manufacturer's protocol. The insert and backbone fragments were then pieced together using Gibson assembly (New England BioLabs Cat #E2621S) following the manufacturer's protocol. Assembled products in the pStx1 staging vector were transformed into chemically-competent Turbo Competent E. coli bacterial cells, plated on LB-Agar plates (LB: Teknova Cat L9315, Agar: Quartzy Cat #214510) containing kanamycin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Correct clones were then cut and pasted into a mammalian expression plasmid (pStX; see FIG. 36) using standard cloning methods. The resultant plasmids were sequenced using Sanger sequencing to ensure correct assembly. Sequences encoding the targeting sequences that target the gene of interest were designed based on CasX PAM locations. Targeting sequence DNA was ordered as single-stranded DNA (ssDNA) oligos (Integrated DNA Technologies) consisting of the targeting sequence and the reverse complement of this sequence. These two oli.gos were annealed together and cloned into pStX individually or in bulk by Golden Gate assembly using T4 DNA Ligase (New England BioLabs Cat #M0202L) and an appropriate restriction enzyme for the plasmid. Golden Gate products were transformed into chemically or electro-competent cells such as NEB Turbo competent E. coli (NEB Cat #C2984I), plated on LB-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) and following the manufacturer's protocol. The resultant plasmids were sequenced using Sanger sequencing to ensure correct ligation. Sequences of the resulting constructs are listed in Table 12.

• TABLE 12
  CasX 395 and 485-491 constructs and corresponding SEQ ID NOs

  Construct	DNA [SEQ ID NO]	Protein [SEQ ID NO]
  CasX 387	3530	3540
  CasX 395	3531	3541
  CasX 485	3532	3542
  CasX 486	3533	3543
  CasX 487	3534	3544
  CasX 488	3535	3545
  CasX 489	3536	3546
  CasX 490	3537	3547
  CasX 491	3538	3548
  CasX 494	3539	3549

Example 12 Generation of RNA Guides
• For the generation of RNA single guides and spacers, templates for in vitro transcription were generated by performing PCR with Q5 polymerase (NEB M0491) according to the recommended protocol, with template oligos for each backbone and amplification primers with the T7 promoter and the spacer sequence. The DNA primer sequences for the T7 promoter, guide and spacer for guides and spacers are presented in Table 13, below. The template oligos, labeled “backbone fwd” and “backbone rev” for each scaffold, were included at a final concentration of 20 nM each, and the amplification primers (T7 promoter and the unique spacer primer) were included at a final concentration of 1 uM each. The sg2, sg32, sg64, and sg174 guides correspond to SEQ ID NOS: 5, 2104, 2106, and 2238, respectively, with the exception that sg2, sg32, and sg64 were modified with an additional 5′ G to increase transcription efficiency (compare sequences in Table 13 to Table 2). The 7.37 spacer targets beta2-microglobulin (B2M). Following PCR amplification, templates were cleaned and isolated by phenol-chloroform-isoamyl alcohol extraction followed by ethanol precipitation.
• In vitro transcriptions were carried out in buffer containing 50 mM Tris pH 8.0, 30 mM MgCl₂, 0.01% Triton X-100, 2 mM spermidine, 20 mM DTT, 5 mM NTPs, 0.5 template, and 100 μg/mL T7 RNA polymerase. Reactions were incubated at 37° C. overnight. 20 units of DNase T (Promega #M6101)) were added per 1 mL of transcription volume and incubated for one hour. RNA products were purified via denaturing PAGE, ethanol precipitated, and resuspended in 1× phosphate buffered saline. To fold the sgRNAs, samples were heated to 70° C. for 5 min and then cooled to room temperature. The reactions were supplemented to 1 mM final MgCl₂ concentration, heated to 50° C. for 5 min and then cooled to room temperature. Final RNA guide products were stored at −80° C.

• TABLE 13
  Sequences for generation of guide RNA

  	Primer
  	Sequence
  	(SEQ	RNA Product
  Primer	ID NO)	(SEQ ID NO)	RNA product
  T7 promoter primer	3550	NA	Used for all
  sg2 backbone fwd	3551	3563	GGUACUGGCGCUUUUAUCUCAUUACUU
  sg2 backbone rev	3552		UGAGAGCCAUCACCAGCGACUAUGUCG
  sg2.7.37 spacer	3553		UAUGGGUAAAGCGCUUAUUUAUCGGAG
  primer			AGAAAUCCGAUAAAUAAGAAGCAUCAA
  			AGGGCCGAGAUGUCUCGCUCCG
  sg32 backbone fwd	3554	3564	GGUACUGGCGCUUUUAUCUCAUUACUU
  sg32 backbone rev	3555		UGAGAGCCAUCACCAGCGACUAUGUCG
  sg32.7.37 spacer	3556		UAUGGGUAAAGCGCCCUCUUCGGAGGG
  primer			AAGCAUCAAAGGGCCGAGAUGUCUCG
  sg64 backbone fwd	3557	3565	GGUACUGGCGCCUUUAUCUCAUUACUU
  sg64 backbone rev	3558		UGAGAGCCAUCACCAGCGACUAUGUCG
  sg64.7.37 spacer	3559		UAUGGGUAAAGCGCUUACGGACUUCGG
  primer			UCCGUAAGAAGCAUCAAAGGGCCGAGA
  			UGUCUCGCUCCG
  sg174 backbone fwd	3560	3566	ACUGGCGCUUUUAUCGgAUUACUUUGA
  sg174 backbone rev	3561		GAGCCAUCACCAGCGACUAUGUCGUAg
  sg174.7.37 spacer	3562		UGGGUAAAGCUCCCUCCUCGGAGGGAG
  primer			CAUCAAAGGGCCGAGAUGUCUCGCUCC
  			G

Example 13 RNP Assembly
• Purified wild-type and RNP of CasX and single guide RNA (sgRNA) were either prepared immediately before experiments or prepared and snap-frozen in liquid nitrogen and stored at −80° C. for later use. To prepare the RNP complexes, the CasX protein was incubated with sgRNA at 1:1.2 molar ratio. Briefly, sgRNA was added to Buffer #1 (25 mM NaPi, 150 mM NaCl, 200 mM trehalose. 1 mM MgCl2), then the CasX was added to the sgRNA solution, slowly with swirling, and incubated at 37° C. for 10 min to form RNP complexes. RNP complexes were filtered before use through a 0.22 μm Costar 8160 filters that were pre-wet with 200 μl Buffer #1. If needed, the RNP sample was concentrated with a 0.5 ml Ultra 100-Kd cutoff filter. (Millipore part #UFC510096), until the desired volume was obtained. Formation of competent RNP was assessed as described in Example 19.
Example 14 Assessing Binding Affinity to the Guide RNA
• Purified wild-type and improved CasX will be incubated with synthetic single-guide RNA containing a 3′ Cy7.5 moiety in low-salt buffer containing magnesium chloride as well as heparin to prevent non-specific binding and aggregation. The sgRNA will be maintained at a concentration of 10 pM, while the protein will be titrated from 1 pM to 100 μM in separate binding reactions. After allowing the reaction to come to equilibrium, the samples will be run through a vacuum manifold filter-binding assay with a nitrocellulose membrane and a positively charged nylon membrane, which bind protein and nucleic acid, respectively. The membranes will be imaged to identify guide RNA, and the fraction of bound vs unbound RNA will be determined by the amount of fluorescence on the nitrocellulose vs nylon membrane for each protein concentration to calculate the dissociation constant of the protein-sgRNA complex. The experiment will also be carried out with improved variants of the sgRNA to determine if these mutations also affect the affinity of the guide for the wild-type and mutant proteins. We will also perform electromobility shift assays to qualitatively compare to the filter-binding assay and confirm that soluble binding, rather than aggregation, is the primary contributor to protein-RNA association.
Example 15 Assessing Binding Affinity to the Target DNA
• Purified wild-type and improved CasX will be complexed with single-guide RNA bearing a targeting sequence complementary to the tamet nucleic acid. The RNP complex will be incubated with double-stranded target DNA containing a PAM and the appropriate target nucleic acid sequence with a 5′ Cy7.5 label on the target strand in low-salt buffer containing magnesium chloride as well as heparin to prevent non-specific binding and aggregation. The target DNA will be maintained at a concentration of 1 nM, while the RNP will be titrated from 1 pM to 100 μM in separate binding reactions, After allowing the reaction to come to equilibrium, the samples will be run on a native 5% polyacrylamide gel to separate bound and unbound target DNA. The gel will be imaged to identify mobility shifts of the target DNA, and the fraction of bound vs unbound DNA will be calculated for each protein concentration to determine the dissociation constant of the RNP-target DNA ternary complex.
Example 16 Assessing Differential PAM Recognition In Vitro
• Purified wild-type and engineered CasX variants will be complexed with single-guide RNA bearing a fixed targeting sequence. The RNP complexes will be added to buffer containing MgCl2 at a final concentration of 100 nM and incubated with 5′ Cy7.5-labeled double-stranded target DNA at a concentration of 10 nM. Separate reactions will be carried out with different DNA substrates containing different PAMs adjacent to the target nucleic acid sequence. Aliquots of the reactions will be taken at fixed time points and quenched by the addition of an equal volume of 50 mM EDTA and 95% formamide. The samples will be run on a denaturing polyacrylamide gel to separate cleaved and uncleaved DNA substrates. The results will be visualized and the rate of cleavage of the non-canonical PAMs by the CasX variants will be determined.
Example 17 Assessing Nuclease Activity for Double-Strand Cleavage
• Purified wild-type and engineered CasX variants will be complexed with single-guide RNA bearing a fixed PM22 targeting sequence. The RNP complexes will be added to buffer containing MgCl2 at a final concentration of 100 nM and incubated with double-stranded target DNA with a 5′ Cv7.5 label on either the target or non-target strand at a concentration of 10 nM. Aliquots of the reactions will be taken at fixed time points and quenched by the addition of an equal volume of 50 mM EDTA and 95% fonnamide. The samples will be run on a denaturing polyacrylamide gel to separate cleaved and uncleaved DNA substrates. The results will be visualized and the cleavage rates of the target and non-target strands by the wild-type and engineered variants will be determined. To more clearly differentiate between changes to target binding vs the rate of catalysis of the nucleolytic reaction itself, the protein concentration will be titrated over a range from 10 nM to 1 uM and cleavage rates will be determined at each concentration to generate a pseudo-Michaelis-Menten fit and determine the kcat* and KM*. Changes to KM* are indicative of altered binding, while changes to kcat* are indicative of altered catalysis.
Example 18 Assessing Target Strand Loading for Cleavage
• Purified wild-type and engineered CasX 119 will be complexed with single-guide RNA bearing a fixed PM/22 targeting sequence. The RNP complexes will be added to buffer containing MgCl2 at a final concentration of 100 nM and incubated with double-stranded target DNA with a 5′ Cy7.5 label On the target strand and a 5′ Cy5 label on the non-target strand at a concentration of 10 nM. Aliquots of the reactions will be taken at fixed time points and quenched by the addition of an equal volume of 50 mM EDTA and 95% formamide. The samples will be run on a denaturing polyacrylamide gel to separate cleaved and uncleaved DNA substrates. The results will be visualized and the cleavage rates of both strands by the variants will be determined. Changes to the rate of target strand cleavage but not non-target strand cleavage would be indicative of improvements to the loading of the target strand in the active site for cleavage. This activity could he further isolated by repeating the assay with a dsDNA substrate that has a gap on the non-target strand, mimicking a pre-cleaved substrate. Improved cleavage of the non-target strand in this context would give further evidence that the loading and cleavage of the target strand, rather than an upstream step, has been improved.
Example 19 CasX:gNA In Vitro Cleavage Assays 1. Determining Cleavage-competent Fraction
• The ability of CasX variants to form active RNP compared to reference CasX was determined using an in vitro cleavage assay. The beta-2 microglobulin (B2M) 7.37 target for the cleavage assay was created as follows. DNA oligos with the sequence TGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGC GCT (non-target strand, NTS; SEQ ID NO: 3567) and TGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGCCCTTAGCTGTGCTCGC GCT (target strand, TS; SEQ ID NO: 3568) were purchased with 5′ fluorescent labels (LI- COR IRDye 700 and 800, respectively). dsDNA targets were formed by mixing the oligos in a 1:1 ratio in lx cleavage buffer (20 mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM TCEP, 5% glycerol, 10 mM MgCl₂), heating to 95° C. for 10 minutes, and allowing the solution to cool to room temperature.
• CasX RNPs were reconstituted with the indicated CasX and guides (see graphs) at a final concentration of 1 _izM with 1.5-fold excess of the indicated guide in 1× cleavage buffer (20 mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM TCEP, 5% glycerol, 10 mM MgCl₂) at 37° C. for 10 min before being moved to ice until ready to use. The 7.37 target was used, along with sgRNAs having spacers complementary to the 7.37 target.
• Cleavage reactions were prepared with final RNP concentrations of 100 nM and a final target concentration of 100 nM. Reactions were carried out at 37° C. and initiated by the addition of the 7.37 target DNA. Aliquots were taken at 5, 10, 30, 60, and 120 minutes and quenched by adding to 95% formamide, 20 mM EDTA. Samples were denatured by heating at 95° C. for 10 minutes and run on a 10% urea-PAGE gel. The gels were imaged with a Li-COR Odyssey CLx and quantified using the LI-COR Image Studio software. The resulting data were plotted and analyzed using Prism. We assumed that CasX acts essentially as a single-turnover enzyme under the assayed conditions, as indicated by the observation that sub-stoichiometric amounts of enzyme fail to cleave a greater-than-stoichiometric amount of target even under extended time-scales and instead approach a plateau that scales with the amount of enzyme present. Thus, the fraction of target cleaved over long time-scales by an equimolar amount of RNP is indicative of what fraction of the RNP is properly formed and active for cleavage. The cleavage traces were fit with a biphasic rate model, as the cleavage reaction clearly deviates from monophasic under this concentration regime, and the plateau was determined for each of three independent replicates. The mean and standard deviation were calculated to determine the active fraction (Table 14). The graphs are shown in FIG. 37.
• Apparent active (competent) fractions were determined for RNPs formed for CasX2+guide 174+7.37 spacer, CasX119+guide 174+7.37 spacer, and CasX459 guide 174+7.37 spacer. The determined active fractions are shown in Table 14. Both CasX variants had higher active fractions than the wild-type CasX2, indicating that the engineered CasX variants form significantly more active and stable RNP with the identical guide under tested conditions compared to wild-type CasX. This may be due to an increased affinity for the sgRNA, increased stability or solubility in the presence of sgRNA, or greater stability of a cleavage-competent conformation of the engineered CasX:sgRNA complex. An increase in solubility of the RNP was indicated by a notable decrease in the observed precipitate formed when CasX457 was added to the sgRNA compared to CasX2. Cleavage-competent fractions were also determined for CasX2.2.7.37, CasX2.32.7.37, CasX2.64.7.37, and CasX2.174.7.37 to be 16±3%, 13±3%, 5±2%, and 22±5%, as shown in FIG. 38.
• The data indicate that both CasX variants and sgRNA variants are able to form a higher degree of active RNP with guide RNA compare to wild-type CasX and wild-type sgRNA.
• 2. In Vitro Cleavage Assays Determining k_cleave for CasX Variants Compared to Wild-Type Reference CasX
• The apparent cleavage rates of CasX variants 119 and 457 compared to wild-type reference CasX were determined using an in vitro fluorescent assay for cleavage of the target 7.37.
• CasX RNPs were reconstituted with the indicated CasX (see FIG. 39) at a final concentration of 1 μM with 1.5-fold excess of the indicated guide in 1× cleavage buffer (20 mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM TCEP, 5% glycerol, 10 mM MgCl2) at 37° C. for 10 min before being moved to ice until ready to use. Cleavage reactions were set up with a final RNP concentration of 200 nM and a final target concentration of 10 nM. Reactions were carried out at 37° C. and initiated by the addition of the target DNA. Aliquots were taken at 0.25, 0.5, 1, 2, 5, and 10 minutes and quenched by adding to 95% formamide, 20 mM EDTA. Samples were denatured by heating at 95° C. for 10 minutes and run on a 10% urea-PAGE gel. The gels were imaged with a LI-COR Odyssey CLx and quantified using the LI-COR Image Studio software. The resulting data were plotted and analyzed using Prism, and the apparent first-order rate constant of non-target strand cleavage (k_cleave) was determined for each CasX:sgRNA combination replicate individually. The mean and standard deviation of three replicates with independent fits are presented in Table 14, and the cleavage traces are shown in FIG. 38.
• Apparent cleavage rate constants were determined for wild-type CasX2, and CasX variants 119 and 457 with guide 174 and spacer 7.37 utilized in each assay. Under the assayed conditions, the k_cleave of CasX2, CasX119, and CasX457 were 0.51±0.01 min⁻¹, 6.29±2.11 min⁻¹, and 3.01±0.90 min⁻¹ (mean±SD), respectively (see Table 14 and FIG. 39). Both CasX variants had improved cleavage rates relative to the wild-type CasX2, though notably CasX119 has a higher cleavage rate under tested conditions than CasX457. As demonstrated by the active fraction determination, however. CasX457 more efficiently forms stable and active RNP complexes, allowing different variants to be used depending on whether the rate of cutting or the amount of active holoenzyme is more important for the desired outcome.
• The data indicate that the CasX variants have a higher level of activity, with K_cleave rates approximately 5 to 10-fold higher compared to wild-type CasX2.
• 3. In Vitro Cleavage Assays: Comparison of Guide Variants to Wild-Type Guides
• Cleavage assays were also performed with wild-type reference CasX2 and reference guide 2 compared to guide variants 32, 64, and 174 to determine whether the variants improved cleavage. The experiments were performed as described above. As many of the resulting RNPs did not approach full cleavage of the target in the time tested, we determined initial reaction velocities (V₀) rather than first-order rate constants. The first two timepoints (15 and 30 seconds) were fit with a line for each CasX:sgRNA combination and replicate. The mean and standard deviation of the slope for three replicates were determined.
• Under the assayed conditions, the V₀ for CasX2 with guides 2, 32, 64, and 174 were 20.4±1.4 nM/min, 18.4±2.4 nM/min, 7.8±1.8 nM/min, and 49.3±1.4 nM/min (see Table 14 and FIG. 40). Guide 174 showed substantial improvement in the cleavage rate of the resulting RNP (˜2.5-fold relative to 2, see FIG. 41), while guides 32 and 64 performed similar to or worse than guide 2. Notably, guide 64 supports a cleavage rate lower than that of guide 2 but performs much better in vivo (data not shown). Some of the sequence alterations to generate guide 64 likely improve in vivo transcription at the cost of a nucleotide involved in triplex formation. Improved expression of guide 64 likely explains its improved activity in vivo, while its reduced stability may lead to improper folding in vitro.

• TABLE 14
  Results of cleavage and RNP formation assays

  			Competent
  RNP Construct	kcleave*	Initial velocity*	fraction
  2.2.7.37		20.4 ± 1.4 nM/inin	16 ± 3%
  2.37.7.37		18.4 ± 2.4 nM/min	13 + 3%
  2.64.7.37		7.8 ± 1.8 nM/min	5 ± 2%
  2.174.7.37	0.51 + 0.01 min−1	49.3 ± 1.4 nM/min	22 + 5%
  119.174.7.37	6.79 + 2.11 min −1		35 ± 6%
  457.174.7.37	3.01 + 0.90 min −1		53 ± 7%
  *Mean and standard deviation

Example 20 Generation and Assay of AAV Vectors Delivering CasX Constructs Targeting SOD1
• This example describes a typical protocol followed to produce and characterize AAV2 vectors packaging CasX molecules and guides.
Materials and Methods:
• For AAV production, the tri-plasmid transfection method was used, using three essential plasmids pTransgene carrying the gene of interest to be packaged in AAV, pRC, and pHelper. DNA encoding CasX and guide RNA were cloned into an AAV transgene cassette, between the ITRs (FIG. 42) to generate the pTransgene plasmid. The constructed transgene plasmid was verified via full-length plasmid sequencing (see Table 15), restriction digestion, and functional tests including in vitro transfection of mammalian cells. Additional plasmids required for AAV production (pRC plasmid and pHelper plasmid) were purchased from commercial suppliers (Aldevron, Takara).
• For AAV production, HEK293/T cells were cultured in FB medium in a 37° C. incubator with 5% CO2. 10-20 1.5 cm dishes of HEK293T cells were used in a single batch of viral production. For a single 15 cm dish, 15 ug of each plasmid was first mixed together in 4 ml of FB medium, and complexed with 145 ug polyethyleneimine (PEI) i.e., at 3 ug PEI/ug of DNA, for 10 mins at room temperature. The ratio of the three plasmids used may be varied to further optimize virus production as needed.
• The PEI-DNA complex was then slowly dripped onto the 15 cm plate of HEK293T cells, and the plate of transfected cells moved back into the incubator. The next day, the medium was changed to FB with 2% FBS (instead of 10% FBS). At 3 days post-transfection, the media from the cells may be collected to increase virus yields. At 5-6 days post-transfection medium and cells were collected. The timing of harvest may be further varied to optimize virus yield.
• The cells were pelleted by centrifugation, and the medium collected from the top. Cells were lysed in a buffer with high salt content and high-salt-active nuclease for ih at 37° C. The cells may also be lysed using additional methods, such as sequential freeze-thaw, or chemical lysis by detergent.
• The medium collected at harvest, and any medium collected at earlier time points, were treated with a 1:5 dilution of a solution containing 40% PEG8000 and 2.5M NaCl, and incubated on ice for 2 h, in order to precipitate AAV. The incubation may also be carried out overnight at 4° C.
• The AAV precipitate from the medium was pelleted by centrifugation, resuspended in high salt content buffer with high-salt-active nuclease and combined with the lysed cell pellet. The combined cell lysate was then clarified by centrifugation and filtration through a 0.45 um filter, and purified on an AAV Poros affinity resin column (Thermofisher Scientific). The virus was eluted from the column into a neutralizing solution. At this stage, the virus may be taken through additional rounds of purification to increase the quality of the virus preparation.
• The eluted virus was then titered via qPCR to quantify the virus yield. For titering, a sample of virus was first digested with DNAse to remove any non-packaged viral DNA, the DNAse deactivated, and then viral capsids disrupted with Proteinase K to expose the packaged viral genomes for titering.
Results:
• Representative titers for AAV packaging DNA encoding a CasX 119 molecule and rRNA guide 64 (119.64) with a spacer having the sequence ATGTTCATGAGTTTGGAGAT; SEQ ID NO: 239 is shown in FIG. 43. Typically, ˜1e13 viral genomes were obtained from one batch of virus production as described here.
• This example demonstrates that i) CasX and a gNA can be cloned into an AAV transgene construct, and ii) CasX and guide can be packaged in an AAV vector and produced at sufficiently high titers.

• TABLE 15
  Sequence of pStx17 Construct

  	Construct	DNA sequence
  	pStX17	SEQ ID NO: 3569

Example 21 Administration of AAV Vectors Encoding a CasX System In Vitro and Evidence of SOD1 Gene Editing Materials and Methods:
• SOD1-GFP reporter cells were seeded at 30 k cells/well in a 96 well plate in 100 μl of FB medium. Confluence of cells was checked the next day, and cells were transduced at 80% confluence with AAV vectors (packaging construct 119.64 targeting SOD1, and SauCas9 targeting SOD1) at a range of doses or multiplicity of infection (MOI), for example from 1e7 to 1 viral genomes per cell. In a separate experiment, neural progenitor cells from the G93A mouse model of ALS (G93A NPCs) were similarly transduced. NPCs are cultured in NPC medium (DMEMF12 with Glutamax, supplemented with 10 mM Hepes (100× Thermofisher #15630080), non-essential amino acids (100× Thermofisher #11140050), penicillin-streptomycin (100×-Pen-Strep; GIBCO #15140-122), 2-mercaptoethanol 1000× (Thermofisher #21985023), B27 without vitamin-A (50×, Thermofisher), N2 (100×, Thermofisher), 20 ng/ml bFGF (Biolegend Cat no #579606), and 20 ng/ml EGF (Thermofisher #PHG0311)) at 37° C. and 5% CO2. The AAV doses were calculated based on viral titers determined by qPCR. Fresh FB medium or NPC medium may be replenished the next day, or as needed. Starting at 5 days post-transduction, and weekly thereafter, a portion of the cells were analyzed via flow cytometry or T7E1 assay.
Results:
• A representative example of SOD1 editing, as demonstrated by percentage of GFP negative cells, at 12 days post-transduction is shown in FIG. 44 and FIG. 45. FIG. 46 shows CasX delivered via AAV, with evidence of editing of G93A NPCs.
• This example demonstrates that CasX constructs targeting SOD1 may be delivered to mammalian cells via AAV, and result in successful editing of the SOD1 locus.
Example 22 In Vitro Transcription for the Generation of Guides and Spacers
• For the generation of RNA single guides and spacers, templates for in vitro transcription were generated by performing PCR with Q5 polymerase (NEB M0491) according to the recommended protocol, with template oligos for each backbone and amplification primers with the T7 promoter and the spacer sequence. The DNA primer sequences for the T7 promoter, guide and spacer for guides and spacers are presented in Table 16, below. The template oligos, labeled “backbone fwd” and “backbone rev” for each scaffold, were included at a final concentration of 20 nM each, and the amplification primers (T7 promoter and the unique spacer primer) were included at a final concentration of 1 uM each. The sg2, sg32, sg64, and sg174 guides correspond to SEQ ID NOS: 5, 2104, 2106, and 2238, respectively, with the exception that sg2, sg32, and sg64 were modified with additional 5′ G to increase transcription efficiency (compare sequences in Table 16 to Table 2). The 7.37 spacer targets beta2-microglobulin (B2M). Following PCR amplification, templates were cleaned and isolated by phenol-chloroform-isoamyl alcohol extraction followed by ethanol precipitation.
• In vitro transcriptions were carried out in buffer containing 50 mM Tris 8.0, 30 mM MgCl₂, 0.01% Triton X-100. 2 mM spermidine, 20 mM DTT, 5 mM NTPs, 0.5 μM template, and 100 μg/mL T7 RNA polymerase. Reactions were incubated at 37° C. overnight. 20 units of DNase I (Promega #M6101)) were added per 1 mL of transcription volume and incubated for one hour. RNA products were purified via denaturing PAGE, ethanol precipitated, and resuspended in 1× phosphate buffered saline. To fold the sgRNAs, samples were heated to 70° C. for 5 min and then cooled to room temperature. The reactions were supplemented to 1 mM final MgCl₂ concentration, heated to 50° C. for 5 min and then cooled to room temperature. Final
• RNA guide products were stored at −80° C.

• TABLE 16
  Sequences for generation of guide RNA

  	Primer
  	Sequence
  	(SEQ
  Primer	ID NO)	(SEQ ID NO)	RNA product
  T7 promoter primer	3550	NA	Used for all
  sg2 backbone fwd	3551	3563	GGUACUGGCGCUUUUAUCUCAUUACUUUGAG
  sg2 backbone rev	3552		AGCCAUCACCAGCGACUAUGUCGUAUGGGUA
  sg2.7.37 spacer	3553		AAGCGCUUAUUUAUCGGAGAGAAAUCCGAUA
  primer			AAUAAGAAGCAUCAAAGGGCCGAGAUGUCUC
  			GCUCCG
  sg32 backbone fwd	3554	3564	GGUACUGGCGCUUUUAUCUCAUUACUUUGAG
  sg32 backbone rev	3555		AGCCAUCACCAGCGACUAUGUCGUAUGGGUA
  sg32.7.37 spacer	3556		AAGCGCCCUCUUCGGAGGGAAGCAUCAAAGG
  primer			GCCGAGAUGUCUCG
  sg64 backbone fwd	3557	3565	GGUACUGGCGCCUUUAUCUCAUUACUUUGAG
  sg64 backbone rev	3558		AGCCAUCACCAGCGACUAUGUCGUAUGGGUA
  sg64.7.37 spacer	3559		AAGCGCUUACGGACUUCGGUCCGUAAGAAGC
  primer			AUCAAAGGGCCGAGAUGUCUCGCUCCG
  sg174 backbone fwd	3560	3566	ACUGGCGCUUUUAUCGgAUUACUUUGAGAGC
  sg174 backbone rev	3561		CAUCACCAGCGACUAUGUCGUAgUGGGUAAA
  sg174.7.37 spacer	3562		GCUCCCUCCUCGGAGGGAGCAUCAAAGGGCC
  primer			GAGAUGUCUCGCUCCG

Example 23 Editing of Gene Targets PCSK9, PMP22, TRAC, SOD1 B2M and HTT
• The purpose of this study was to evaluate the ability of the CasX variant 119 and gNA variant 174 to edit nucleic acid sequences in six gene targets.
Materials and Methods
• Spacers for all targets except B2M and SOD1 were designed in an unbiased manner based on PAM requirements (TTC or CTC) to target a desired locus of interest. Spacers targeting B2M and SOD1 had been previously identified within targeted exons via lentiviral spacer screens carried out for these genes. Designed spacers for the other targets were ordered from integrated DNA Technologies (IDT) as single-stranded DNA (ssDNA) oligo pairs. ssDNA spacer pairs were annealed together and cloned via Golden Gate cloning into a base mammalian-expression plasmid construct that contains the following components: codon optimized Cas X 119 protein+NLS under an EF1A promoter, guide scaffold 174 under a U6 promoter, carbenicillin and puromycin resistance genes. Assembled products were transformed into chemically-competent E. coli, plated on Lb-Agar plates (LB: Teknova Cat #L9315, Agar: Quartzy Cat #214510) containing carbenicillin and incubated at 37° C. Individual colonies were picked and miniprepped using Qiagen Qiaprep spin Miniprep Kit (Qiagen Cat #27104) following the manufacturer's protocol. The resulting plasmids were sequenced through the guide scaffold region via Sanger sequencing (Quintara Biosciences) to ensure correct ligation.
• HEK 293T cells were grown in Dulbecco's Modified Eagle Medium (DMEM; Corning Cellgro, #10-013-CV) supplemented with 10% fetal bovine serum (FBS; Seradigm, #1500-500), 100 Units/ml penicillin and 100 mg/ml streptomycin (100x-Pen-Strep; GIBCO #15140-122), sodium pyruvate (100×, Thermofisher #11360070), non-essential amino acids (100× Thermofisher #11140050), HEPES buffer (100× Thermofisher #15630080), and 2-mercaptoethanol (1000× Thermofisher #21985023). Cells were passed every 3-5 days using TryplE and maintained in an incubator at 37° C. and 5% CO2.
• On day 0, HEK293T cells were seeded in 96-well, flat-bottom plates at 30 k cells/well. On day 1, cells were transfected with 100 ng plasmid DNA using Lipofectamine 3000 according to the manufacturer's protocol. On day 2, cells were switched to FB medium containing puromycin. On day 3, this media was replaced with fresh FB medium containing puromycin. The protocol after this point diverged depending on the gene of interest. Day 4 for PCSK9, PMP22, and TRAC: cells were verified to have completed selection and switched to FB medium without puromycin. Day 4 for B2M, SOD1, and HTT: cells were verified to have completed selection and passed 1:3 using TryplE into new plates containing FB medium without puromycin. Day 7 for PCSK9, PMP22, and TRAC: cells were lifted from the plate, washed in dPBS, counted, and resuspended in Quick Extract (Lucigen, QE09050) at 10,000 cells/μl. Genomic DNA was extracted according to the manufacturer's protocol and stored at −20° C. Day 7 for B2M, SOD1, and HTT: cells were lifted from the plate, washed in dPBS, and genomic DNA was extracted with the Quick-DNA Miniprep Plus Kit (Zymo, D4068) according to the manufacturer's protocol and stored at −20° C.
• NGS Analysis: Editing in cells from each experimental sample was assayed using next generation sequencing (NGS) analysis. All PCRs were carried out using the KAPA HiFi HotStart ReadyMix PCR Kit (KR0370). The template for genomic DNA sample PCR was 5 μl of genomic DNA in QE at 10 k cells/μL for PCSK9, PMP22, and TRAC. The template for genomic DNA sample PCR was 400 ng of genomic DNA in water for B2M, SOD1, and HTT. Primers were designed specific to the target genomic location of interest to form a target amplicon. These primers contain additional sequence at the 5′ ends to introduce Illumina read and 2 sequences. Further, they contain a 7 nt randomer sequence that functions as a unique molecular identifier (UMI). Quality and quantification of the amplicon was assessed using a Fragment Analyzer DNA analyzer kit (Agilent, dsDNA 35-1500 bp). Aniplicons were sequenced on the Illutnina Miseq according to the manufacturer's instructions. Resultant sequencing reads were aligned to a reference sequence and analyzed for indels. Samples with editing that did not align to the estimated cut location or with unexpected alleles in the spacer region were discarded.
Results
• In order to validate the editing effected by the CasX:gNA 119.174 at a variety of genetic loci, a clonal plasmid transfection experiment was performed in HEK 293T Multiple spacers (Table 17) were designed and cloned into an expression plasmid encoding the CasX 119 nuclease and guide 174 scaffold. HEK 293T cells were transfected with plasmid DNA, selected with puromycin, and harvested for genomic DNA six days post-transfection. Genomic DNA was analyzed via next generation sequencing (NGS) and aligned to a reference DNA sequence for analysis of insertions or deletions (indels). CasX:gNA 119.174 was able to efficiently generate indels across the 6 target genes, as shown in FIGS. 47 and 48. Indel rates varied between spacers, but median editing rates were consistently at 60% or higher, and in some cases, indel rates as high as 91% were observed. Additionally, spacers with non-canonical CTC PAMs were demonstrated to be able to generate indels with all tested target genes (FIG. 49).
• The results demonstrate that the CasX variant 119 and gNA variant 174 can consistently and efficiently generate indels at a wide variety of genetic loci in human cells. The unbiased selection of many of the spacers used in the assays shows the overall effectiveness of the 119.174 RNP molecules to edit genetic loci, while the ability to target to spacers with both a. TTC and a CTC PAM demonstrates its increased versatility compared to reference CasX that edit only with the TTC PAM.

• TABLE 17
  Spacer sequences targeting each genetic locus.

  Gene	Spacer	PAM	Spacer Sequence	SEQ ID NO:
  PCSK9	6.1	TTC	GAGGAGGACGGCCTGGCCGA	3570
  PCSK9	6.2	TTC	ACCGCTGCGCCAAGGTGCGG	3571
  PCSK9	6.4	TTC	GCCAGGCCGTCCTCCTCGGA	3572
  PCSK9	6.5	TTC	GTGCTCGGGTGCTTCGGCCA	3573
  PCSK9	6.3	TTC	ATGGCCTTCTTCCTGGCTTC	3574
  PCSK9	6.6	TTC	GCACCACCACGTAGGTGCCA	3575
  PCSK9	6.7	TTC	TCCTGGCTTCCTGGTGAAGA	3576
  PCSK9	6.8	TTC	TGGCTTCCTGGTGAAGATGA	3577
  PCSK9	6.9	TTC	CCAGGAAGCCAGGAAGAAGG	3578
  PCSK9	6.10	TTC	TCCTTGCATGGGGCCAGGAT	3579
  PMP22	18.16	TTC	GGCGGCAAGTTCTGCTCAGC	3580
  PMP22	18.17	TTC	TCTCCACGATCGTCAGCGTG	3581
  PMP22	18.18	CTC	ACGATCGTCAGCGTGAGTGC	3582
  PMP22	18.1	TTC	CTCTAGCAATGGATCGTGGG	3583
  TRAC	15.3	TTC	CAAACAAATGTGTCACAAAG	3584
  TRAC	15.4	TTC	GATGTGTATATCACAGACAA	3585
  TRAC	15.5	TTC	GGAATAATGCTGTTGTTGAA	3586
  TRAC	15.9	TTC	AAATCCAGTGACAAGTCTGT	3587
  TRAC	15.10	TTC	AGGCCACAGCAGTGTTGCTC	3588
  TRAC	15.21	TTC	AGAAGACACCTTCTTCCCCA	3589
  TRAC	15.22	TTC	TCCCCAGCCCAGGTAAGGGC	3590
  TRAC	15.23	TTC	CCAGCCCAGGTAAGGGCAGC	3591
  HTT	5.1	TTC	AGTCCCTCAAGTCCTTCCAG	3592
  HTT	5.2	TTC	AGCAGCAGCAGCAGCAGCAG	3593
  HTT	5.3	TTC	TCAGCCGCCGCCGCAGGCAC	3594
  HTT	5.4	TTC	AGGGTCGCCATGGCGGTCTC	3595
  HTT	5.5	TTC	TCAGCTTTTCCAGGGTCGCC	3596
  HTT	5.7	CTC	GCCGCAGCCGCCCCCGCCGC	3597
  HTT	5.8	CTC	GCCACAGCCGGGCCGGGTGG	3598
  HTT	5.9	CTC	TCAGCCACAGCCGGGCCGGG	3599
  HTT	5.10	CTC	CGGTCGGTGCAGCGGCTCCT	3600
  SOD1	8.56	TTC	CCACACCTTCACTGGTCCAT	3601
  SOD1	8.57	TTC	TAAAGGAAAGTAATGGACCA	3602
  SOD1	8.58	TTC	CTGGTCCATTACTTTCCTTT	3603
  SOD1	8.2	TTC	ATGTTCATGAGTTTGGAGAT	239
  SOD1	8.68	TTC	TGAGTTTGGAGATAATACAG	3604
  SOD1	8.59	TTC	ATAGACACATCGGCCACACC	3605
  SOD1	8.47	TTC	TTATTAGGCATGTTGGAGAC	3606
  SOD1	8.62	CTC	CAGGAGACCATTGCATCATT	3607
  B2M	7.120	TTC	GGCCTGGAGGCTATCCAGCG	3608
  B2M	7.37	TTC	GGCCGAGATGTCTCGCTCCG	3609
  B2M	7.43	CTC	AGGCCAGAAAGAGAGAGTAG	3610
  B2M	7.119	CTC	CGCTGGATAGCCTCCAGGCC	3611
  B2M	7.14	TTC	TGAAGCTGACAGCATTCGGG	3612

Example 24 Design and Evaluation of Improved CasX Variants by Deep Mutational Evolution
• The purpose of the experiments was to identify and engineer novel CasX protein variants with enhanced genome editing efficiency relative to wild-type CasX. To cleave DNA efficiently in living cells, the CasX protein must efficiently perform the following functions: i) form and stabilize the R-loop structure consisting of a targeting guide RNA annealed to a complementary genomic target site in a DNA:RNA hybrid; and ii) position an active nuclease domain to cleave both strands of the DNA at the target sequence. These two functions can each be enhanced by altering the biochemical or structural properties of the protein, specifically by introducing amino acid mutations or exchanging protein domains in an additive or combinatorial fashion.
• To construct CasX protein variants with improved properties, an overall approach was chosen in which bacterial assays and hypothesis-driven approaches were first used to identify candidate mutations to enhance particular functions, after which increasingly stringent human genome editing assays were used in a stepwise manner to rationally combine cooperatively function-enhancing mutations in order to identify CasX variants with enhanced editing properties.
Materials and Methods: Cloning and Media
• Restriction enzymes, PCR reagents, and cloning strains of E. coli were obtained from New England Biolabs. All molecular biology and cloning procedures were performed according to the manufacturer's instructions. PCR was performed using Q5 polymerase unless otherwise specified. All bacterial culture growth was performed in 2XYT media (Teknova) unless otherwise specified. Standard plasmid cloning was performed in Turbo® E. coli unless otherwise specified. Standard final concentrations of the following antibiotics were used where indicated: carbenicillin: 100 μg/mL; kanamycin: 60 μg/mL; chloramphenicol: 25 μg/mL.
Molecular Biology of Protein Library Construction
• Four libraries of CasX protein variants were constructed using plasmid recoinbineering in E. coli strain EcNR2 (Addgene ID: 26931), and the overall approach to protein mutagenesis was termed Deep Mutational Evolution (DME), which is schematically shown in FIG. 50. Three libraries were constructed corresponding to each of three cleavage-inactivating mutations made to the reference CasX protein open reading frame of Planctomycetes, SEQ ID NO:2 (“STX2”), rendering the CasX catalytically dead (dCasX). These three mutations are referred to as D1 (with a D659A substitution), D2 (with an E756A substitution), or D3 (with a D922A substitution). A fourth library was composed of all three mutations in combination, referred to as DDD (D659A; E756A; D922A substitutions). These libraries were constructed by introducing desired mutations to each of the four starting plasmids. Briefly, an oligonucleotide library was obtained from Twist Biosciences and prepared for recombineering (see below). A final volume of 50 μL of 1 μM oligonucleotides, plus 10 ng of pSTX1 encoding the dCasX open reading frame (composed of either D1, D2, or D3) was electroporated into 50 μL of induced, washed, and concentrated EcNR2 using a 1 mm electroporation cuvette (BioRad GenePulser). A Harvard Apparatus ECM 630 Electroporation System was used with settings 1800 kV, 200 Ω, 25 μF. Three replicate electroporations were performed, then individually allowed to recover at 30° C. for 2 hr in 1 mL of SOC (Teknova) without antibiotic. These recovered cultures were titered on LB plates with kanamycin to determine the library size. 2XYT media and kanamycin was then added to a final volume of 6 mL and grown for a further 16 hours at 30° C. Cultures were miniprepped (QIAprep Spin Miniprep Kit) and the three replicates were then combined, completing a round of plasmid recombineering. A second round of recombineering was then performed, using the resulting miniprepped plasmid from round 1 as the input plasmid.
• Oligo library synthesis and maturation: A total of 57751 unique oligonucleotide sequences designed to result in either amino acid insertion, substitution, or deletion at each codon position along the STX 2 open reading frame were synthesized by Twist Biosciences, among which were included so-called ‘recombineering oligos’ that included one codon to represent each of the twenty standard amino acids and codons with flanking homology when encoded in the plasmid pSTX1. The oligo library included flanking 5′ and 3′ constant regions used for PCR amplification. Compatible PCR primers include oSH7:

• 	(universal forward; SEQ ID NO: 3613)
  	5′AACACGTCCGTCCTAGAACT
  	and
  	oSH8:
  	(universal reverse; SEQ ID NO: 3614)
  	5′ACTTGGTTACGCTCAACACT (see reference table).

  
  The entire oligo pool was amplified as 400 individual 100 μL reactions. The protocol was optimized to produce a clean band at 164 bp. Finally, amplified oligos were digested with a restriction enzyme (to remove primer annealing sites, which would otherwise form scars during recombineering), and then cleaned, for example, with a PCR clean-up kit (to remove excess salts that may interfere with the electroporation step). Here, a 600 μL final volume BsaI restriction digest was performed, with 30 μg DNA+30 μL BsaI enzyme, which was digested for two hours at 37° C.
• For DME1: after two rounds of recombineering were completed, plasmid libraries were cloned into a bacterial expression plasmid, pSTX2. This was accomplished using a BsmbI Golden Gate Cloning approach to subclone the library of STX genes into an expression compatible context, resulting in plasmid pSTX3. Libraries were transformed into Turbo® E. coli (New England Biolabs) and grown in chloramphenicol for 16 hours at 37° C., followed by miniprep the next day.
• For DME2: protein libraries from DME1 were further cloned to generate a new set of three libraries for further screening and analysis. All subcloning and PCR was accomplished within the context of plasmid pSTX1. Library D1 was discontinued and libraries D2 and D3 were kept the same. A new library, DDD, was germerated from libraries D2 and D3 as follows. First, libraries D2 and D3 were PCR amplified such that the Dead 1 mutation. E756A, was added to all plasmids in each library, followed by blunt ligation, transformation, and miniprep, resulting in library A (D1+D2) and library B (D1+D3). Next, another round of PCR was performed to add either mutation D3 or D2, respectively, to library A and B, generating PCR products A′ and B′. At this point, A′ and B′ were combined in equimolar amounts, then blunt ligated, transformed, and miniprepped to generate a new library, DDD, containing all three dead mutations in each plasmid.
Bacterial CRISPR Interference (CRISPRi) Screen
• A dual-color fluorescence reporter screen was implemented, using monomeric Red Fluorescent Protein (mRFP) and Superfolder Green Fluorescent Protein (stUFP), based on Qi L S, et cal. Cell 152:1173-1183 (2013). This screen was utilized to assay gene-specific transcriptional repression mediated by programmable DNA binding of the CasX system. This strain of E coli expresses bright green and red fluorescence under standard culturing conditions or when grown as colonies on agar plates. Under a CRISPRi system, the CasX protein is expressed from an anhydrotetracycline (aTc)-inducible promoter on a plasmid containing a p15A replication origin (plasmid pSTX3; chloramphenicol resistant), and the sgRNA is expressed from a minimal constitutive promoter on a plasmid containing a CoIE1 replication origin (pSTX4, non-targeting spacer, or pSTX5, GFP-targeting spacer #1; carbenicillin resistant). When the CRISPRi coli strain is co-transformed with both plasmids, genes targeted by the spacer in pSTX4 are repressed; in this case GFP repression is observed, the degree to which is dependent on the function of the targeting CasX protein and sgRNA. In this system, RFP fluorescence can serve as a normalizing control. Specifically, RFP fluorescence is unaltered and independent of functional CasX based CRISPRi activity. CRISPRi activity can be tuned in this system by regulating the expression of the CasX protein; here, all assays used an induction concentration of 20 nM aTc final concentration in growth media.
• Libraries of CasX protein were initially screened using the above CRISPRi system After co-transformation and recovery, libraries were either: 1) plated on LB agar plus appropriate antibiotics and titered such that individual colonies could be picked, or 2) grown for eight hours in 2XYT media with appropriate antibiotics and sorted on a MA900 flow cytometry instrument (Sony). Variants of interest were detected using either standard Sanger sequencing of picked colonies (UC Berkeley Barker Sequencing Facility) or NGS sequencing of miniprepped plasmid (Massachusetts General Hospital COB DNA Core Next-Generation Sequencing Service).
• Plasmids were miniprepped and the protein sequence was PCR-amplified, then tagmented using a Nextera kit (Illumina) to fragment the amplicon and introduce indexing adapters for sequencing on a 150 paired end HiSeq 2500 (VC Berkeley Genomics Sequencing Lab).
• Bacterial ccdB Plasmid Clearance Selection
• A dual-plasmid selection system was used to assay clearance of a toxic plasmid by CasX DNA cleavage. Briefly, the arabinose-inducible plasmid pRLO63.3 expressing toxic protein ccdB results in death when transformed into E. coli strain BW25113 and grown under permissive conditions. However, growth is rescued if the plasmid is cleared successfully by dsDNA cleavage, and in particular by plasmid pSTX3 co-expressing CasX protein and a guide RNA targeting the plasmid pBLO63.3. CasX protein libraries from DME1, without the catalytically inactivating mutations D1, D2, or D3, were subcloned into plasmid pSTX3. These plasmid libraries were transformed into BW25113 carrying pBLO63.3 by electroporation (200 ng of plasmid into 50 uL of electrocompetent cells) and allowed to recover in 2 m l of SOC media at 37° C. at 200 rpm shaking for 25 minutes, after which 1 uL of 1 M IPTG was added. Growth was continued for an additional 40 minutes, after which cultures were evenly divided across a 96-well deep-well block and grown in selective media for 4.5 hrs at 37° C. or 45° C. at 750 rpm. Selective media consists of the following: 2XYT with chloramphenicol+10 mM arabinose+500 μM IPTG+2 nM arc (concentrations final). Following growth, plasmids were miniprepped to complete one round of selection, and the resulting DNA was used as input for a subsequent round. Seven rounds of selection were performed on CasX protein libraries. CasX variant Sanger sequencing or NGS was performed as described above.
NGS Data Analysis
• Paired end reads were trimmed for adapter sequences with cutadapt (version 2.1), and aligned to the reference with bowtie2 (v2.3.4.3). The reference was the entire amplicon sequence prior to tagmentation in the Nextera protocol. Each catalytically inactive CasX variant was aligned to its respective amplicon sequence. Sequencing reads were assessed for amino acid variation from the reference sequence. In short, the read sequence and aligned reference sequence were translated (in frame), then realigned and amino acid variants were called. Reads with poor alignment or high error rates were discarded mapq <20 and estimated error rate 4%; Estimated error rate was calculated using per-base phred quality scores))). Mutations at locations of poor-quality sequencing were discarded (phred score <20). Mutations were labeled for being single substitutions, insertions, or deletions, or other higher-order imitations, or outside the protein-coding sequence of the amplicon. The number of reads that supported each set of mutations was determined. These read counts were normalized for sequencing depth (mean normalization), and read counts from technical replicates were averaged by taking the geometric mean. Enrichment was calculated within each CasX variant by averaging the enrichment for each gate.
Molecular Biology of Variants
• In order to screen variants of interest, individual variants were constructed using standard molecular biology techniques. All mutations were built on STX2 using a staging vector and Gibson cloning. To build single mutations, universal forward (5′→3′) and reverse (3′→5′) primers were designed on either end of the protein sequence that had homology to the desired backbone for screening (sec Table 18). Primers to create the desired mutations were also designed (F primer and its reverse complement) and used with the universal F and R primers for amplification, thus producing two fragments. In order to add multiple mutations, additional primers with overlap were designed and more PCR fragments were produced. For example, to construct a triple mutant, four sets of F/R primers were designed. The resulting PCR fragments were gel extracted and the screening vector was digested with the appropriate restriction enzymes then gel extracted. The insert fragments and vector were then assembled using Gibson assembly master mix, transformed, and plated using appropriate LB agar+antibiotic. The clones were Sanger sequenced and correct clones were chosen.
• Finally, spacer cloning was performed to target the guide RNA to a gene of interest in the appropriate assay or screen. The sequence verified non-targeting clone was digested with the appropriate golden gate enzyme and cleaned using DNA Clean and Concentrator kit (Zymo). The oligos for the spacer of interest were annealed. The annealed spacer was ligated into digested and cleaned vector using a standard Golden Gate Cloning protocol. The reaction was transformed and plated on LB agar+antibiotic. The clones were singer sequenced and correct clones were chosen.

• TABLE 18
  Primer sequences

  Screening vector	F primer sequence	R primer sequence
  pSTX6	SAH24:	SAH25:
  	TTCAGGTTGGACCGGTGCCACCATGGCCCC	TTTTGGACTAGTCACGGCGOGC
  	AAAGAAGAAGCGGAAGGTCAGCCAAGAG	TTCCAG (SEQ ID NO: 3616)
  	ATCAAGAGAATCAACAAGATCAGA (SEQ
  	ID NO: 3615)
  pSTX16 or	oIC539:	oIC540:
  pSTX34	ATGGCCCCAAAGAAGAAGCGGAAGGTCTC	TACCTTTCTCTTCTTTTTTGGAC
  	TAGACAAG (SEQ ID NO: 3617)	TAGTCACGG (SEQ ID NO: 3618)

GFP Editing by Plasmid Lipofection of HEK293T Cells
• Either doxycycline inducible GFP (iGFP) reporter HEK293T cells or SOD1-GFP reporter HEK293T cells were seeded at 20-40 k cells/well in a 96 well plate in 100 μl of FB medium and cultured in a 37° C. incubator with 5% CO2. The following day, confluence of seeded cells was checked. Cells were ˜75% confluent at time of transfection. Each CasX construct was transfected at 100-500 ng per well using Lipofectamine 3000 following the manufacturer's protocol, into 3 wells per construct as replicates. SaCas9 and SpyCas9 targeting the appropriate gene were used as benchmarking controls. For each Cas protein type, a non-targeting plasmid was used as a negative control, After 24-48 hours of puromycin selection at 0.3-3 μg/ml to select for successfully transfected cells, followed by 1-7 days of recovery in FB medium, GFP fluorescence in transfected cells was analyzed via flow cytometry. In this process, cells were gated for the appropriate forward and side scatter, selected for single cells and then gated for reporter expression (Attune Nxt Flow Cytometer, Thermo Fisher Scientific) to quantify the expression levels of fluorophores. At least 10,000 events were collected for each sample. The data were then used to calculate the percentage of edited cells.
GFP Editing by Lentivirus Transduction of HEK293T Cells
• Lentivirus products of plasmids encoding CasX proteins, including controls, CasX variants, and/or CasX libraries, were generated in a Lenti-X 293T Cell Line (Takara) following standard molecular biology and tissue culture techniques. Either iGFP HEK293T cells or SOD1-GFP reporter HEK293T cells were transduced using lenti virus based on standard tissue culture techniques. Selection and fluorescence analysis was performed as described above, except the recovery time post-selection was 5-21 days. For Fluorescence-Activated Cell Sorting (FACS), cells were gated as described above on a MA900 instrument (Sony). Genomic DNA was extracted by QuickExtract™ DNA Extraction Solution (Lucigen) or Genomic DNA Clean & Concentrator (Zymo).
Engineering of CasX Protein 2 to CasX 119
• Prior work had demonstrated that CasX RNP complexes composed of functional wild-type CasX protein from Planctomycetes (hereafter referred to as CasX protein 2 {or STX2, or STX protein 2, SEQ ID NO: 2} and CasX sgRNA 1 {or STX sgRNA 1, SEQ ID NO: 4}) are capable of inducing dsDNA cleavage and gene editing of mammalian genomes (Liu, J J et al Nature, 566, 218-223 (2019)). However, previous observations of cleavage efficiency were relatively low (˜30% or less), even under optimal laboratory conditions. These poor rates of genome editing may be insufficient for the wild-type CasX CRISPR systems to serve as therapeutic genome-editing molecules. in order to efficiently perform genome editing, the CasX protein must effectively perform two central functions: (i) form and stabilize the R-loop, and (ii) position the nuclease domain for cleavage of both DNA strands. Under conditions in which CasX RNP can access genomic DNA, genome editing rates will he partly governed by the ability of the CasX protein to perform these functions (the other controlling component being the guide RNA). The optimization of both functions is dependent on the complex sequence-function relationship between the linear chain of amino acids encoding the CasX protein and the biochemical properties of the fully formed, cleavage competent RNP. As amino acid mutations that enhance each of these functions can be combined to cumulatively result in a highly engineered CasX protein exhibiting greatly enhanced genome editing efficiency sufficient for human therapeutics, an overall engineering approach was devised in which mutations enhancing function (i) were identified, mutations enhancing function (ii) were identified, and then rational stacking (or combination) of multiple beneficial mutations would be used to construct CasX variants capable of efficient genome editing. Function (i), stabilization of the R-loop, is by itself sufficient to interfere with gene expression in living cells even in the absence of DNA nuclease activity, a phenomenon known as CRISPR interference (CRISPRi). It was determined that a bacterial CRISPRi assay would be well-suited to identifying mutations enhancing this function. Similarly, a bacterial assay testing for double-stranded DNA (dsDNA) cleavage would be capable of identifying mutations enhancing function (ii). A toxic plasmid clearance assay was chosen to serve as a bacterial selection strategy and identify relevant amino acid changes. These sets of mutations were then validated to provide an enhancement to human genome editing activity, and served as the foundation for more extensive and rational combinatorial testing across increasingly stringent assays.
• The identification of mutations enhancing core functions was performed in an engineering cycle of protein library design, molecular biology construction of libraries, and high-throughput assay of the libraries. Potential improved variants of the STX2 protein were either identified by NGS of a high-throughput biological assay, sequenced directly as clones from a population, or designed de novo for specific hypothesis testing. For high-throughput assays of functions (i) or (ii), a comprehensive and unbiased design approach to mutagenesis was used for initial diversification. Plasmid recombineering was chosen as a sufficiently comprehensive and rapid method for library construction and was performed in a promoterless staging vector pSTX1 in order to minimize library bias throughout the cloning process. A comprehensive oligonucleotide pool encoded all possible single amino acid substitutions, insertions, and deletions in the STX2 sequence was constructed by DME, the first round of library construction and screening is hereafter referred to as DME (FIG. 50).Two high-throughput bacterial assays were chosen to identify potential improved variants from the diverse set of mutations in DME1. As discussed above, we reasoned that a CRISPRi bacterial screen would identify mutations enhancing function (i). While CRISPRi uses a catalytically inactive form of the CasX protein, many specific characteristics together influence the total enhancement of this fim.ction, such as expression efficiency, folding rate, protein stability, or stability of the R-loop (including binding affinity to the sgRNA or DNA). DME1 libraries were constructed on the dCasX mutant templates and individually screened. Screening was performed as Fluorescence-Activated Cell Sorting (FACS) of GFP repression in a previously validated dual-color CRISPRi scheme.
Results:
• For each of the DME1, DME2 and DME3 libraries, the three libraries exhibited a different baseline CRISPRi activity, thereby serving as independent, yet related, screens. For each library, gates of varying stringency were drawn around the population of interest, and sorted cell populations were deep sequenced to identify CasX mutations enhancing GFP repression (FIG. 51). A second high-throughput bacterial assay was developed to assess dsDNA cleavage in E. coli by way of selection (see methods). When this assay is performed under selective conditions, a functional STX2 RNP can exhibit ˜1000- to 10,000-fold increase in colony forming units compared to nonfunctional CasX protein (FIG. 52). Multiple rounds of liquid media selections were performed for the cleavage-competent libraries of DME Sequential rounds of colony picking and sequencing identified mutations to enhance function (ii). Several mutations were observed with increasing frequency with prolonged selection. One mutation of note, the deletion of proline 793, was first observed in round four at a frequency of two out of 36 sequenced colonies. After round five, the frequency increased to six out of 36 sequenced colonies. In round seven, it was observed in ten out of 48 sequenced colonies. This round-over-round enrichment suggested mutations observed in these assays could potentially enhance function (ii) of the CasX protein. Selected mutations observed across these assays can be found in table 19 as follows:

• TABLE 19
  Selected mutations observed in bacterial
  assays or function (i) or (ii)

  Pos.	Ref.	Alt.*	Assay

  2	Q	R	45 C ccdb colony
  72	T	S	D2 CRISPRi
  80	A	T	37 C ccdb colony
  111	R	K	45 C ccdb colony
  119	G	C	45 C ccdb colony
  121	E	D	37 C ccdb colony
  153	T	I	37 C ccdb colony
  166	R	S	D2 CRISPRi
  203	R	K	45 C ccdb colony
  270	S	W	37 C ccdb colony
  346	D	Y	45 C ccdb colony
  361	D	A	D1 CRISPRi
  385	E	A	D3 CRISPRi
  386	E	R	45 C ccdb colony
  390	K	R	D3 CRISPRi
  399	F	L	45 C ccdb colony
  421	A	G	D2 CRISPRi
  433	S	N	45 C ccdb colony
  489	D	S	D3 CRISPRi
  536	F	S	D3 CRISPRi
  546	I	V	D2 CRISPRi
  552	E	A	D3 CRISPRi
  591	R	I	37 C ccdb colony
  595	E	G	D3 CRISPRi
  636	A	D	D3 CRISPRi
  657	—	G	D1 CRISPRi
  661	—	L	D1 CRISPRi
  661	—	A	D1 CRISPRi
  663	N	S	D1 CRISPRi
  679	S	N	D2 CRISPRi
  695	G	H	45 C ccdb colony
  696	—	P	45 C ccdb colony
  707	A	D	D3 CRISPRi
  708	A	K	45 C ccdb colony
  712	D	Q	37 C ccdb colony
  732	D	P	D1 CRISPRi
  751	A	S	D3 CRISPRi
  774	—	G	D1 CRISPRi
  788	A	W	D2 CRISPRi
  789	Y	T	D1 CRISPRi
  789	Y	D	D2 CRISPRi
  791	G	M	45 C ccdb colony
  792	L	E	45 C ccdb colony
  793	P	—	45 C ccdb colony
  793	—	AS	45 C ccdb colony
  793	P	T	45 C ccdb colony
  793	P	—	D1 CRISPRi
  793	—	F	D2 CRISPRi
  794	—	PG	45 C ccdb colony
  794	—	PS	45 C ccdb colony
  795	—	AS	37 C ccdb colony
  795	—	AS	45 C ccdb colony
  796	—	AG	37 C ccdb colony
  797	—	AS	45 C ccdb colony
  797	Y	L	45 C ccdb colony
  799	S	A	D3 CRISPRi
  867	S	G	45 C ccdb colony
  889	—	L	37 C ccdb colony
  897	L	M	45 C ccdb colony
  922	D	K	D1 CRISPRi
  963	Q	P	D2 CRISPRi
  975	K	Q	D2 CRISPRi
  *substitution, insertion, or deletion, positions are indicated relative to SEQ ID NO: 2
  Pos.: Position; Ref.: Reference; Alt: Alternative

• The mutations observed in the bacterial assays above were selected for their potential to enhance CasX protein functions (i) or (ii), but desirable mutations will enhance at least one function while simultaneously remaining compatible with the other. To test this, mutations were tested for their ability to improve human cell genome editing activity overall, which requires both functions acting in concert. A HEK293T GFP editing assay was implemented in which human cells containing a stably-integrated inducible GFP (iGFP) gene were transduced with a plasmid that expresses the CasX protein and sgRNA 2 with spacers to target the RNP to the GFP gene. Mutations identified in bacterial screens, bacterial selections, as well as mutations chosen de novo from biochemical hypotheses resulting from inspection of the published Cryo-EM structure of the homologous DphCasX protein, were tested for their relative improvement to human genome editing activity as quantified relative to the parent protein STX 2 (FIG. 53), with the greatest improvement demonstrated for construct 119, shown at the bottom of FIG. 53. Several dozen of the proposed function-enhancing mutations were found to improve human cell genome editing susbstantially, and selected mutations from these assays can be found in Table 20 as follows:

• TABLE 20
  Selected single mutations observed to enhance genome editing

  			Fold-Improvement
  Position	Reference	Alternative*	(average of two GFP spacers)

  379	L	R	1.4
  708	A	K	2.13
  620	T	P	1.84
  385	E	P	1.19
  857	Y	R	1.95
  658	I	V	1.94
  399	F	L	1.64
  404	L	K	2.23
  793	P	—	1.23
  252	Q	K	1.12**
  *substitution, insertion, or deletion, positions relative to SEQ ID NO: 2
  **calculated as the average improvement across four variants with and without the mutation

• The overall engineering approach taken here relies on the central hypothesis that individual mutations enhancing each function can he additively combined to obtain greatly enhanced CasX variants with improved editing capability, which was supported by the findings as described below; CasX variant 119 (indicated by the star in FIG. 54) exhibited a 23.9-fold improvement relative to the wild-type CasX. To test this, the single mutations were first identified if they enhanced overall editing activity. Of particular note here, a substitution of the hydrophobic leucine 379 in the helical II domain to a positively charged arginine resulted in a 1.40 fold-improvement in editing activity. This mutation might provide favorable ionic interactions with the nearby phosphate backbone of the DNA target strand (between PAM-distal bp 22 and 23), thus stabilizing R-loop formation and thereby enhancing function (i). A second hydrophobic to charged mutation, alanine 708 to lysine, increased editing activity by 2.13-fold, and might provide additional ionic interactions between the RuvC domain and the sgRNA 5′ end, thus plausibly enhancing function (i) by increasing the binding affinity of the protein for the sgRNA and thereby increasing the rate of R-loop formation. The deletion of proline 793 improved editing activity by 1.23-fold by shortening a loop between an alpha helix and a beta sheet in the RuvC domain, potentially enhancing function (ii) by favorably altering nuclease positioning for dsDNA cleavage Overall, several dozen single mutations were found to improve editing activity, including mutations identified from each of the bacterial assays as well as mutations proposed from de novo hypothesis generation. To further identify those mutations that enhanced function in a cooperative manner, rational CasX variants composed of combinations of multiple mutations were tested (FIG. 53). An initial small combinatorial set was designed and assayed, of which CasX variant 119 emerged. as the overall most improved editing molecule, with a 2.8-fold improved editing efficiency compared to the STX2 wild-type protein. Variant 119 is composed of the three single mutations L379R, A708K, and [P793], demonstrating that their individual contributions to enhancement of function are additive.
SOD1-GFP Assay Development.
• To assess CasX variants with greatly improved genome-editing activity, we sought to develop a more stringent genome editing assay. The iGFP assay provides a relatively facile editing target such that STX protein 2 in the assays above exhibited an average editing efficiency of 41% and 16% with GFP targeting spacers 4.76 and 4.77 respectively. As protein variants approach 2-fold or greater efficiency improvements, the assay becomes saturated. Therefore a new HEK293T cell line was developed with the GFP sequence integrated in-frame at the C-terminus of the endogenous human gene SOD1, termed the SOD1-GFP line. This cell line served as a new, more stringent, assay to measure the editing efficiency of several hundred additional CasX protein variants (FIG. 54). Additional mutations were identified from bacterial assays, including a second iteration of DME library construction and screening, as well as utilizing hypothesis-driven approaches. Further exploration of combinatorial improved variants was also performed in the SOD1-GFP assay.
• In light of the SOD1-GFP assay results, measured efficiency improvements were no longer saturated, and Cask variant 119 (indicated by the star in FIG. 54) exhibited a 23.9-fold improvement relative to the wild-type CasX (average of two spacers), with several constructs exhibiting enhanced activity relative to the CasX 119 construct. Alternatively, the dynamic rane of the iGFP assay could be increased (though perhaps not completely unsaturated) by reducing the baseline activity of the WT CasX protein, namely by using sgRNA variant 1 rather than 2. Under these more stringent conditions of the iGFP assay, CasX variant 119 exhibited a 15.3-fold improvement relative to the wild-type CasX using the same spacers. Intriguingly, CasX variant 119 also exhibited substantial editing activity with spacers utilizing each of the four NTCN PAM sequences, while WT CasX only edited above 1% with spacers utilizing TTCN and ATCN PAM sequences (FIG. 55), demonstrating the ability of the CasX variant to effectively edit using an expanded spectrum of PAM sequences.
CasX Function Enhancement by Extensive Combinatorial Mutagenesis.
• Potential improved variants tested in the variety of assays above provided a dataset from which to select candidate lead proteins. Over 300 proteins were assessed in individual clonal assays and of these, 197 single mutations were assessed; the remaining ˜100 proteins contained combinatorial combinations of these mutations. Protein variants were assessed via three different assays (plasmid p6 by iGFP, plasmid p6 by SOD1-GFP, or plasmid p16 by SOD1-GFP). While single mutants led to significant improvements in the iGFP assay (with fraction GFP—greater than 50%), these single-mutants all performed poorly in the SOD1-GFP p6 backbone assay (fraction GFP—less than 10%). However, proteins containing multiple, stacked mutations were able to successfully inactivate GFP in this more stringent assay, indicating that stacking of improved mutations could substantially improve cleavage activity.
• Individual mutations observed to enhance function often varied in their capacity to additively improve editing activity when combined with additional mutations. To rationally quantify these epistatic effects and further improve genome editing activity, a subset of mutations was identified that had each been added to a protein variant containing at least one other mutation, and where both proteins (with and without the mutation) were tested in the same experimental context (assay and spacer; 46 mutations total). To determine the effect due to that mutation, the fraction of GFP-cells was compared with and without the mutation. For each protein/experimental context, the mutation effect was quantified as: 1) substantially improving the activity (f_v>1.1 fo where fo is the fraction GFP—without the mutation, and f_v is the fraction GFP—with the mutation), 2) substantially worsening the activity (f_v<0.9f₀), or 3) not affecting activity (neither of the other conditions are met). An overall score per mutation was calculated (s), based on the fraction of protein/experiment contexts in which the mutation substantially improved activity, minus the fraction of contexts in which the mutation substantially worsened activity. Out of the 46 mutations obtained, only 13 were associated with consistently increased activity (s≥0.5), and 18 mutations substantially decreased activity (S≤−0.5). Importantly, the distinction between these mutations was only clear when examining epistatic interactions across a variety of variant contexts: all of these mutations had comparable activity in the iGFP assay when measured alone.
• The above quantitative analysis allowed the systematic design of an additional set of highly engineered CasX proteins composed of single mutations enhancing function both individually and in combination, First, seven out of the top 13 mutations were chosen to be stacked (the other 6 variants comprised the three variants A708K, [P793] and L379R that were included in all proteins, and another two that affected redundant positions; see FIG. 14). These mutations were iteratively stacked onto three different versions of the CasX protein: CasX 119, 311, and 365; proceeding to add only one mutation (e.g., Y857R), to adding several mutations in combination. In order to maximize the combination of enhancements for both function (i) and function (ii), individual mutations were rationally chosen to maintain a diversity of biochemical properties multiple mutations that substitute a hydrophobic residue with a negatively charged residue were avoided. The resulting ˜30 protein variants had between five and 10 individual mutations relative to STX2 (mode=7 mutations). The proteins were tested in a lipofection assay in a new backbone context (p34) with guide scaffold 64, and most showed improvement relative to protein 119. The most improved variant of this set, protein 438, was measured to be >20% improved relative to protein 119 (see Table 21 below).
• Lentiviral Transduction iGFP Assay Development
• As discussed above regarding the iGFP assay, enhancements to the CasX system had likely resulted in the lipofection assay becoming saturated—that is, limited by the dynamic range of the measurement. To increase the dynamic range, a new assay was designed in which many fewer copies of the CasX gene are delivered to human cells, consisting of lentiviral trausductions in a new backbone context, plasmid pSTX34 (see FIG. 35). Under this more stringent delivery modality, the dynamic range was sufficient to observe the improvements of CasX protein variant 119 in the context of a further improved sgRNA, namely sgRNA variant 174. Improved variants of both the protein and sgRNA were found to additively combine to produce yet further improved CasX CRISPR systems. Protein variant 119 and sgRNA variant 174 were each measured to improve iGFP editing activity by approximately an order of magnitude when compared with wild-type CasX protein 2 (SEQ ID NO: 2) in complex with sgRNA 1 (SEQ ID NO: 4) under the lipofection iGFP assay (FIG. 56). Moreover, improvements to editing activity from the protein and sgRNA appear to stack nearly linearly; while individually substituting CasX 2 for CasX 119, or substituting sgRNA 174 for sgRNA 1, produces a ten-fold improvement, substituting both simultaneously produces at least another ten-fold improvement (FIG. 57). Notably, this range of activity improvements exceeds the dynamic range of either assay. However, the overall activity improvement can be estimated by calculating the fold change relative to the sample 2.174, which was measured precisely in both assays. The enhancement of the highly engineered CasX CRISPR system 119.174 over wild type CasX CRISPR system 2.1 resulted in a 259-fold improvement in genome editing efficiency in human cells (+/−58, propagated standard deviation, as shown in FIG. 57), supporting that, under the conditions of the assay, the engineering of both the CasX and the guide led to dramatic improvements in editing efficiency compared to wild-type CasX and guide.
Engineering of Domain Exchange Variants
• One problematic limitation of mutagenesis-based directed evolution is the combinatorial increase of the numbers of possible sequences that result as one takes larger steps in sequence-space. To overcome this, the swapping of protein domains from homologous sequences of different CasX proteins was evaluated as an alternative approach. To take advantage of the phylogenetic data available for the CasX CRISPR system, alignments were made between the CasX 1 (SEQ ID NO:) and CasX 2 (SEQ ID NO: 2) protein sequences, and domains were annotated for exchange in the context of improved CasX protein variant 119. To benchmark CasX 119 against the top designed combinatorial CasX protein variants and the top domain exchanged variants, all within the context of improved sgRNA 174, a stringent iGFP lentiviral transduction assay was performed. Protein variants from each class were identified as improved relative to CasX variant 119 (FIG. 58), and fold changes are represented in Table 21. For example, at day 13, CasX 119.174 with GFP spacer 4.76 leads to phenotype disruption in only ˜60% of cells, while CasX variant 491 in the same context results in >90% phenotypic editing. To summarize, the compared proteins contained the following number of mutations relative to the WI CasX protein 2: 119=3 point mutations; 438=7 point mutations; 488=protein 119, with NTSB and helical Ib domains from CasX 1 (67 mutations total); 491=5 point mutations, with NTSB and helical Ib domains from CasX 1 (69 mutations total).

• TABLE 21
  CasX variant improvements over CasX variant 119 in the iGFP lentiviral
  transduction assay, in the context of improved sgRNA 174.

  	Fold-change	Fold-change
  Cas X	editing activity,	editing activity,
  Protein	spacer 4.76*	spacer 4.77*
  119	1.00	1.00
  438	1.22	1.21
  488	1.41	2.43
  491	1.55	3.03
  *relative to CasX 119

• The results demonstrate that the application of rationally-designed libraries, screening, and analysis methods into a technique we have termed Deep Mutational Evolution to scan fitness landscapes of both the CasX protein and guide RNA enabled the identification and validation of mutations which enhanced specific functions, contributing to the improvement of overall genome editing activity. These datasets enabled the rational combinatorial design of further improved CasX and guide variants disclosed herein.
Example 25 Design and Evaluation of Improved Guide RNA Variants
• The existing CasX platform based on wild-type sequences for dsDNA editing in human cells achieves very low efficiency editing outcomes when compared with alternative CRISPR systems (Liu, J J et al Nature, 566, 218-223 (2019)). Cleavage efficiency of genomic DNA is governed, in large part, by the biochemical characteristics of the CasX system, which in turn arise from the sequence-function relationship of each of the two components of a cleavage-competent CasX RNP: a CasX protein complexed with a sgRNA. The purpose of the following experiments was to create and identify gRNA scaffold variants with enhanced editing properties relative to wild-type CasX:gNA RNP through a program of comprehensive mutagenesis and rational approaches.
Methods
• Methods for High-Throughput sgRNA Library Screens
  1) Molecular Biology of sgRNA Library Construction
• To build a library of sgRNA variants, primers were designed to systematically mutate each position encoding the reference gRNA scaffold of SEQ ID NO: 5, where mutations could he substitutions, insertions, or deletions. In the following in vivo bacterial screens for sgRNA mutations, the sgRNA (or mutants thereof) was expressed from a minimal constitutive promoter on the plasmid pSTX4. This minimal plasmid contains a ColE1 replication origin and carbenicillin antibiotic resistance cassette, and is 2311 base pairs in length, allowing standard Around-the-Hom PCR and blunt ligation cloning (using conventional methodologies). Forward primers KST223-331 and reverse primers KST332-440 tile across the sgRNA sequence in one base-pair increments and were used to amplify the vector in two sequential PCR steps. In step 1. 108 parallel PCR reactions were performed for each type of mutation, resulting in single base mutations at each designed position. Three types of mutations were generated. To generate base substitution mutations, forward and reverse primers were chosen in matching pairs beginning with KST224+KST332. To generate base insertion mutations, forward and reverse primers were chosen in matching pairs beginning with KST223+KST332. To generate base deletion mutations, forward and reverse primers were chosen in matching pairs beginning with KST225+KST332. After Step 1 PCR, samples were pooled into an equimolar manner, blunt-ligated, and transformed into Turbo E. coli (New England Biolabs), followed by plasmid extraction the next day. The resulting plasmid library theoretically contained all possible single mutations. In Step 2, this process of PCR and cloning was then repeated using the Step 1 plasmid library as the template for the second set of PCRs, arranged as above, to generate all double mutations. The single mutation library from Step 1 and the double mutation library from Step 2 were pooled together.
• After the above cloning steps, the library diversity was assessed with next generation sequencing (see below section for methods) (see FIG. 59). It was confirmed that the majority of the library contained more than one mutation (‘other’) category. A substantial fraction of the library contained single base substitutions, deletions, and insertions (average representation within the library of 1/18,000 variants for single substitutions, and up to 1/740 variants for single deletions).
• 2) Assessing Library Diversity with Next Generation Sequencing.
• For NGS analysis. genomic DNA was amplified via PCR with primers specific to the scaffold region of the bacterial expression vector to form a target amplicon. These primers contain additional sequence at the 5′ ends to introduce Illumina read (see Table 22 for sequences). Typical PCR conditions were: lx Kapa. Hifi buffer, 300 nM dNTPs, 300 nM each primer, 0.75 ul of Kapa. Hifi Hotstart DNA polymerase in a 50 μl reaction. On a thermal cycler, incubate for 95° C. for 5 min; then 16-25 cycles of 98° C. for 15 s, 60° C. for 20 s. 72° C. for 1 min; with a final extension of 2 min at 72° C. Amplified DNA product was purified with Ampure XP DNA cleanup kit, with elution in 30 ul of water. A second PCR step was done with indexing adapters to allow multiplexing on the Illumina platform. 20 μl of the purified product from the previous step was combined with 1× Kapa GC buffer, 300 nM dNTPs, 200 nM each primer, 0.75 μl of Kapa. Hifi Hotstart DNA polymerase in a 50 μl reaction. On a thermal cycler, cycle for 95° C. for 5 min, then 18 cycles of 98° C. for 15 s, 65° C. for 15 s, 72° C. for 30 s, with a final extension of 2 min at 72° C. Amplified DNA product was purified with Anipure XP DNA cleanup kit, with elution in 30 μl of water. Quality and quantification of the amplicon was assessed using a Fragment Analyzer DNA analyzer kit (Agilent, dsDNA 35-1500 bp).

• TABLE 22
  primer sequences.

  	Primer	SEQ ID NO
  	PCR1 Fwd	3619
  	PCR2 Rvs	3620
  	PCR2 Fwd	3621
  	PCR2 Rvs v1 001	3622
  	PCR2_Rvs_v1_002	4294
  	PCR2_Rvs_v1_003	4295
  	PCR2_Rvs_v1_004	4296
  	PCR2_Rvs_v1_005	4297
  	PCR2_Rvs_v1_006	4298
  	PCR2_Rvs_v1_007	4299
  	PCR2_Rvs_v1_008	4300
  	PCR2_Rvs_v1_009	4301
  	PCR2_Rvs_v1_010	4302
  	PCR2_Rvs_v1_011	4303
  	PCR2_Rvs_v1_012	4304
  	PCR2_Rvs_v1_013	4305
  	PCR2_Rvs_v1_014	4306
  	PCR2_Rvs_v1_015	4307
  	PCR2_Rvs_v1_016	4308
  	PCR2_Rvs_v1_017	4309
  	PCR2_Rvs_v1_018	4310
  	PCR2_Rvs_v1_019	4311
  	PCR2_Rvs_v1_020	4312
  	PCR2_Rvs_v1_021	4313
  	PCR2_Rvs_v1_022	4314
  	PCR2_Rvs_v1_023	4315
  	PCR2_Rvs_v1_024	4316
  	PCR2_Rvs_v1_025	4317
  	PCR2_Rvs_v1_026	4318
  	PCR2_Rvs_v1_027	4319
  	PCR2_Rvs_v1_028	4320
  	PCR2_Rvs_v1_029	4321
  	PCR2_Rvs_v1_030	4322
  	PCR2_Rvs_v1_031	4323
  	PCR2_Rvs_v1_032	4324
  	PCR2_Rvs_v1_033	4325
  	PCR2_Rvs_v1_034	4326
  	PCR2_Rvs_v1_035	4327
  	PCR2_Rvs_v1_036	4328
  	PCR2_Rvs_v1_037	4329
  	PCR2_Rvs_v1_038	4330
  	PCR2_Rvs_v1_039	4331
  	PCR2_Rvs_v1_040	4332
  	PCR2_Rvs_v1_041	4333
  	PCR2_Rvs_v1_042	4334
  	PCR2_Rvs_v1_043	4335
  	PCR2_Rvs_v1_044	4336
  	PCR2_Rvs_v1_045	4337
  	PCR2_Rvs_v1_046	4338
  	PCR2_Rvs_v1_047	4339
  	PCR2_Rvs_v1_048	4340
  	PCR2_Rvs_v2_001	4341
  	PCR2_Rvs_v2_002	4342
  	PCR2_Rvs_v2_003	4343
  	PCR2_Rvs_v2_004	4344
  	PCR2_Rvs_v2_005	4345
  	PCR2_Rvs_v2_006	4346
  	PCR2_Rvs_v2_007	4347
  	PCR2_Rvs_v2_008	4348
  	PCR2_Rvs_v2_009	4349
  	PCR2_Rvs_v2_010	4350
  	PCR2_Rvs_v2_011	4351
  	PCR2_Rvs_v2_012	4352
  	PCR2_Rvs_v2_013	4353
  	PCR2_Rvs_v2_014	4354
  	PCR2_Rvs_v2_015	4355
  	PCR2_Rvs_v2_016	4356
  	PCR2_Rvs_v2_017	4357
  	PCR2_Rvs_v2_018	4358
  	PCR2_Rvs_v2_019	4359
  	PCR2_Rvs_v2_020	4360
  	PCR2_Rvs_v2_021	4361
  	PCR2_Rvs_v2_022	4362
  	PCR2_Rvs_v2_023	4363
  	PCR2_Rvs_v2_024	4364
  	PCR2_Rvs_v2_025	4365
  	PCR2_Rvs_v2_026	4366
  	PCR2_Rvs_v2_027	4367
  	PCR2_Rvs_v2_028	4368
  	PCR2_Rvs_v2_029	4369
  	PCR2_Rvs_v2_030	4370
  	PCR2_Rvs_v2_031	4371
  	PCR2_Rvs_v2_032	4372
  	PCR2_Rvs_v2_033	4373
  	PCR2_Rvs_v2_034	4374
  	PCR2_Rvs_v2_035	4375
  	PCR2_Rvs_v2_036	4376
  	PCR2_Rvs_v2_037	4377
  	PCR2_Rvs_v2_038	4378
  	PCR2_Rvs_v2_039	4379
  	PCR2_Rvs_v2_040	4380
  	PCR2_Rvs_v2_041	4381
  	PCR2_Rvs_v2_042	4382
  	PCR2_Rvs_v2_043	4383
  	PCR2_Rvs_v2_044	4384
  	PCR2_Rvs_v2_045	4385
  	PCR2_Rvs_v2_046	4386
  	PCR2_Rvs_v2_047	4387
  	PCR2_Rvs_v2_048	4388
  	PCR2_fwd_v1_univ	4389
  	PCR2_fwd_v2_univ	4390
  	PCR2_fwd_v2_001	4391
  	PCR2_fwd_v2_002	4392
  	PCR2_fwd_v2_003	4393
  	PCR2_fwd_v2_004	4394
  	PCR2_fwd_v2_005	4395
  	PCR2_fwd_v2_006	4396
  	PCR2_fwd_v2_007	4397
  	PCR2_fwd_v2_008	4398
  	PCR2_fwd_v2_009	4399
  	PCR2_fwd_v2_010	4400
  	PCR2_fwd_v2_011	4401
  	PCR2_fwd_v2_012	4402

3) Bacterial CRISPRi (CRISPR Interference) Assay
• A dual-color fluorescence reporter screen was implemented, using monomeric Red Fluorescent Protein (mRFP) and Superfolder Green Fluorescent Protein (sfGFP), based on Qi L S, et al. (Cell 152, 5, 1173-1183 (2013)). This screen was utilized to assay gene-specific transcriptional repression mediated by programmable DNA binding of the CasX system). This strain of E. coli expresses bright green and red fluorescence under standard culturing conditions or when grown as colonies on agar plates. Under a CRISPRi system, the CasX protein is expressed from an anhydrotetracycline (aTc)-inducible promoter on a plasmid containing a p15A replication origin (plasmid pSTX3, chloramphenicol resistant), and the sgRNA is expressed from a minimal constitutive promoter on a plasmid containing a ColE1 replication origin (pSTX41, non-targeting spacer, or pSTX5, GFP-targeting spacer #1; carbenicillin resistant). When the E. coli strain is co-transformed with both plasmids, genes targeted by the spacer in pSTX4 are repressed; in this case GFP repression is observed, the degree to which is dependent on the function of the targeting CasX protein and sgRNA. In this system, RFP fluorescence can serve as a normalizing control. Specifically, RFP fluorescence should be unaltered and independent of functional CasX based CRISPRi activity. CRISPRi activity can be tuned in this system by regulating the expression of the CasX protein; here, all assays used an induction concentration of 20 nM anhydrotetracycline (aTc) final concentration in growth media.
• Libraries of sgRNA were constructed to assess the activity of sgRNA variants in complex with three cleavage-inactivating mutations made to the reference CasX protein open reading frame of Planctomycetes, SEQ ID NO: 2, rendering the CasX catalytically dead (dCasX). These three mutations are referred to as D1 (with a D659A substitution), D2 (with a E756A substitution), or D3 (with a D922A substitution). A fourth library, composed of all three mutations in combination is referred to as DDD (D659A; E756A; D922A substitutions).
• Libraries of sgRNA were screened for activity using the above CRISPRi system with either D2, D3, or DDD. After co-transformation and recovery, libraries were grown for 8 hours in 2xyt media with appropriate antibiotics and sorted on a Sony MA900 flow cytometry instrument. Each library version was sorted with three different gates (in addition to the naive, unsorted library). Three different sort gates were employed to extract GFP-cells: 10%, 1%, and “F” which represents ˜0.1% of cells, ranked by GFP repression. Finally, each sort was done in two technical replicates. Variants of interest were detected using either Sanger sequencing of picked colonies (UC Berkeley Barker Sequencing Facility) or NGS sequencing of ininiprepped plasmid (Massachusetts General Hospital CCM DNA Core Next-Generation Sequencing Service) or NGS sequencing of PCR amplicons, produced with primers that introduced indexing adapters for sequencing on an illumina platform (see section above). Amplicons were sent for sequencing with Novogene (Beijing, China) for sequencing on an Illumina Hiseq, with 150 cycle, paired-end reads. Each sorted sample had at least 3 million reads per technical replicate, and at least 25 million reads for the naive samples. The average read count across all samples was 10 million reads.
4) NGS Data Analysis
• Paired end reads were trimmed for adapter sequences with cutadapt (version 2.1), merged to form a single read with flash2 (v2.2.00), and aligned to the reference with bowtie2 (v2.3.4.3). The reference was the entire amplicon sequence, which includes ˜30 base pairs flanking the Planctomyces reference guide scaffold from the plasmid backbone having the sequence:

• (SEQ ID NO: 3623)

  TGACAGCTAGCTCAGTCCTAGGTATAATACTAGTTACTGGCGCTTTTA

  TCTCATTACTTTGAGAGCCATCACCAGCGACTATGTCGTATGGGTAAA

  GCGCTTATTTATCGGAGAGAAATCCGATAAATAAGAAGCATCAAAGCT

  GGAGTTGTCCCAATTCTTCTAGAG

• Variants between the reference and the read were determined from the bowtie2 output. In brief, custom software in python (analyzeDME/bin/bam_to_variants.py) extracted single-base variants from the reference sequence using the cigar string and nod string from each alignment. Reads with poor alignment or high error rates were discarded (mapq <20 and estimated error rate >4%; estimated error rate was calculated using per-base phred quality scores). Single-base variants at locations of poor-quality sequencing were discarded (phred score <20). Immediately adjacent single-base variants were merged into one mutation that could span multiple bases. Mutations were labeled for being single substitutions, insertions, or deletions, or other higher-order mutations, or outside the scaffold sequence.
• The number of reads that supported each set of mutations was determined. These read counts were normalized for sequencing depth (mean nomialization), and read counts from technical replicates were averaged by taking the geometric mean.
• To obtain enrichment values for each scaffold variant, the number of normalized reads for each sorted sample were compared to the average of the normalized read counts for D2 and D3, which were highly correlated (FIG. 59B). The naive DDD sample was not sequenced. To obtain the enrichment for each catalytically dead. CasX variant, the log of the enrichment values across the three sort gates were averaged.
• Methods for Individual Validation of sgRNA Activity in Human Cell Assays
  1) Individual sgRNA Variant Construction
• In order to screen variants of interest, individual variants were constructed using standard molecular biology techniques. All mutations were built on the reference CasX (SEQ ID NO: 2) using a staging vector and Gibson cloning. To build single mutations, a universal forward (5′→3′) and reverse (3′→5′) primer were designed on either end of the encoded protein sequence that had homology to the desired backbone for screening (see Table 23 below) Primers to create the desired mutations were also designed (F pruner and its reverse complement) and used with the universal F and R primers for amplification; thus producing two fragments. In order to add multiple mutations, additional primers with overlap were designed and more PCR fragments were produced. For example, to construct a triple mutant, four sets of F/R primers were designed. The resulting PCR fragments were gel extracted. These fragments were subsequently assembled into a screening vector (see Table 23), by digesting the screening vector backbone with the appropriate restriction enzymes and gel extraction. The insert fragments and vector were then assembled using Gibson assembly master mix, transformed, and plated using appropriate LB agar+antibiotic. The clones were Sanger sequenced and correct clones were chosen.
• Finally, spacer cloning was performed to target the guide RNA to a gene of interest in the appropriate assay or screen. The sequence-verified non-targeting clone was digested with the appropriate Golden Gate enzyme and cleaned using DNA Clean and Concentrator kit (Zymo). The oligos for the spacer of interest were annealed. The annealed spacer was ligated into a digested and cleaned vector using a standard Golden Gate Cloning protocol. The reaction was transformed into Turbo E. coli and plated on LB agar+carbenicillin, and allowed to grow overnight at 37° C. individual colonies were picked the next day, grown for eight hours in 2XYT carbenicillin at 37° C., and miniprepped. The clones were Sanger sequenced and correct clones were chosen.

• TABLE 23
  Primer sequences

  Screening vector	F primer sequence	R primer sequence
  pSTX6	SAH24:	SAH25:
  	TTCAGGTTGGACCGGTGCCACCATGGCCCC	TTTTGGACTAGTCACGGCGOGC
  	AAAGAAGAAGCGGAAGGTCAGCCAAGAG	TTCCAG (SEQ ID NO: 3616)
  	ATCAAGAGAATCAACAAGATCAGA (SEQ
  	ID NO: 3615)
  pSTX16 or	oIC539:	oIC540:
  pSTX34	ATGGCCCCAAAGAAGAAGCGGAAGGTCTC	TACCTTTCTCTTCTTTTTTGGAC
  	TAGACAAG (SEQ ID NO: 3617)	TAGTCACGG (SEQ ID NO: 3618)

2) GFP Editing by Plasmid Lipofection of HEK293T Cells
• Either doxycycline-inducible GIP (iGFP) reporter HEK293T cells or SOD1-GFP reporter HEK293T cells were seeded at 20-40 k cells/well in a 96 well plate in 100 μl of FB medium and cultured in a 37° C. incubator with 5% CO₂. The following day, confluence of seeded cells was checked. Cells were ˜75% confluent at time of transfection. Each CasX construct was transfected at 100-500 ng per well using Lipofectamine 3000 following the manufacturer's protocol, into 3 wells per construct as replicates. SaCas9 and SpyCas9 targeting the appropriate gene were used as benchmarking controls. For each Cas protein type, a non-targeting plasmid was used as a negative control.
• After 24-48 hours of puromycin selection at 0.3-3 μg/ml to select for successfully transfected cells, followed by 1-7 days of recovery in FB medium, GFP fluorescence in transfected cells was analyzed via flow cytometry. In this process, cells were gated for the appropriate forward and side scatter, selected for single cells and then gated for reporter expression (Attune Nxt Flow Cytometer, Thermo Fisher Scientific) to quantify the expression levels of fluorophores. At least 10,000 events were collected for each sample. The data were then used to calculate the percentage of edited cells.
3) GFP Editing by Lentivirus Transduction of HEK293T Cells
• Lentivirus products of plasmids encoding CasX proteins, including controls, CasX variants, and/or CasX libraries, were generated in a Lenti-X 293T Cell Line (Takara) following standard molecular biology and tissue culture techniques. Either iGFP I-IEK293T cells or SOD1-GFP reporter HEK293T cells were transduced using lentivirus based on standard tissue culture techniques. Selection and fluorescence analysis was performed as described above, except the recovery time post-selection was 5-21 days. For Fluorescence-Activated Cell Sorting (FACS), cells were gated as described above on a MA900 instrument (Sony), Genomic DNA was extracted by QuickExtracfrm DNA Extraction Solution (Lucigen) or Genomic DNA Clean & Concentrator (Zymo)
Results:
• Engineering of sgRNA 1 to 174
  1) sgRNA Derived from Metagenomics of Bacterial Species Improved Function in Human Cells
• An initial improvement in CasX RNP cleavage activity was found by assessing new metagenomic bacterial sequences for possible CasX guide scaffolds. Prior work demonstrated that Deltaproteobacteria sgRNA (SEQ ID NO: 4) could form a functional RNA-guided nuclease complex with CasX proteins, including the Deltaproteobacteria CasX (SEQ ID NO:1 or Planctomycetes CasX (SEQ ID NO: 2). Structural characterization of this complex allowed. identification of structural elements within the sgRNA (FIGS. 60A-60C). However, a sgRNA scaffold from Planctomycetes was never tested. A second tracrRNA was identified from Planctomycetes, which was made into an sgRNA with the same method as was used for Deltaproteobacteria tracrRNA-crRNA (SEQ ID NO: 5) (Liu, J J et al Nature, 566, 218-223 (2019)). These two sgRNA had similar structural elements, based on RNA secondary structure prediction algorithms, including three stem loop structures and possible triplex formation (FIG. 61).
• Characterization the activity of Planctomycetes CasX protein complexed with the Deltaproteobacteria sgRNA (hereafter called RNP 2.1, wherein the CasX protein has the sequence of SEQ ID NO: 2) and Planctomycetes CasX protein complexed with scaffold 2 sgRNA (hereafter called RNP 2.2) showed clear superiority of RNP 2.2 compared to the others in a GFP-lipofection assay (see Methods) (FIG. 62). Thus, this scaffold formed the basis of our molecular engineering and optimization.
2) Improving Activity of CasX RNP Through Comprehensive RNA Scaffold Mutagenesis Screen.
• To find mutations to the guide RNA scaffold that could improve dsDNA cleavage activity of the CasX RNP, a large diversity of insertions, deletions and substitutions to the gRNA scaffold 2 were generated (see Methods). This diverse library was screened using CRISPRi to determine variants that improved DNA-binding capabilities and ultimately improved cleavage activity in human cells. The library was generated through a process of pooled primer cloning as described in the Materials and Methods. The CRISPRi screen was carried out using three enzymatically-inactive versions of CasX (called D2, D3, and DDD; see Methods). Library variants with improved DNA binding characteristics were identified through a high-throughput soiling and sequencing approach. Scaffold variants from cells with high GFP repression (i.e., low fluorescence) were isolated and identified with next generation sequencing. The representation of each variant in the GFP-pool was compared to its representation in the naive library to form an enrichment score per variant (see Materials and Methods). Enrichment was reproducible across the three catalytically dead-CasX variants (FIG. 64).
• Examining the enrichment scores of all single variants revealed mutable locations within the guide scaffold, especially the extended stem (FIGS. 63A-63C). The top-20 enriched single variants outside of the extended stem are listed in Table 24. In addition to the extended stem, these largely cluster into four regions: position 55 (scaffold stein bubble), positions 15-19 (triplex loop), position 27 (triplex), and in the 5′ end of the sequence ( positions 1, 2, 4, 8). While the majority of these top-enriched variants were consistently enriched across all three catalytically dead CasX versions, the enrichment at position 27 was variable, with no evident enrichment in the D3 CasX (data not shown).
• The enrichment of different structural classes of variants suggested that the RNP activity might be improved by distinct mechanisms. For example, specific mutations within the extended stem were enriched relative to the WT scaffold. Given that this region does not substantially contact the CasX protein (FIG. 60A), we hypothesize that mutating this region may improve the folding stability of the gRNA scaffold, while not affecting any specific protein-binding interaction interfaces. On the other hand, 5′ mutations could be associated with increased transcriptional efficiency. In a third mechanism, it was reasoned that mutations to the scaffold stem bubble or triplex could lead to increased stability through direct contacts with the CasX protein, or by affecting allosteric mechanisms with the RNP. These distinct mechanisms to improve RNP binding support that these mutations could be stacked or combined to additively improve activity.

• TABLE 24
  Top enriched single-variants outside of extended stem.

  				log2
  Position	Annotation	Reference	Alternate	enrichment	Region

  55	insertion	—	G	2.37466	scaffold stem
  					bubble
  55	insertion	—	T	1.9.3584	scaffold stem
  					bubble
  15	insertion	—	T	1.65155	triplex loop
  17	insertion	—	T	1.56605	triplex loop
  4	deletion	T	—	1.48676	5′ end
  27	insertion	—	C	1.26385	triplex
  16	insertion	—	C	1.26025	triplex loop
  19	insertion	—	T	1.25306	triplex loop
  18	insertion	—	G	1.22628	triplex loop
  2	deletion	A	—	1.17690	5′ end
  17	insertion	—	A	1.16081	triplex loop
  18	substitution	C	T	1.10247	triplex loop
  18	insertion	—	A	1.04716	triplex loop
  16	substitution	C	T	0.97399	triplex loop
  8	substitution	G	C	0.95127	pseudoknot
  16	substitution	C	A	0.89373	triplex loop
  27	insertion	—	A	0.86722	triplex
  1	substitution	T	C	0.83183	5′ end
  18	deletion	C	—	0.77641	triplex loop
  19	insertion	—	G	0.76838	triplex loop

  
  3) Assessing RNA Scaffold Mutants in dsDNA Cleavage Assay in Human Cells
• The CRISPRi screen is capable of assessing binding capacity in bacterial cells at high throughput. However it does not guarantee higher cleavage activity in human cell assays. We next assessed a large swath of individual scaffold variants for cleavage capacity in human cells using a plasmid lipofection in HEK cells (see Materials and Methods). In this assay, human HEK293T cells containing a stably-integrated GFP gene were transduced with a plasmid (p16) that expresses reference Cast protein (Stx2) (SEQ ID NO: 2) and sgRNA comprising the gRNA scaffold variant and spacers 4.76 (having sequence UGUGGUCGGGGUAGCGGCUG (SEQ ID NO: 3624) and 4.77 (having sequence UCAAGUCCGCCAUGCCCGAA (SEQ ID NO: 3625)) to target the RNP to knockdown the GFP gene. Percent GFP knockdown was assayed using flow cytometry. Over a hundred scaffold variants were tested in this assay.
• The assay resulted in largely reproducible values across different assay dates for spacer 4.76, while exhibiting more variability for spacer 4.77 (FIG. 69). Spacer 4.77 was generally less active for the wild-type RNP complex, and the lower overall signal may have contributed to this increased variability. Comparing the cleavage activity across the two spacers showed generally correlated results (r 0.652; FIG. 70). Because of the increased noise in spacer 4.77 measurements, the reported cleavage activity per scaffold was taken as the weighted average between the measurements on each scaffold, with the weights equal to the inverse squared error. This weighting effectively down-weights the contribution from high-error measurements.
• A subset of sequences was tested in both the HEK-iGFP assay and the CRISPRi assay. Comparing the CRISPRi enrichment score to the GFP cleavage activity showed that highly-enriched variants had cleavage activity at or exceeding the wildtype RNP (FIG. 63C). Two variants had high cleavage activity with low enrichment scores (C18G and T17G); interestingly, these substitutions are at the same position as several highly-enriched insertions (FIG. 71).
• Examining all scaffolds tested in the HEK-iGFP assay revealed certain features that consistently improved cleavage activity. We found that the extended stem could often be completely swapped out for a different stein, with either improved or equivalent activity (e.g., compare scaffolds of SEQ ID NO: 2101-2105, 2111, 2113, 2115; all of which have replaced the extended stem, with increased activity relative to the reference, as seen in Table 5). We specifically focused on two stems with different origins: a truncated version of the wildtype stem, with the loop sequence replaced by the highly stable UUCG tetraloop (stem 42). The other (stem 46) was derived from Uvsx bacteriophage T4 mRNA, which in its biological context is important for regulation of reverse transcription of the bacteriophage genome (Tuerk et al. Proc Nati Acad Sci USA. 85(5):1364 (1988)). The top-performing gRNA scaffolds all had one of these two extended stem versions (e.g., SEQ ID NOS: 2160 and 2161).
• Appending ribozymes to the 3′ end often resulted in functional scaffolds (e.g., see SEQ ID NO: 2182 with equivalent activity to the WT guide in this assay {Table 5}). On the other hand, adding to the 5′ end generally hurt cleavage activity. The best-performing 5′ ribozyme construct (SEQ ID NO: 2208) had cleavage activity <40% of the WT guide in the assay.
• Certain single-point mutations were generally good, or at least not harmful, including T10C, which was designed to increase transcriptional efficiency in human cells by removing the four consecutive T's at the 5′ start of the scaffold (Kiyama and Oishi, Nucleic Acids Res., 24:4577 (1996)). C18G was another helpful mutation, which was obtained from individual colony picking from the CRISPRi screen. The insertion of C at position 27 was highly-enriched in two out of the three dCasX versions of the CRISPRi screen. However, it did not appear to help cleavage activity. Finally, insertion at position 55 within the RNA bubble substantially improved cleavage activity (i.e., compare SEQ ID NO: 2236, with a {circumflex over ( )}G55 insertion to SEQ ID NO: 2106 in Table 5).
4) Further Stacking of Variants in Higher-Stringency Cleavage Assays
• Scaffold mutations that proved beneficial were stacked together to form a set of new variants that were tested under more stringent criteria: a plasmid lipofection assay in human HEK-293t cells with the GFP gene knocked into the SOD1 allele, which we observed was generally harder to knock down. Of this batch of variants, guide scaffold 158 was identified as a. top-performer (FIG. 65). This scaffold had a modified extended stem (Uvsx), with additional mutations to fully base pair the extended stem ([A99] and G65U). It also contained mutations in the triplex loop (C18G) and in the scaffold stern bubble ({circumflex over ( )}G55).
• In a second validation of improved DNA editing capacity, sgRNAs were delivered to cells with low-MOI lentiviral transduction, and with distinct targeting sequences to the SOD1 gene (see Methods); spacers were 8.2 (having sequence AUGUUCAUGAGUUUGGAGAU (SEQ ID NO: 3626)), and 8.4 (having sequence UCGCCAUAACUCGCUAGGCC (SEQ ID NO: 3627)) (results shown in FIG. 66). Additionally, 5′ truncations of the initial GT of guide scaffolds 158 and 64 were deleted (forming scaffolds 174 and 175 respectively). This assay showed dominance of guide scaffold 174: the variant derived from guide scaffold 158 with 2 bases truncated from the 5′ end (FIG. 66). A schematic of the secondary structure of scaffold 174 is shown in FIG. 67.
• In sum, our improved guide scaffold 174 showed marked improvement over our starting reference guide scaffold (scaffold 1 from Deltaproteobacteria, SEQ NO:4), and substantial improvement over scaffold 2 (SEQ ID NO: 5) (FIG. 68). This scaffold contained a swapped extended stem (replacing 32 bases with 14 bases), additional mutations in the extended stem ([A99] and G65U), a mutation in the triplex loop (C18G), and in the scaffold stem bubble ({circumflex over ( )}G55) (where all the numbering refers to the scaffold 2), Finally, the initial T was deleted from scaffold 2, as well as the G that had been added to the 5′ end in order to enhance transcriptional efficiency. The substantial improvements seen with guide scaffold 174 came collectively from the indicated mutations.
Example 26 Editing of RHO in ARPE19 RHO-GFP Cells
• The purpose of the experiment was to demonstrate the ability of CasX to edit the RHO locus using the CasX variants 438, 488 and 491, guide 174 variant, and spacers targeting Exon of the RHO gene. Spacers were chosen based on PAM availability in the locus without prior knowledge of potential activity.
• To facilitate assessment of editing outcomes, an ARPE19 RHO-GFP reporter cell line was first generated by knocking into ARPE19 cells a transgene cassette that constitutively expresses Exon 1 of the human RHO gene linked to GFP. The modified cells were expanded by serial passage every 3-5 days and maintained in Fibroblast (FB) medium, consisting of Dulbecco's Modified Eagle Medium (DMEM: Corning Cellgro, #10-013-CV) supplemented with 10% fetal bovine serum (FBS; Seradigm, #1500-500), and 100 Units/mL penicillin and 100 mg/mL streptomycin (100×-Pen-Strep; GMCO #15140-122), and can additionally include sodium pyruvate (100×, Thermofisher #11360070), non-essential amino acids (100× Thermofisher #11140050), HEPES buffer (100× Thermofisher #15630080), and 2-mercaptoethanol (1000× Thermofisher #21985023). The cells were incubated at 37° C. and 5% CO2. After 1-2 weeks, GFP+ cells were bulk sorted into FB medium. The reporter lines were expanded by serial passage every 3-5 days and maintained in FB medium in an incubator at 37° C. and 5% CO2. Reporter clones were generated by a limiting dilution method. The clonal lines were characterized via flow cytometry, genomic sequencing, and functional modification of the RHO locus using a previously validated RHO targeting CasX molecule. The optimal reporter lines were identified as ones that i) had a single copy of GFP correctly integrated per cell ii) maintained doubling times equivalent to unmodified cells, and iii) resulted in reduction in GFP fluorescence upon disruption of the RHO gene when assayed using the methods described below.
• ARPE19 RHO-GFP reporter cells, constructed using cell line generation methods described above, were used for this experiment. Cells were seeded at 20-40 k cells/well in a 96 well plate in 100 μL of FB medium and cultured in a 37° C. incubator with 5% CO2. The following day, lentiviral vectors packaging each CasX and guide construct (e.g., see Table 25 for sequences) were used to transduce cells at a high multiplicity of infection (MOI), using 3 wells per construct as replicates. A lentivirus packaging a non-targeting construct was used as a negative control. Cells were selected for successful transduction with puromycin at 0.3-3 μg/ml for 24-48 hours followed by recovery in FB medium. Edited cells were analyzed by flow cytometry 14 days after transduction. Briefly, cells were sequentially gated for live cells, single cells, and fraction of GFP-negative cells.
• Results: The graph in FIG. 72 shows the results of flow cytometry analysis of Cas-mediated editing at the RHO locus in APRE19 RHO-GFP cells 14 days post-transfection. Eighteen different spacers (indicated by the individual data points) targeting the RHO Exon locus were used for each of the different CasX variants (438, 488, and 491) used in this experiment. Each data point is an average measurement of 3 replicates for an individual spacer. The median values for the constructs were: 438 (48.4); 488 (59.0) and 491 (56.4), indicating that under the conditions of the assay, each of the CasX variants with appropriate guides were able to specifically edit in APRE19 RHO-GFP reporter cells at a high level while the construct with a non-targeting spacer resulted in no editing (data not shown)

• TABLE 25
  Guide encoding sequences

  SPACER SEQUENCE

  	174 GUIDE + SPACER SEQUENCE
  Spacer	(SEQ ID NO)	(SEQ ID NO)

  11.13	3628	3646
  11.14	3629	3647
  11.15	3630	3648
  11.16	3631	3649
  11.17	3632	3650
  11.18	3633	3651
  11.19	3634	3652
  11.20	3635	3653
  11.21	3636	3654
  11.22	3637	3655
  11.23	3638	3656
  11.24	3639	3657
  11.25	3640	3658
  11.26	3641	3659
  11.27	3642	3660
  11.28	3643	3661
  11.29	3644	3662
  11.1	3645	3663

Example 27 Design of Improved Guides Based on Predicted Secondary Structure Stability Methods
• A computational method was employed to predict the relative stability of the ‘target’ secondary structure, compared to alternative, non-functional secondary structures. First, the ‘target’ secondary structure of the gRNA was determined by extracting base-pairs formed within the RNA in the CryoEM structure for CasX 1.1. For prediction of RNA secondary structure, the program RNAfold was used (version 2.4.14). The ‘target’ secondary structure was converted to a ‘constraint string’ that enforces bases to be paired with other bases, or to be unpaired. Because the triplex is unable to be modeled in RNAfold, the bases involved in the triplex are required to be unpaired in the constraint string, whereas all bases within other stems (pseudoknot, scaffold, and extended stems) were required to be appropriately paired. For guide scaffolds 2 (SEQ ID NO:5), 174 (SEQ ID NO:2238), and 175 (SEQ ID NO:2239), this constraint string was constructed based on sequence alignment between the scaffold and scaffold 1 (SEQ ID NO:4) outside of the extended stem, which can have minimal sequence identity, Within the extended. stem, bases were assumed to be paired according to the predicted secondary structure for the isolated extended stem sequence. See Table 26 for a subset of sequences and their constraint strings.

• TABLE 26
  Constraint strings to represent the ‘target secondary structure’ in RNAfold algorithm.

  Name	Constraint string
  Scaffold 3 (w/5′ truncation as in CryoEM	(((((.xxx.........xxxxx))))).((.((((((((...))))).)))))...(((((((((((((((.......))))))
  structure)	))))).))))..xxxxx
  Scaffold 2	....(((((.xxx.........xxxxx.)))))....((((((((...))))).))).....((.(((((((((((((......))))
  	)))))))))..))..xxxxx
  Scaffold 374	...(((((.xxx.........xxxxx.)))))....((((((((...)))))..))).....((((((((....))))))))..xx
  	xxx
  Scaffold 175	...(((((.xxx.........xxxxx.)))))....((((((((...))))).))).....((.(((((((((....))))))))).
  	.))..xxxxx

• Secondary structure stability of the ensemble of structures that satisfy the constraint was obtained, using the command: ‘RNAfold-p0-noPS-C’ And taking the ‘free energy of ensemble’ in kcal/mol (ΔG_constraint). The prediction was repeated without the constraint to get the secondary structure stability of the entire ensemble that includes both the target and alternative structures, using the command: ‘RNAfold-p0-noPS’ and taking the ‘free energy of ensemble’ in kcal/mol (ΔG_all).
• The relative stability of the target structure to alternate structures was quantified as the difference between these two ΔG values: ΔΔG=ΔG_constraint_ΔG_all. A sequence with a large value for ΔΔG is predicted to have many competing alternate secondary structures that would make it difficult for the RNA to fold into the target binding-competent structure. A sequence with a low value for ΔΔG is predicted to be more optimal in terms of its ability to fold into a binding-competent secondary structure.
Results
• A series of new scaffolds was designed to improve scaffold activity based on existing data and new hypotheses. Each new scaffold comprised a set of mutations that, in combination, were predicted to enable higher activity of dsDNA cleavage. These mutations fell into the following categories: First, mutations in the 5′ unstructured region of the scaffold were predicted to increase transcription efficiency or otherwise improve activity of the scaffold. Most commonly, scaffolds had the 5′ “GU” nucleotides deleted (scaffolds 181-220: SEQ ID NOS: 2242-2280). The “U” is the first nucleotide (U1) in the reference sequence SEQ ID NO:5. The G was prepended to increase transcription efficiency by U6 polymerase. However, removal of these two nucleotides was shown, surprisingly, to increase activity (FIG. 66). Additional mutations at the 5′ end include (a) combining the GU deletion with A2G, such that the first transcribed base is the G at position 2 in the reference scaffold (scaffold 199: SEQ ID NO:2259); (h) deleting only U1 and keeping the prepended G (scaffold 200: SEQ ID NO:2260); and (c) deleting the U at position 4, which is predicted to be unstructured and was found to be beneficial when added to scaffold 2 in a high-throughput CRISPRi assay (scaffold 208: SEQ ID NO:2268).
• A second class of mutations was to the extended stem region, The sequence for this region was chosen from three possible options: (a) a “truncated stem loop” which has a shorter loop sequence than the reference sequence extended stem (the scaffolds 64 and 175 contain this extended stem: SEQ ID NOS: 2106 and 2239, respectively) (b) Uvsx hairpin with additional loop-distal mutations [A99] and G65T to fully base-pair the extended stem (the scaffold 174: SEQ ID NO: 2238 contains this extended stem); or (c) an “MS2(U15C)” hairpin with the same additional loop-distal mutations [A99] and G65T as in (b). These three extended stems classes were present in scaffolds with high activity (e.g. see FIG. 65), and their sequences can be found in Table 27.

• TABLE 27
  Sequences of extended stem regions used in novel scaffolds.

  		Incorporated in Scaffolds
  Extended stem name	Extended stem sequence	(SEQ ID NO)
  truncated stem loop	GCGCUUACGGACUUCGGUCCGUAAGAAGC	2239, 2242-2244, 2246, 2255-2258
  	(SEQ ID NO: 4291)
  UvsX, -99 G65T	GCUCCCUCUUCGGAGGGAGC (SEQ ID	2238, 2245, 2250-2254, 2259-2280
  	NO: 4292)
  MS2(U15C), -99 G65T	GCUCACAUGAGGAUCACCCAUGUGAGC	2249
  	(SEQ ID NO: 4293)

• Thirdly, a set of mutations was designed to the triplex loop region. This region was not resolved in the CryoEM structure of CasX 1.1, likely because it does not form base-pairs and thus is more flexible. This region tolerates mutations, with certain mutations having beneficial effects on RNP binding, based on CRISPRi data from scaffold 2 (FIG. 63). The C18G substitution within the triplex loop was already incorporated in the scaffold 174. The following mutations were added to scaffold 174, that were not immediately adjacent to the C 18G substitution in order to limit potential negative epistasis between these mutations: {circumflex over ( )}U 15 (insertion of U before nucleotide 15 in scaffold 2), {circumflex over ( )}U17, and C16A (scaffolds 208, 210, and 209: SEQ ID NOS: 2268, 2270, 2269, respectively).
• Fourth, a set of mutations was designed to systematically stabilize the target secondary structure for the scaffold. For background, RNA polymers fold into complex three-dimensional structures that enforce their function. In the CasX RNP, the RNA scaffold forms a structure comprising secondary structure elements such as the pseudoknot stem, a triplex, a scaffold stem-loop, and an extended stem-loop, as evident in the Cryo-EM characterization of the CasX RNP 1.1. These structural elements likely help enforce a three dimensional structure that is competent to bind the CasX protein, and in turn enable conformational transitions necessary for enzymatic function of the RNP. However, an RNA sequence can fold into alternate secondary structures that compete with the formation of the target secondary structure. The propensity of a given sequence to fold into the target versus alternate secondary structures was quantified using computational prediction, similar to the method described in (Jarmoskaite, I., et al. 2019. A quantitative and predictive model for RNA binding by human pumilio proteins. Molecular Cell 74(5), pp. 966-981.e18.) for correcting observed binding equilibrium constants for a distinct protein-RNA interaction, and using RNAfold (Lorenz, R., Bernhart, S. H., Honer Zu Siederdissen, C., et al. 2011. ViennaRNA Package 2.0. Algorithms for Molecular Biology 6, p. 26.) to predict secondary structure stability (see Methods).
• A series of mutations were chosen that were predicted to help stabilize the target secondary structure, in the following regions: The pseudoknot is a base-paired stem that forms between the 5′ sequence of the scaffold and sequence 3′ of the triplex and triplex loop. This stem is predicted to comprise 5 base-pairs, 4 of which are canonical Watson-Crick pairs and the fifth is a noncanonical G:A wobble pair. Converting this G:A wobble to a Watson Crick pair is predicted to stabilize alternative secondary structures relative to the target secondary structure (high ΔΔG between target and alternative secondary structure stabilities; Methods). This aberrant stability comes from a set of secondary structures in which the triplex bases are aberrantly paired. However, converting the G to an A or a C (for an A:A wobble or CA wobble) was predicted to lower the AAG value (G8C or G8A added to scaffolds 174 and 175+C18G). A second set of mutations was in the triplex loop: including a U15C mutation and a C18G mutation (for scaffold 175 that does not already contain this variant), Finally, the linker between the pseudoknot stem and the scaffold stem was mutated at position 35 (U35A), which was again predicted to stabilize the target secondary structure relative to alternatives.
• Scaffolds 189-198 (SEQ ID NOS:2250-2258) included these predicted mutations on top of scaffolds 174 or 175, individually and in combination. The predicted change in ΔΔG for each of these scaffolds is given in Table 28 below. This algorithm predicts a much stronger effect on ΔΔG with combining multiple of these mutations into a single scaffold.

• TABLE 28
  Predicted effect on target secondary structure stability
  of incorporating specific mutations individually
  or in combination to scaffolds 174 or 175.

  			Effect of mutation(s)
  		Scaffold	ΔΔG_mut-
  Starting		ΔΔG	ΔΔG_starting_scaffold
  scaffold	Mutation(s)	(kcal/mol)	(kcal/mol)

  174	—	0.17	—
  174	G8A	−0.74	−0.91
  174	G8C	−0.32	−0.49
  174	U15C	−0.02	−0.19
  174	U35A	−0.22	−0.39
  174	G8A, U15C, U35A	−1.34	−1.51
  175	—	3.23	—
  175	G8A	3.15	−0.08
  175	G8C	3.15	−0.08
  175	U35A	3.07	−0.16
  175	U15C	0.78	−2.45
  175	Cl8G	0.43	−2.80
  175	G8A, T15C, C18G, T35A	−1.03	−4.26

• A fifth set of mutations was designed to test whether the triplex bases could be replaced by an alternate set of three nucleotides that are still able to form triplex pairs (Scaffolds 212-220: SEQ ID NOS:2272-2280). A subset of these substitutions are predicted to prevent formation of alternate secondary structures.
• A sixth set of mutations were designed to change the pseudoknot-triplex boundary nucleotides, which are predicted to have competing effects on transcription efficiency and triplex formation. These include scaffolds 201-206 (SEQ ID NOS:2261.-2266).
Example 28 In Vitro Cleavage Assays with NTC PAMs
• In vitro cleavage assays were performed essentially as described in Example 19, using CasX 2 (SED ID NO:2), CasX 119, and CasX 438 complexed with single guide 174 with spacer 7.37 targeted against B2M. Fluorescently labeled dsDNA targets that would be complementary with a 7.37 spacer and either a ITC, CTC, CTC, or ATC PAM were used (The DNA sequences used to generate each dsDNA substrate are shown in Table 29. The PAM sequences for each are bolded. TS—target strand. NTS—Non-target strand). Target DNA was incubated with a 20-fold excess of the indicated RNP and the amount of cleaved target was determined at the indicated. time points. The monophasic fit of the combined replicates is shown. During the assay, samples were taken at at 0.25, 0.5, 1, 2, 5, 10, 30, and 60 minutes. Gels were imaged with an Amersham Typhoon and quantified using the IQTL 8,2 software. Apparent first-order rate constants for non-target strand cleavage (k_cleave) were determined for each Casx:sgRNA complex on each target. Rate constants for targets with non-TTC PAM were compared to the TIC PAM target to determine whether the relative preference for each PAM was altered for a given CasX variant. The results are shown in FIG. 73 (the monophasic fit of the combined replicates is shown) and Table 30. For all Cas X variants, the TTC PAM target sequence supported the highest cleavage rate, followed by the ATC, then the CTC, and finally the GTC target sequence. The CTC target supported cleavage 3.5-4.3% as fast as the TTC target; the GTC target supported cleavage 1.0-1.4% as fast; and the ATC target supported cleavage 6.5-8.3% as fast. Despite the lower k_cleave rates for the non-TTC PAM, the cleavage rates of the variants allow targets with ATC or CTC PAMs to be cleaved nearly completely within 10 minutes, and these increased cleavage rates relative to the wild-type CasX may be sufficient for effective genome editing in a human cell, supporting the utility of the CasX variants haying an increased ability to utilize a larger spectrum of PAM sequences.

• TABLE 29
  Sequences of DNA substrates used in in vitro PAM cleavage assay.

  Assay
  Combination	DNA Substrate Sequence*
  7.37 TTC	AGCGCGAGCACAGCTAAGGCCACGGAGCGAGACATCTCGGCCCGAATGCTGTCAGCTTCA (SEQ
  PAM TS	ID NO: 4404)
  7.37 TTC	TGAAGCTGACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCT (SEQ
  PAM NTS	ID NO: 4405)
  7.37 CTC	AGCGCGAGCACAGCTAAGGCCACGGAGCGAGACATCTCGGCCCGAGTGCTGTCAGCTTCA (SEQ
  PAM TS	ID NO: 4406)
  7.37 CTC	TGAAGCTGACAGCACTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCT (SEQ
  PAM NTS	ID NO: 4407)
  7.37 GTC	AGCGCGAGCACAGCTAAGGCCACGGAGCGAGACATCTCGGCCCGACTGCTGTCAGCTTCA (SEQ
  PAM TS	ID NO: 4408)
  7.37 GTC	TGAAGCTGACAGCAGTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCT (SEQ
  PAM NTS	ID NO: 4409)
  7.37 ATC	AGCGCGAGCACAGCTAAGGCCACGGAGCGAGACATCTCGGCCCGATTGCTGTCAGCTTCA (SEQ
  PAM TS	ID ND: 4410)
  7.37 ATC	TGAAGCTGACAGCAATCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCT (SEQ
  PAM NTS	ID NO: 4411)
  *PAM indicated in bold

• TABLE 30
  Cleavage Rates

  kcleave Rate*

  CasX	TTC	CTC	GTC	ATC

  2	0.267 min−1	9.29E−3 min−1	3.75E−3 min −1	1.87E−2 min−1
  		(0.035)	(0.014)	(9.070)
  119	8.33 min−1	0.303 min−1	8.64E−2 min−1	0.540 min−1
  		(0.036)	(0.010)	(0.065)
  438	4.94 min−1	0.212 min−1	1.31E−2 min−1	0.408 min−1
  		(0.043)	(0.013)	(0.083)
  *For all non-NTC PAMs, the relative cleavage rate as compared to the TTC rate for that variant is shown in parentheses.

Claims (75)

1. A variant of a reference CasX protein (CasX variant), wherein:

a. the CasX variant comprises at least one modification in the reference CasX protein wherein the reference CasX protein comprises the sequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3; and

b. the CasX variant exhibits at least one improved characteristic as compared to the reference CasX protein.

2. The CasX variant of claim 1, wherein the improved characteristic of the CasX variant is selected from the group consisting of: improved folding of the CasX variant; improved binding affinity to a guide nucleic acid (gNA); improved binding affinity to a target DNA; improved ability to utilize a greater spectrum of one or more PAM sequences, including ATC, CTC, GTC, or TTC, in the editing of target DNA; improved unwinding of the target DNA; increased editing activity; improved editing efficiency; improved editing specificity; increased nuclease activity; increased target strand loading for double strand cleavage; decreased target strand loading for single strand nicking; decreased off-target cleavage; improved binding of non-target DNA strand; improved protein stability; improved protein solubility; improved protein:gNA complex (RNP) stability; improved protein:gNA complex solubility; improved protein yield; improved protein expression; improved fusion characteristics or a combination thereof.

3. The Cas X variant of claim 1, wherein the at least one modification comprises:

a. at least one amino acid substitution in a domain of the CasX variant;

b. at least one amino acid deletion in a domain of the CasX variant;

c. at least one amino acid insertion in a domain of the CasX variant;

d. a substitution of all or a portion of a domain from a different CasX;

e. a deletion of all or a portion of a domain of the CasX variant; or f. any combination of (a)-(e).

4. (canceled)

5. The CasX variant of claim 1, wherein the at least one modification is in a domain selected from:

a. a non-target strand binding (NTSB) domain;

b. a target strand loading (TSL) domain;

c. a helical I domain;

d. a helical II domain;

e. an oligonucleotide binding domain (OBD); or

f. a RuvC DNA cleavage domain.

6. The CasX variant of claim 5 wherein:

the at least one modification in the TSL domain comprises an amino acid substitution of one or more of amino acids Y857, S890, and S932 of SEQ ID NO: 2;

the at least one modification in the helical I domain comprises an amino acid substitution of one or more of amino acids S219, L249, E259, Q252, E292, L307, or D318 of SEQ ID NO: 2;

the at least one modification in the helical II domain comprises an amino acid substitution of one or more of amino acids D361, L379, E385, E386, D387, F399, L404, R458, C477, or D489 of SEQ ID NO: 2;

the at least one modification in the OBD comprises an amino acid substitution of one or more of amino acids F536, E552, T620, or I658 of SEQ ID NO: 2; and/or

the at least one modification in the RuvC DNA cleavage domain comprises an amino acid substitution of one or more of amino acids K682, G695, A708, V711, D732, A739, D733, L742, V747, F755, M771, M779, W782, A788, G791, L792, P793, Y797, M799, Q804, S819, or Y857 or a deletion of amino acid P793 of SEQ ID NO: 2.

7-16. (canceled)

17. The CasX variant of claim 5, wherein the modification results in an increased ability to edit the target DNA.

18. The CasX variant of claim 1, wherein the CasX variant is capable of forming a ribonuclear protein complex (RNP) with a guide nucleic acid (gNA).

19. The CasX variant of claim 1, wherein the at least one modification comprises:

a. a substitution of 1 to 100 consecutive or non-consecutive amino acids in the CasX variant;

b. a deletion of 1 to 100 consecutive or non-consecutive amino acids in the CasX variant;

c. an insertion of 1 to 100 consecutive or non-consecutive amino acids in the CasX; or

d. any combination of (a)-(c).

20. (canceled)

21. The CasX variant of claim 1, wherein the CasX variant comprises two or more modifications in one domain or wherein the CasX variant comprises modifications in two or more domains.

22-32. (canceled)

33. The CasX variant of claim 1, wherein the at least one modification compared to the reference CasX sequence of SEQ ID NO: 2 is selected from one or more of:

a. an amino acid substitution of L379R;

b. an amino acid substitution of A708K;

c. an amino acid substitution of T620P;

d. an amino acid substitution of E385P;

e. an amino acid substitution of Y857R;

f. an amino acid substitution of I658V;

g. an amino acid substitution of F399L;

h. an amino acid substitution of Q252K;

i. an amino acid substitution of L404K; and

j. an amino acid deletion of P793.

34. The CasX variant of claim 1, wherein the CasX variant has a sequence selected from the group consisting of the sequences of Tables 3, 8, 9, 10 and 12, a sequence selected from the group consisting of SEQ ID NOS: 258-327, 3508-3520, and 4412-4415, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99% sequence identity thereto.

35. (canceled)

36. The CasX variant of claim 1, further comprising a substitution of an NTSB and/or a helical lb domain from a different CasX, wherein the substituted NTSB and/or the helical lb domain is from the reference CasX of SEQ ID NO: 1.

37-38. (canceled)

39. The CasX variant of claim 1, further comprising a heterologous protein or domain thereof fused to the CasX, wherein the heterologous protein or domain thereof comprises one or more nuclear localization signals (NLS) selected from the group of sequences consisting of PKKKRKV (SEQ ID NO: 352), KRPAATKKAGQAKKKK (SEQ ID NO: 353), PAAKRVKLD (SEQ ID NO: 354), RQRRNELKRSP (SEQ ID NO: 355), NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 356), RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 357), VSRKRPRP (SEQ ID NO: 358), PPKKARED (SEQ ID NO: 35), PQPKKKPL (SEQ ID NO: 360), SALIKKKKKMAP (SEQ ID NO: 361), DRLRR (SEQ ID NO: 362), PKQKKRK (SEQ ID NO: 363), RKLKKKIKKL (SEQ ID NO: 364), REKKKFLKRR (SEQ ID NO: 365), KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 366), RKCLQAGMNLEARKTKK (SEQ ID NO: 367), PRPRKIPR (SEQ ID NO: 368), PPRKKRTVV (SEQ ID NO: 369), NLSKKKKRKREK (SEQ ID NO: 370), RRPSRPFRKP (SEQ ID NO: 371), KRPRSPSS (SEQ ID NO: 372), KRGINDRNFWRGENERKTR (SEQ ID NO: 373), PRPPKMARYDN (SEQ ID NO: 374), KRSFSKAF (SEQ ID NO: 375), KLKIKRPVK (SEQ ID NO: 376), PKKKRKVPPPPAAKRVKLD (SEQ ID NO: 377), PKTRRRPRRSQRKRPPT (SEQ ID NO: 378), SRRRKANPTKLSENAKKLAKEVEN (SEQ ID NO: 379), KTRRRPRRSQRKRPPT (SEQ ID NO: 380), RRKKRRPRRKKRR (SEQ ID NO: 381), PKKKSRKPKKKSRK (SEQ ID NO: 382), HKKKHPDASVNFSEFSK (SEQ ID NO: 383), QRPGPYDRPQRPGPYDRP (SEQ ID NO: 384), LSPSLSPLLSPSLSPL (SEQ ID NO: 385), RGKGGKGLGKGGAKRHRK (SEQ ID NO: 386), PKRGRGRPKRGRGR (SEQ ID NO: 387), and PKKKRKVPPPPKKKRKV (SEQ ID NO: 389) or any one of SEQ ID NOS: 3540-3549; wherein the one or more NLS are positioned at or near the C-terminus of the CasX protein, at or near at the N-terminus of the CasX protein, or at or near the N-terminus and at or near the C-terminus of the CasX protein.

40-43. (canceled)

44. The CasX variant of claim 2, wherein one or more of the improved characteristics of the CasX variant is at least about 1.1 to about 100-fold or more improved relative to the reference CasX proteins of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.

45-46. (canceled)

47. The CasX variant of claim 1, wherein a ribonucleoprotein (RNP) comprising the CasX variant exhibits greater editing efficiency and/or binding of a target sequence in the target DNA when any one of the PAM sequences TTC, ATC, GTC, or CTC is located 1 nucleotide 5′ to the non-target strand of the protospacer having identity with the targeting sequence of the gNA in a cellular assay system compared to the editing efficiency and/or binding of an RNP comprising a reference CasX protein in a comparable assay system.

48-53. (canceled)

54. The CasX variant of claim 1, wherein the CasX variant protein comprises a nuclease domain having nickase activity, the CasX variant protein comprises a nuclease domain having double-stranded cleavage activity, or wherein the CasX protein is a catalytically inactive CasX (dCasX) protein, and wherein the dCasX and the gNA retain the ability to bind to the target DNA.

55-56. (canceled)

57. The CasX variant of claim 54, wherein the CasX protein is catalytically inactive (dCasX) and wherein the dCasX comprises a mutation at residues:

a. D672, and/or E769, and/or D935 corresponding to the CasX protein of SEQ ID NO:1; or

b. D659, and/or E756, and/or D922 corresponding to the CasX protein of SEQ ID NO: 2.

58. (canceled)

59. The CasX variant of claim 1, wherein the CasX variant comprises a first domain from a first CasX protein and second domain from a second CasX protein different from the first CasX protein.

60-62. (canceled)

63. The CasX variant of claim 59, wherein the first domain comprises a portion of the sequence selected from the group consisting of amino acids 1-56, 57-100, 101-191, 192-332, 333-509, 510-660, 661-824, 825-934, and 935-986 of SEQ ID NO: 1 and the second domain comprises a portion of the sequence selected from the group consisting of amino acids 1-58, 59-102,103-192, 193-333, 334-501, 502-647, 648-812, 813-921, and 922-978 of SEQ ID NO: 2.

64. (canceled)

65. The CasX variant of claim 1, wherein the CasX variant comprises at least one chimeric domain comprising a first part from a first CasX protein and a second part from a second CasX protein different from the first CasX protein.

66-70. (canceled)

71. The CasX variant of claim 1, comprising a sequence selected from the group consisting of SEQ ID NOS: 247-337, 3301-3493, 3498-3501, 3505-3520, 3540-3549 and 4412-4415.

72-76. (canceled)

77. A variant of a reference guide nucleic acid scaffold (gNA variant) capable of binding a reference CasX protein or a CasX variant, wherein:

a. the gNA variant comprises at least one modification compared to the reference guide nucleic acid scaffold sequence; and

b. the gNA variant exhibits one or more improved characteristics compared to the reference guide nucleic acid scaffold comprising a sequence selected from the group consisting of SEQ ID NOS: 4-16.

78. The gNA variant of claim 77, wherein the one or more improved characteristics is selected from the group consisting of: improved stability; improved solubility; improved transcription of the gNA; improved resistance to nuclease activity; increased folding rate of the gNA; decreased side product formation during folding; increased productive folding; improved binding affinity to a CasX protein; improved binding affinity to a target DNA when complexed with the CasX protein; improved gene editing when complexed with the CasX protein; improved specificity of editing when complexed with the CasX protein; and improved ability to utilize a greater spectrum of one or more PAM sequences, including ATC, CTC, GTC, or TTC, in the editing of target DNA when complexed with the CasX protein.

79. (canceled)

80. The gNA variant of claim 77, wherein the at least one modification comprises:

a. at least one nucleotide substitution in a region of the gNA variant;

b. at least one nucleotide deletion in a region of the gNA variant;

c. at least one nucleotide insertion in a region of the gNA variant;

d. a substitution of all or a portion of a region of the gNA variant;

e. a deletion of all or a portion of a region of the gNA variant; or

f. any combination of (a)-(e); wherein the region of the gNA variant is selected from the group consisting of extended stem loop, scaffold stem loop, triplex, and pseudoknot.

81. (canceled)

82. The gNA variant of claim 80, wherein the scaffold stem further comprises a bubble, a triplex loop region, or a 5′ unstructured region.

83-84. (canceled)

85. The gNA variant of claim 77, wherein the at least one modification comprises:

a. a substitution of 1 to 15 consecutive or non-consecutive nucleotides in the gNA variant in one or more regions;

b. a deletion of 1 to 10 consecutive or non-consecutive nucleotides in the gNA variant in one or more regions;

c. an insertion of 1 to 10 consecutive or non-consecutive nucleotides in the gNA variant in one or more regions;

d. a substitution of the scaffold stem loop or the extended stem loop with an RNA stem loop sequence from a heterologous RNA source with proximal 5′ and 3′ ends; or

e. any combination of (a)-(d).

86. The gNA variant of claim 77, comprising an extended stem loop region comprising at least 10, at least 100, at least 500, at least 1000, or at least 10,00010,000 nucleotides.

87-88. (canceled)

89. The gNA variant of claim 85, wherein the extended RNA stem loop comprises a sequence selected from MS2, Qβ, U1 hairpin II, Uvsx, or PP7 stem loops.

90. The gNA variant of claim 85, wherein the at least one modification compared to the reference guide scaffold of SEQ ID NO: 5 is selected from one or more of:

a. a C18G substitution in the triplex loop;

b. a G55 insertion in the stem bubble;

c. a U1 deletion;

d. a modification of the extended stem loop wherein

i. a 6 nt loop and 13 loop-proximal base pairs are replaced by a Uvsx hairpin; and

ii. a deletion of A99 and a substitution of G64U that results in a loop-distal base that is fully base-paired.

91-92. (canceled)

93. The gNA variant of claim 77, wherein the gNA variant further comprises a targeting sequence wherein the targeting sequence is complementary to the target DNA sequence.

94. The gNA variant of claim 93, wherein the targeting sequence has 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 nucleotides.

95. (canceled)

96. The gNA variant of claim 93, wherein the gNA is a single-guide gNA comprising the scaffold sequence linked to the targeting sequence.

97. The gNA variant of claim 77, wherein the one or more of the improved characteristics of the CasX variant is at least about 1.1 to about 100-fold or more improved relative to the reference gNA of SEQ ID NO: 4 or SEQ ID NO: 5.

98-102. (canceled)

103. The gNA variant of claim 77, wherein the scaffold of the gNA variant sequence comprises a sequence selected from the group of sequences of SEQ ID NOS: 2101-2280, or having at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto.

104. The gNA variant of claim 103, wherein the scaffold of the gNA variant sequence consists of a sequence selected from the group of sequences of SEQ ID NOS: 2101-2280.

105-107. (canceled)

108. The gNA variant of claim 77, further comprising a protein binding motif and/or a thermostable stem loop.

109-119. (canceled)

120. A gene editing pair comprising:

a variant of a reference CasX protein (CasX variant) wherein:

a. the CasX variant comprises at least one modification in the reference CasX protein; and

b. the CasX variant exhibits at least one improved characteristic as compared to the reference CasX protein; and

a guide nucleic acid (gNA variant) comprising a variant of a reference guide nucleic acid scaffold capable of binding a reference CasX protein or the CasX variant, wherein:

c. the gNA variant comprises at least one modification compared to the reference guide nucleic acid scaffold sequence; and

d. the gNA variant exhibits one or more improved characteristics compared to the reference guide nucleic acid scaffold comprising a sequence selected from the group consisting of SEQ ID NOS: 4-16; and

e. the gNA variant comprises a targeting sequence, wherein the targeting sequence is complementary to a target DNA sequence.

121-136. (canceled)

137. A method of editing a target DNA, comprising contacting the target DNA with a gene editing pair comprising:

a variant of a reference CasX protein (CasX variant), wherein:

a. the CasX variant comprises at least one modification in the reference CasX protein; and

b. the CasX variant exhibits at least one improved characteristic as compared to the reference CasX protein; and

a guide nucleic acid variant (gNA variant) comprising a variant of a reference guide nucleic acid scaffold (gNA variant) capable of binding a reference CasX protein or the CasX variant, wherein:

c. the gNA variant comprises at least one modification compared to the reference guide nucleic acid scaffold sequence; and

d. the gNA variant exhibits one or more improved characteristics compared to the reference guide nucleic acid scaffold comprising a sequence selected from the group consisting of SEQ ID NOS: 4-16; and

e. the gNA variant comprises a targeting sequence, wherein the targeting sequence is complementary to the target DNA sequence;

wherein the contacting results in editing or modification of the target DNA.

138-159. (canceled)

160. The method of claim 137, wherein the method comprises contacting the eukaryotic cell with a vector encoding or comprising the CasX protein and the gNA, and optionally further comprising the donor template.

161. The method of claim 160, wherein the vector is an Adeno-Associated Viral (AAV) vector; a lentiviral vector, a non-viral particle or a virus-like particle (VLP).

162-177. (canceled)

178. A polynucleotide encoding:

a variant of a reference CasX protein (CasX variant), wherein:

a. the CasX variant comprises at least one modification in the reference CasX protein, wherein the reference CasX protein; and

b. the CasX variant exhibits at least one improved characteristic as compared to the reference CasX protein; and/or

a variant of a reference guide nucleic acid scaffold (gNA variant) capable of binding a reference CasX protein or a CasX variant, wherein:

c. the gNA variant comprises at least one modification compared to the reference guide nucleic acid scaffold sequence; and

d. the gNA variant exhibits one or more improved characteristics compared to the reference guide nucleic acid scaffold comprising a sequence selected from the group consisting of SEQ ID NOS: 4-16.

179. (canceled)

180. A vector comprising the polynucleotide of claim 178.

181-189. (canceled)

190. The gene editing pair of claim 120, wherein the CasX protein and the gNA are associated together in a ribonuclear protein complex (RNP).

191-200. (canceled)

201. A kit, comprising:

a variant of a reference CasX protein (CasX variant) wherein:

a. the CasX variant comprises at least one modification in the reference CasX protein; and

b. the CasX variant exhibits at least one improved characteristic as compared to the reference CasX protein and/or

a variant of a reference guide nucleic acid scaffold (gNA variant) capable of binding a reference CasX protein or a CasX variant, wherein:

c. the gNA variant comprises at least one modification compared to the reference guide nucleic acid scaffold sequence; and

d. the gNA variant exhibits one or more improved characteristics compared to the reference guide nucleic acid scaffold comprising a sequence selected from the group consisting of SEQ ID NOS: 4-16;

and a container.

202-222. (canceled)

Images