WO2021030666A1 - Édition de bases par transglycosylation - Google Patents

Édition de bases par transglycosylation Download PDF

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WO2021030666A1
WO2021030666A1 PCT/US2020/046320 US2020046320W WO2021030666A1 WO 2021030666 A1 WO2021030666 A1 WO 2021030666A1 US 2020046320 W US2020046320 W US 2020046320W WO 2021030666 A1 WO2021030666 A1 WO 2021030666A1
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cas9
fusion protein
sequence
domain
protein
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David R. Liu
Jaron August McClure MERCER
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The Broad Institute, Inc.
President And Fellows Of Harvard College
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1022—Transferases (2.) transferring aldehyde or ketonic groups (2.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases RNAses, DNAses

Definitions

  • Targeted editing of nucleic acid sequences is a highly promising approach for the study of gene function and also has the potential to provide new therapies for genetic diseases, including those caused by point mutations.
  • Point mutations represent the majority of known human genetic variants associated with disease. Developing robust methods to introduce and correct point mutations is therefore important in understanding and treating diseases with a genetic component.
  • Base editing involves the conversion of a specific nucleic acid base into another at a targeted genomic locus. For certain approaches, this can be achieved without requiring double-stranded DNA breaks (DSB).
  • Engineered base editors are capable of editing many targets with high efficiency, often achieving editing of 30-70% of cells following a single treatment, without selective enrichment of the cell population for editing events.
  • Base editors are typically fusions of a Cas (“CRISPR-associated”) domain and a nucleotide modification domain (e.g., a natural or evolved deaminase, such as a cytidine deaminase, e.g., APOBEC1 (“apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1”), CDA (“cytidine deaminase”), and AID (“activation-induced cytidine deaminase”)) domains.
  • base editors may also include proteins or domains that alter cellular DNA repair processes to increase the efficiency and/or stability of the resulting single-nucleotide change.
  • cytosine base editors convert target C:G base pairs to T:A base pairs
  • adenosine base editors convert A:T base pairs to G:C base pairs.
  • C-to-T, G-to-A, A-to-G, T-to-C, C- to-U, and A-to-U enable the targeted installation of ah possible transition mutations (C-to-T, G-to-A, A-to-G, T-to-C, C- to-U, and A-to-U)
  • SNPs single nucleotide polymorphisms
  • C-to-T base editors use a cytidine deaminase to convert cytidine to uridine in the single- stranded DNA loop created by the Cas9 (“CRISPR-associated protein 9”) domain.
  • CRISPR-associated protein 9 The opposite strand is nicked by Cas9 to stimulate DNA repair mechanisms that use the edited strand as a template, while a fused uracil glycosylase inhibitor slows excision of the edited base.
  • DNA repair leads to a C:G to T:A base pair conversion.
  • This class of base editor is described in U.S. Patent Publication No. 2017/0121693, published May 4, 2017, which issued on January 1, 2019 as U.S.
  • Patent No. 10,167,457 each of which is incorporated herein by reference.
  • a major limitation of base editing is the inability to generate transversion (purine ⁇ - pyrimidine) changes, which are needed to correct the remaining -38% of known human pathogenic SNPs. See Komor, A.C. et al, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature 533, 420-424 (2016); and Landrum, M.J. et al, ClinVar: public archive of relationships among sequence variation and human phenotype, Nucleic Acids Res. 42, D980-985 (2014), each of which is incorporated herein by reference.
  • transversions can only be repaired by nuclease-mediated formation of a double-stranded break (DSB) followed by homology directed repair (HDR), which is typically inefficient, especially in non-mitotic cells, and leads to undesired by-products, such as indels (insertions and deletions) and translocations.
  • DLB double-stranded break
  • HDR homology directed repair
  • transversion base editors requires the development of a new editing strategy, such as the manipulation of endogenous DNA repair pathways or a different nucleobase chemical transformation.
  • the present disclosure describes novel transversion base editors using an innovative transglycosylation strategy. The present disclosure greatly expands the capabilities of base editing.
  • the present disclosure provides for thymine-to-guanine or “TGBE” (or adenine-to-cytosine or “ACBE”) transversion base editors which satisfy the need in the art for the installation of targeted single -base transversion nucleobase changes in a target nucleotide sequence, e.g., a genome.
  • TGBE thymine-to-guanine
  • ACBE adenine-to-cytosine
  • the present disclosure provides for methods of making TGBE base editors, as well as methods of using TGBE base editors or nucleic acid molecules encoding such TGBE base editors in applications including editing a nucleic acid molecule, e.g., a genome.
  • This new strategy allows for the efficient and specific transversion of T-to-G or A-to-C using the base editors described herein.
  • transglycosylation strategy an enzyme-catalyzed substitution of a thymine for a guanine is performed at the deoxyribose-nucleobase glycosidic bond (see FIG. 2).
  • a transglycosylase enzyme recognizes a target thymine base within a target sequence.
  • the transglycosylase e.g., an active site aspartate residue
  • guanine replaces the active site transglycosylase amino acid residue in a nucleophilic attack, re-forming a glycosidic bond with the deoxyribose.
  • the cell s replication and repair machinery replaces the mismatched adenosine with a cytosine. A desired T:A to G:C transversion is thus achieved.
  • a guanine or deazaguanine derivative e.g., 7-cyano-7-deazaguanine (abbreviated PreQ 0 ) (also referrec to as 7-cyano-7- carbaguanine) or 7-amino-methyl-7-deazaguanine (abbreviated PreQi), replaces the excised thymine.
  • PreQ 0 7-cyano-7-deazaguanine
  • PreQi 7-amino-methyl-7-deazaguanine
  • the cell’s mismatch repair machinery converts the 2'-deoxy-7-cyano-7-deazaguanosine (dPreQo) or 2'-deoxy-7-amino-methyl-7- deazaguanosine (dPreQi) product of this reaction to a guanosine, thereby completing the T- to-G change.
  • dPreQo 2'-deoxy-7-cyano-7-deazaguanosine
  • dPreQi 2'-deoxy-7-amino-methyl-7- deazaguanosine
  • Targeted transglycosylation is achieved by the use of a fusion protein comprising a nucleic acid programmable D/RNA binding protein (napR/DNAbp), or more particularly, a nucleic acid programmable DNA binding protein (napDNAbp) domain, a transglycosylase domain, and optionally a linker connecting these two domains (see FIG. 1).
  • the napDNAbp domain may comprise a catalytically dead Cas9 (“dCas9”) or Cas9 nickase (“nCas9”).
  • the base editor fusion protein comprises (i) a napDNAbp, and (ii) a transglycosylase.
  • the napDNAbp may be a Cas9 domain.
  • the napDNAbp domain may be a CasX (Casl2e), CasY (Casl2d), Cpfl, C2cl, C2c2 (Casl3a), C2c3 (Casl2c), GeoCas9, CjCas9, Casl2a, Casl2b, Casl2g, Casl2h, Casl2i, Casl3b, Casl3c, Casl3d, Casl4, Csn2, an xCas9, an SpCas9-NG, an LbCasl2a, an AsCasl2a, a Cas9-KKH, a circularly permuted Cas9, an Argonaute (Ago) domain, a
  • the napDNAbp domain may be a nuclease active Cas9 domain, a nuclease inactive Cas9 (dCas9) domain, or a Cas9 nickase (nCas9) domain.
  • the napDNAbp domain may be a Cas9 domain derived from S. pyogenes, or an SpCas9.
  • the transglycosylase domain comprises a wild-type tRNA guanine transglycosylase (TGT), or a variant thereof, e.g., a TGT that substitutes a first nucleobase (i.e., a thymine) for a second nucleobase at a ribose- nucleobase glycosidic bond.
  • the second nucleobase may be a guanine or a guanine derivative (e.g., a deazaguanine derivative, such as PreQi or PreQo).
  • the transglycosylase comprises any one of the amino acid sequences of SEQ ID NOs: 5-8, 10, and 15-25. In particular embodiments, the transglycosylase domain comprises any one of the amino acid sequences of SEQ ID NOs: 10 and 15-17. In particular embodiments, the transglycosylase domain comprises the sequence of SEQ ID NO: 10. In particular embodiments, the transglycosylase domain is an E. coli TGT, or a variant thereof. In other embodiments, the transglycosylase domain is an E. coli deazapurine-in-DNA, gene A protein (DpdA), or a variant thereof.
  • DpdA gene A protein
  • the fusion proteins described herein may comprise any of the following structures: NH2-[transglycosylase domain] -[napDNAbp domain]-COOH; or Nth- [napDNAbp domain] -[transglycosylase domain]-COOH, wherein each instance of “]-[” comprises an optional linker.
  • the linker fusing the napDNAbp domain and transglycosylase domain may be any suitable amino acid linker sequence, polymer (natural or synthetic), functional group, covalent bond, or combination thereof.
  • exemplary linkers include any of the following amino acid sequences: S GGS S GGS S GSETPGTSES ATPES S GGS S GGS (SEQ ID NO: 11); SGGSGGSGGS (SEQ ID NO: 12); GGG; GGGS (SEQ ID NO: 1); SGGGS (SEQ ID NO: 2); SGSETPGTSESATPES (SEQ ID NO: 48); or SGGS (SEQ ID NO: 14).
  • complexes comprising any of the fusion proteins described herein and a guide RNA bound to the napDNAbp domain of the fusion protein are provided.
  • the disclosure provides nucleic acids or vectors encoding any of the base editor fusion proteins, or domains thereof, described herein.
  • the nucleic acid sequences may be codon-optimized for expression in the cells of any organism of interest (e.g., human). In certain embodiments, the nucleic acid sequence is codon-optimized for expression in human cells.
  • cells containing the nucleic acids, cells containing the vectors, and cells containing the complexes described herein are provided. Further provided are cells containing purified fusion proteins, or domains thereof, as described herein.
  • the disclosure provides a pharmaceutical composition comprising any of the fusion proteins described herein and a pharmaceutically acceptable excipient.
  • the pharmaceutical composition further comprises a gRNA.
  • the disclosure provides a pharmaceutical composition comprising a nucleic acid or vector encoding any of the disclosed fusion proteins.
  • the nucleic acid or vector further encodes a gRNA.
  • the disclosure provides a kit comprising a nucleic acid construct that includes (i) a nucleic acid sequence encoding any of the fusion proteins described herein; (ii) a heterologous promoter that drives expression of the sequence of (i); and optionally an expression construct encoding a guide RNA backbone and the target sequence.
  • kits comprising a fusion protein as provided herein, a gRNA having complementarity to a target sequence, cofactor proteins, buffers, media, and/or target cells.
  • methods for targeted nucleic acid editing typically comprise i) contacting a nucleic acid sequence with a complex comprising any of the fusion proteins described herein and a guide nucleic acid, wherein the double-stranded DNA comprises a target T:A (or A:T) nucleobase pair; and ii) editing the thymine (or adenine) of the T:A (or A:T) nucleobase pair.
  • the methods may further comprise iii) cutting or nicking a strand of the double-stranded DNA (e.g ., nicking the non-edited strand of the DNA).
  • methods of treatment using the base editors described herein are provided.
  • the methods described herein may comprise treating a subject having or at risk of developing a disease, disorder, or condition, comprising administering to the subject a fusion protein as described herein, a polynucleotide as described herein, a vector as described herein, or a pharmaceutical composition as described herein.
  • FIG. 1 is a schematic illustration showing an exemplary fusion protein of the disclosure.
  • a fusion protein comprising an nCas9 domain linked to a transglycosylase enzyme is targeted to the correct thymine nucleobase through the hybridization of a single guide RNA (“sgRNA”) to a complementary sequence of nucleic acid.
  • the transglycosylase exchanges the thymine nucleobase with a guanine nucleobase.
  • Depicted here is the transglycosylase-DNA intermediate of the transglycosylation reaction, in which the enzyme is covalently bound to the deoxyribose sugar at the 1 ' position after the thymine base has been excised.
  • FIG. 2 depicts the catalyzed conversion of thymine to guanine by the disclosed base editors.
  • a transglycosylase enzyme recognizes a target thymine base within a target sequence to which the sgRNA has complementarity.
  • the transglycosylase e.g., at an active site aspartate residue
  • a free guanine replaces the active site residue in a backside attack, re-forming a deoxyribose-glycosidic bond.
  • the cell’s mismatch repair machinery converts the mismatched adenine to a cytosine, thereby completing the desired T:A to G:C mutation.
  • FIG. 3 depicts a possible chemical mechanism for a tRNA guanine transglycosylase (“TGT”) mediated exchange of thymine with guanine.
  • TGT tRNA guanine transglycosylase
  • FIG. 4 shows the second nucleobase substrates ( . ⁇ ? ., the bases added, or substituted in, to the target sequence) accepted by known types of transglycosylases, along with the ribose-substituted products generated in the RNA base exchange reactions catalyzed by these transglycosylases. All of the transglycosylase types shown are adapted to accept guanine as a first nucleobase substrate (i.e ., the base that is excised out of the target sequence). For instance, eukaryotic TGTs are capable of replacing guanine in RNA with queosine (Q) and queosine derivatives.
  • Q queosine
  • bacterial DpdAs are capable of replacing guanine in RNA with 7-amido-7-deazaguanine (ADG).
  • ADG 7-amido-7-deazaguanine
  • G + archaeosine
  • RM system restriction modification system
  • FIG. 5 depicts an exemplary assay for selection of evolved variants of bacterial transglycosylases that are effective at recognizing a (DNA) thymine base as a first nucleobase substrate.
  • Plasmids containing mutagenized E. coli TGT-dCas9 fusion proteins and targeting guide RNAs (sgRNAs), and selection plasmids containing an inactivated spectinomycin resistance gene with a mutation at the active site that requires A:T to C:G editing to correct are transformed into E. coli cells, which are plated onto agar media containing spectinomycin and sucrose.
  • sgRNAs targeting guide RNAs
  • FIGs. 6A-6B depict in vitro data showing that E. coli TGT will act on DNA hairpins, wherein the sequence surrounding a target guanine in the hairpin has been altered.
  • FIG. 6A shows the base exchange reaction that was performed, wherein a tritiated guanine base was added to a mix that included E.
  • FIG. 6B shows that the target guanine was successfully replaced with tritiated G across four different trinucleotide sequences. Abreviation: DPM, disintegrations per minute.
  • accessory plasmid refers to a plasmid comprising a gene required for the generation of infectious viral particles under the control of a conditional promoter.
  • transcription from the conditional promoter of the accessory plasmid is typically activated, directly or indirectly, by a function of the gene to be evolved.
  • the accessory plasmid serves the function of conveying a competitive advantage to those viral vectors in a given population of viral vectors that carry a version of the gene to be evolved able to activate the conditional promoter or able to activate the conditional promoter more strongly than other versions of the gene to be evolved.
  • only viral vectors carrying an “activating” version of the gene to be evolved will be able to induce expression of the gene required to generate infectious viral particles in the host cell, and, thus, allow for packaging and propagation of the viral genome in the flow of host cells.
  • Vectors carrying non-activating versions of the gene to be evolved will not induce expression of the gene required to generate infectious viral vectors, and, thus, will not be packaged into viral particles that can infect fresh host cells.
  • Exemplary accessory plasmids have been described, for example in U.S. Patent Pub. No. 2018/0087046, published on March 29, 2018, which is incorporated by reference herein.
  • Base editing is a genome editing technology that involves the conversion of a specific nucleic acid base into another at a targeted genomic locus. In certain embodiments, this can be achieved without requiring double- stranded DNA breaks (DSB).
  • DSB double- stranded DNA breaks
  • CRISPR-based systems begin with the introduction of a DSB at a locus of interest. Subsequently, cellular DNA repair enzymes mend the break, commonly resulting in random insertions or deletions (indels) of bases at the site of the DSB.
  • base-to-base changes there are 12 possible base-to-base changes that may occur via individual or sequential use of transition (i.e ., a purine-to-purine change or pyrimidine-to-pyrimidine change) or transversion ⁇ i.e., a purine-to-pyrimidine or pyrimidine-to-purine) editors. These include:
  • C-to-T base editor (or “CTBE”). This type of editor converts a C:G Watson-Crick nucleobase pair to a T:A Watson-Crick nucleobase pair. Because the corresponding Watson-Crick paired bases are also interchanged as a result of the conversion, this category of base editor may also be referred to as a G-to-A base editor (or “GABE”). o A-to-G base editor (or “AGBE”). This type of editor converts a A:T Watson-Crick nucleobase pair to a G:C Watson-Crick nucleobase pair. Because the corresponding Watson-Crick paired bases are also interchanged as a result of the conversion, this category of base editor may also be referred to as a T-to-C base editor (or “TCBE”).
  • C-to-T base editor or “CTBE”. This type of editor converts a C:G Watson-Crick nucleobase pair to a T:A Watson-Crick nucleobase pair. Because the corresponding
  • this category of base editor may also be referred to as a C-to-A base editor (or “CABE”).
  • CABE C-to-A base editor
  • A-to-T base editor or “ATBE”. This type of editor converts a A:T Watson-Crick nucleobase pair to a T:A Watson-Crick nucleobase pair.
  • this category of base editor may also be referred to as a T-to-A base editor (or “TABE”).
  • TABE T-to-A base editor
  • ACBE A-to-C base editor
  • This type of editor converts a A:T Watson-Crick nucleobase pair to a C:G Watson-Crick nucleobase pair. Because the corresponding Watson-Crick paired bases are also interchanged as a result of the conversion, this category of base editor may also be referred to as a T-to-G base editor (or “TGBE”).
  • the fusion protein comprises a nuclease-inactive Cas9 (dCas9) fused to a transglycosylase which binds a nucleic acid in a guide RNA- programmed manner via the formation of an R-loop but does not cleave the nucleic acid.
  • the dCas9 domain of the fusion protein may include a D10A and an H840A mutation.
  • the fusion protein comprises a Cas9 nickase (nCas9) fused to a transglycosylase.
  • the nCas9 domain of the fusion protein may include a D10A or an H840A mutation (which renders the Cas9 domain capable of cleaving only one strand of a nucleic acid duplex), as described in PCT/US2016/058344, filed on October 22, 2016, and published as WO 2017/070632 on April 27, 2017), which is incorporated herein by reference.
  • the DNA cleavage domain of S. pyogenes Cas9 includes two subdomains, the HNH nuclease subdomain and the RuvCl subdomain.
  • the HNH subdomain cleaves the strand complementary to the gRNA (the “targeted strand,” or the strand at which editing or transglycosylation occurs), whereas the RuvCl subdomain cleaves the non-complementary strand containing the PAM sequence (the “non-targeted strand”, or the strand at which editing or transglycosylation does not occur).
  • the fusion protein comprises a Cas9 nickase fused to a transglycosylase, e.g., a transglycosylase which converts a thymine nucleobase to a guanine.
  • base editors encompasses the base editors described herein as well as any base editor known or described in the art at the time of this filing or developed in the future.
  • Cas9 or “Cas9 nuclease” or “Cas9 domain” refers to a CRISPR associated protein 9, or variant thereof, and embraces any naturally occurring Cas9 from any organism, any naturally-occurring Cas9, any Cas9 homolog, ortholog, or paralog from any organism, and any variant of a Cas9, naturally-occurring or engineered. More broadly, a Cas9 protein, domain, or moiety is a type of nucleic acid programmable D/RNA binding protein (napR/DNAbp),” or more specifically, a “nucleic acid programmable DNA binding protein (napDNAbp)”.
  • napR/DNAbp nucleic acid programmable D/RNA binding protein
  • napDNAbp nucleic acid programmable DNA binding protein
  • Cas9 is not meant to be limiting and may be referred to as a “Cas9 or variant thereof.” Exemplary Cas9 proteins are described herein and also described in the art. The present disclosure is unlimited with regard to the particular Cas9 that is employed in the base editors of the disclosure.
  • proteins comprising Cas9 or fragments thereof are referred to as “Cas9 variants.”
  • a Cas9 variant shares homology to Cas9, or a fragment thereof.
  • Cas9 variants include functional fragments of Cas9.
  • a Cas9 variant is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to wild type Cas9.
  • the Cas9 variant may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32,
  • the Cas9 variant comprises a fragment of Cas9 (e.g., a gRNA binding domain or a DNA-cleavage domain), such that the fragment is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the corresponding fragment of wild type Cas9.
  • a fragment of Cas9 e.g., a gRNA binding domain or a DNA-cleavage domain
  • the fragment has at least 30%, at least 35%, 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%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identity to the amino acid length of a corresponding wild type Cas9.
  • dCas9 refers to a nuclease-inactive Cas9 or nuclease-dead Cas9, or a variant thereof, and embraces any naturally occurring dCas9 from any organism, any naturally-occurring dCas9 equivalent, any dCas9 homolog, ortholog, or paralog from any organism, and any mutant or variant of a dCas9, naturally-occurring or engineered.
  • the term dCas9 is not meant to be particularly limiting and may be referred to as a “dCas9 or equivalent.”
  • nCas9 or “Cas9 nickase” refers to a Cas9 or a variant thereof, which cleaves or nicks only one of the strands of a target cut site thereby introducing a nick in a double strand DNA molecule rather than creating a double strand break. This can be achieved by introducing appropriate mutations in a wild-type Cas9 which inactives one of the two endonuclease activities of the Cas9.
  • any suitable mutation which inactivates one Cas9 endonuclease activity but leaves the other intact is contemplated, such as one of D10A or H840A mutations in the wild-type Cas9 amino acid sequence (e.g., SEQ ID NO: 9) may be used to form the nCas9.
  • the D10A mutation is used to form the nCas9.
  • a population of nucleic acids is subjected to multiple rounds of (a) replication, (b) mutation, and (c) selection to produce a desired evolved product, for example, a nucleic acid encoding a protein with a desired activity, wherein the multiple rounds can be performed without investigator interaction, and wherein the processes under (a)-(c) can be carried out simultaneously.
  • the evolution procedure is carried out in vitro, for example, using cells in culture as host cells.
  • a continuous evolution process relies on a system in which a gene of interest is provided in a nucleic acid vector that undergoes a life-cycle including replication in a host cell and transfer to another host cell, wherein a critical component of the life-cycle is deactivated and reactivation of the component is dependent upon a desired mutation in the gene of interest.
  • a critical component of the life-cycle is deactivated and reactivation of the component is dependent upon a desired mutation in the gene of interest.
  • the nucleic acid vector of the continuous evolution system that comprises the gene of interest is a a viral vector, a microparticle, a nanoparticle, a lipid particle, or naked DNA (e.g., a mobilization plasmid).
  • transfer of the gene of interest from cell to cell is via infection, transfection, transduction, conjugation, or uptake of naked DNA, and efficiency of cell-to-cell transfer (e.g., transfer rate) is dependent on the activity of a product encoded by the gene of interest.
  • the nucleic acid vector is a phage harboring the gene of interest, and the efficiency of phage transfer (via infection) is dependent on an activity of the gene of interest in that a protein required for the generation of phage particles (e.g., pill for M13 phage) is expressed in the host cells only in the presence of the desired activity of the gene of interest.
  • a protein required for the generation of phage particles e.g., pill for M13 phage
  • the nucleic acid vector is a retroviral vector, for example, a lentiviral or vesicular stomatitis virus vector harboring the gene of interest, and the efficiency of viral transfer from cell to cell is dependent on an activity of the gene of interest in that a protein required for the generation of viral particles (e.g ., an envelope protein, such as VSV-g) is expressed in the host cells only in the presence of the desired activity of the gene of interest.
  • a retroviral vector for example, a lentiviral or vesicular stomatitis virus vector harboring the gene of interest
  • a protein required for the generation of viral particles e.g ., an envelope protein, such as VSV-g
  • the nucleic acid vector is a DNA vector, for example, in the form of a mobilizable plasmid DNA, comprising the gene of interest, that is transferred between bacterial host cells via conjugation, and the efficiency of conjugation-mediated transfer from cell to cell is dependent on the activity of the gene of interest in that a protein required for conjugation-mediated transfer (e.g., traA or traQ) is expressed in the host cells only in the presence of the desired activity of the gene of interest.
  • Host cells contain F plasmid lacking one or both of those genes.
  • some embodiments provide a continuous evolution system, in which a population of viral vectors comprising a gene of interest to be evolved replicates in a flow of host cells, e.g., a flow through a lagoon, wherein the viral vectors are deficient in a gene encoding a protein that is essential for the generation of infectious viral particles, and wherein that gene is comprised in the host cell under the control of a conditional promoter that can be activated by a gene product encoded by the gene of interest, or a mutated version thereof.
  • the activity of the conditional promoter depends on a desired function of a gene product encoded by the gene of interest.
  • Viral vectors in which the gene of interest has not acquired a mutation conferring the desired function, will not activate the conditional promoter, or only achieve minimal activation, while any mutation in the gene of interest that confers the desired mutation will result in activation of the conditional promoter. Since the conditional promoter controls an essential protein for the viral life cycle, activation of this promoter directly corresponds to an advantage in viral spread and replication for those vectors that have acquired an advantageous mutation.
  • CRISPR is a family of DNA sequences (i.e., CRISPR clusters) in bacteria and archaea that represent snippets of prior infections by a virus that have invaded the prokaryote.
  • the snippets of DNA are used by the prokaryotic cell to detect and destroy DNA from subsequent attacks by similar viruses and effectively constitute, along with an array of CRISPR-associated proteins (including Cas9 and homologs thereof) and CRISPR-associated RNA, a prokaryotic immune defense system.
  • CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
  • tracrRNA trans-encoded small RNA
  • me endogenous ribonuclease 3
  • Cas9 protein a trans-encoded small RNA
  • the tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA.
  • Cas9/crRNA/tracrRNA endonucleolytic ally cleaves linear or circular nucleic acid target complementary to the RNA. Specifically, the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3 '-5' exonucleolytically.
  • RNA-binding and cleavage typically requires protein and both RNAs.
  • single guide RNAs (“sgRNA”, or simply “gRNA”) can be engineered so as to incorporate embodiments of both the crRNA and tracrRNA into a single RNA species — the guide RNA.
  • sgRNA single guide RNAs
  • Cas9 recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus non-self.
  • CRISPR biology as well as Cas9 nuclease sequences and structures are well known to those of skill in the art (see, e.g., “Complete genome sequence of an Ml strain of Streptococcus pyogenes.” Ferretti J.J., el al, Proc. Natl. Acad. Sci. U.S.A.
  • Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference.
  • a “CRISPR system” refers collectively to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated (“Cas”) genes, including sequences encoding a Cas gene, a tracr (trans-activating CRISPR) sequence (e.g. tracrRNA or an active partial tracrRNA), a tracr mate sequence (encompassing a “direct repeat” and a tracrRNA-processed partial direct repeat in the context of an endogenous CRISPR system), a guide sequence (also referred to as a “spacer” in the context of an endogenous CRISPR system), or other sequences and transcripts from a CRISPR locus.
  • a tracr trans-activating CRISPR
  • a tracr mate sequence encompassing a “direct repeat” and a tracrRNA-processed partial direct repeat in the context of an endogenous CRISPR system
  • a guide sequence also referred to as a “spacer” in the context of an
  • the tracrRNA of the system is complementary (fully or partially) to the tracr mate sequence present on the guide RNA.
  • the term “effective amount,” as used herein, refers to an amount of a biologically active agent that is sufficient to elicit a desired biological response.
  • an effective amount of a base editor may refer to the amount of the base editor that is sufficient to edit a target site nucleotide sequence, e.g., a genome.
  • an effective amount of a base editor provided herein e.g., of a fusion protein comprising a nuclease-inactive Cas9 domain and a nucleotide modification domain (e.g., a transglycosylase domain) may refer to the amount of the fusion protein that is sufficient to induce editing of a target site specifically bound and edited by the fusion protein.
  • an effective amount of a base editor provided herein may refer to the amount of the fusion protein sufficient to induce editing having the following characteristics: > 50% product purity, ⁇ 5% indels, and/or an editing window of 2-8 nucleotides.
  • an effective amount of a base editor may refer to the amount of the fusion protein sufficient to induce editing of > 45% product purity, ⁇ 10% indels, a ratio of intended point mutations to indels that is at least 5:1, and/or an editing window of 2-10 nucleotides.
  • an agent e.g., a fusion protein, a nuclease, a transglycosylase, a hybrid protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide
  • an agent e.g., a fusion protein, a nuclease, a transglycosylase, a hybrid protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide
  • the desired biological response e.g., on the specific allele, genome, or target site to be edited, on the target cell or tissue (i.e ., the cell or tissue to be edited), and on the agent being used.
  • the term “evolved base editor” or “evolved base editor variant” refers to a base editor formed as a result of mutagenizing a reference base editor.
  • the term also refers to embodiments in which the nucleotide modification domain is evolved or a separate domain is evolved.
  • Mutagenizing a reference base editor may comprise mutagenizing a transglycosylase — by a continuous evolution method (e.g., PACE), wherein the evolved transglycosylase has one or more amino acid variations introduced into its amino acid sequence relative to the amino acid sequence of the transglycosylase.
  • Amino acid sequence variations may include one or more mutated residues within the amino acid sequence of a reference base editor, e.g., as a result of a change in the nucleotide sequence encoding the base editor that results in a change in the codon at any particular position in the coding sequence, the deletion of one or more amino acids (e.g., a truncated protein), the insertion of one or more amino acids, or any combination of the foregoing.
  • the evolved base editor may include variants in one or more components or domains of the base editor (e.g., variants introduced into a transglycosylase domain, or a variant introduced into combinations of these domains).
  • fusion protein refers to a hybrid polypeptide which comprises protein domains from at least two different proteins.
  • One protein may be located at the amino-terminal (N-terminal) portion of the fusion protein or at the carboxy-terminal (C-terminal) protein thus forming an “amino-terminal fusion protein” or a “carboxy-terminal fusion protein,” respectively.
  • a protein may comprise different domains, for example, a nucleic acid binding domain (e.g., the gRNA binding domain of Cas9 that directs the binding of the protein to a target site) and a nucleic acid cleavage domain or a catalytic domain of a nucleic-acid editing protein.
  • any of the proteins provided herein may be produced by any method known in the art.
  • the proteins provided herein may be produced via recombinant protein expression and purification, which is especially suited for fusion proteins comprising a peptide linker.
  • Methods for recombinant protein expression and purification are well known, and include those described by Green and Sambrook, Molecular Cloning: A Laboratory Manual (4 th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)), the entire contents of which are incorporated herein by reference.
  • a suitable host cell refers to a cell that can host, replicate, and transfer a phage vector useful for a continuous evolution process as provided herein.
  • a suitable host cell is a cell that can be infected by the viral vector, can replicate it, and can package it into viral particles that can infect fresh host cells.
  • a cell can host a viral vector if it supports expression of genes of viral vector, replication of the viral genome, and/or the generation of viral particles.
  • One criterion to determine whether a cell is a suitable host cell for a given viral vector is to determine whether the cell can support the viral life cycle of a wild-type viral genome that the viral vector is derived from.
  • a suitable host cell would be any cell that can support the wild-type M13 phage life cycle.
  • Suitable host cells for viral vectors useful in continuous evolution processes are well known to those of skill in the art, and the disclosure is not limited in this respect.
  • the viral vector is a phage and the host cell is a bacterial cell.
  • the host cell is an E. coll cell. Suitable E.
  • a fresh host cell can, however, have been infected by a viral vector unrelated to the vector to be evolved or by a vector of the same or a similar type but not carrying the gene of interest.
  • the host cell is a prokaryotic cell, for example, a bacterial cell.
  • the host cell is an E. coli cell.
  • the host cell is a eukaryotic cell, for example, a yeast cell, an insect cell, or a mammalian cell.
  • the type of host cell will, of course, depend on the viral vector employed, and suitable host cell/viral vector combinations will be readily apparent to those of skill in the art.
  • the host cells are E. coli cells expressing the Fertility factor, also commonly referred to as the F factor, sex factor, or F-plasmid.
  • the F-factor is a bacterial DNA sequence that allows a bacterium to produce a sex pilus necessary for conjugation and is essential for the infection of E. coli cells with certain phage, for example, with M13 phage.
  • the host cells for M13-PACE are of the genotype F'proA + B +
  • AlacIZYA araD139 A(ara,leu)7697 mcrA
  • linker refers to a chemical group or a molecule linking two molecules or domains, e.g., nCas9 and a transglycosylase.
  • a linker joins a dCas9 and modification domain (e.g., a transglycosylase).
  • the linker is positioned between, or flanked by, two groups, molecules, or other domains and connected to each one via a covalent bond, thus connecting the two.
  • the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein).
  • the linker is an organic molecule, group, polymer, or synthetic chemical domain.
  • Chemical domains include, but are not limited to, amide, urea, carbamate, carbonate, an ester, acetal, ketal, phosphoramidite, hydrazone, imine, oxime, disulfide, silyl, hydrazine, hydrazone, thiol, imidazole, carbon-carbon bond, carbon-heteroatom bond, and azo domains.
  • the linker may comprise a moiety derived from a click chemistry reaction (e.g., triazole, diazole, diazine, sulfide bond, maleimide ring, succinimide ring, ester, amide).
  • the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated.
  • mutation refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue; a deletion or insertion of one or more residues within a sequence; or a substitution of a residue within a sequence of a genome in a subject to be corrected. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue.
  • Mutations can include a variety of categories, such as single base polymorphisms, microduplication regions, indel, and inversions, and is not meant to be limiting in any way. Mutations can include “loss-of- function” mutations which is the normal result of a mutation that reduces or abolishes a protein activity.
  • loss-of-function mutations are recessive, because in a heterozygote the second chromosome copy carries an unmutated version of the gene coding for a fully functional protein whose presence compensates for the effect of the mutation.
  • a loss-of-function mutation is dominant, one example being haploinsufficiency, where the organism is unable to tolerate the approximately 50% reduction in protein activity suffered by the heterozygote.
  • This is the explanation for a few genetic diseases in humans, including Marfan syndrome which results from a mutation in the gene for the connective tissue protein called fibrillin.
  • Mutations also embrace “gain-of-function” mutations, which is one which confers an abnormal activity on a protein or cell that is otherwise not present in a normal condition.
  • gain-of-function mutations are in regulatory sequences rather than in coding regions, and can therefore have a number of consequences. For example, a mutation might lead to one or more genes being expressed in the wrong tissues, these tissues gaining functions that they normally lack. Alternatively the mutation could lead to overexpression of one or more genes involved in control of the cell cycle, thus leading to uncontrolled cell division and hence to cancer. Because of their nature, gain-of-function mutations are usually dominant.
  • nucleic acid molecules or polypeptides e.g., Cas9 or transglycosylases
  • nucleic acid molecule or polypeptides e.g., Cas9 or transglycosylases
  • the nucleic acid molecule or the polypeptide is at least substantially free from at least one other component with which they are naturally associated in nature and/or as found in nature (e.g ., an amino acid sequence not found in nature).
  • nucleic acid refers to RNA as well as single- and/or double-stranded DNA. Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecule.
  • a nucleic acid molecule may be a non-naturally occurring molecule, e.g., a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurring nucleotides or nucleosides.
  • the terms “nucleic acid,” “DNA,” “RNA,” and/or similar terms include nucleic acid analogs, e.g., analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc.
  • nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications.
  • a nucleic acid sequence is presented in the 5' to 3' direction unless otherwise indicated.
  • a nucleic acid is or comprises natural nucleosides (e.g., adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5- bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenine, 8-
  • nucleic acid programmable D/RNA binding protein refers to any protein that may associate (e.g., form a complex) with one or more nucleic acid molecules (i.e., which may broadly be referred to as a “napR/DNAbp-programming nucleic acid molecule” and includes, for example, guide RNA in the case of Cas systems) which direct or otherwise program the protein to localize to a specific target nucleotide sequence (e.g., a gene locus of a genome) that is complementary to the one or more nucleic acid molecules (or a portion or region thereof) associated with the protein, thereby causing the protein to bind to the nucleotide sequence at the specific target site.
  • a specific target nucleotide sequence e.g., a gene locus of a genome
  • napR/DNAbp embraces napDNAbps such as CRISPR Cas9 proteins, as well as Cas9 equivalents, homologs, orthologs, or paralogs, whether naturally occurring or non-naturally occurring (e.g ., engineered or modified), and may include a Cas9 equivalent from any type of CRISPR system (e.g., type II, V, VI), including Cpfl (a type-V CRISPR-Cas systems), C2cl (a type V CRISPR-Cas system), C2c2 (a type VI CRISPR-Cas system, also known as Casl3a), C2c3 (a type V CRISPR-Cas system, also known as Casl2c), dCas9, GeoCas9, CjCas9, Casl2a, Casl2b, Casl2g, Casl2h, Casl2i, Casl3b, Casl3c, Casl3d, Casl4,
  • Cas homologs and variants such as an xCas9, an SpCas9- NG, an LbCasl2a, an AsCasl2a, a Cas9-KKH, a SmacCas9, and a Spy-macCas9.
  • Cas-equivalents are described in Makarova et al, “C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector,” Science 2016; 353 (6299), the contents of which are incorporated herein by reference.
  • nucleic acid programmable DNA binding protein that may be used in connection with this disclosure are not limited to CRISPR-Cas systems.
  • the disclosure embraces any such programmable protein, such as the Argonaute protein from Natronobacterium gregoryi (NgAgo) which may also be used for DNA-guided genome editing.
  • NgAgo-guide DNA system does not require a PAM sequence or guide RNA molecules, which means genome editing can be performed simply by the expression of generic NgAgo protein and introduction of synthetic oligonucleotides on any genomic sequence. See Gao et al, DNA- guided genome editing using the Natronobacterium gregoryi Argonaute. Nature Biotechnology 2016; 34(7):768-73, which is incorporated herein by reference.
  • the napR/DNAbp is a RNA-programmable nuclease, when in a complex with an RNA, may be referred to as a nuclease:RNA complex.
  • the bound RNA(s) is referred to as a guide RNA (gRNA).
  • gRNAs can exist as a complex of two or more RNAs, or as a single RNA molecule.
  • gRNAs that exist as a single RNA molecule may be referred to as single-guide RNAs (sgRNAs), though “gRNA” is used interchangeably to refer to guide RNAs that exist as either single molecules or as a complex of two or more molecules.
  • gRNAs that exist as single RNA species comprise two domains: (1) a domain that shares homology to a target nucleic acid (e.g., and directs binding of a Cas9 (or equivalent) complex to the target); and (2) a domain that binds a Cas9 protein.
  • domain (2) corresponds to a sequence known as a tracrRNA, and comprises a stem-loop structure.
  • domain (2) is homologous to a tracrRNA as depicted in Figure IE of Jinek et al., Science 337:816-821(2012), the entire contents of which is incorporated herein by reference.
  • gRNAs e.g., those including domain 2
  • a gRNA comprises two or more of domains (1) and (2), and may be referred to as an “extended gRNA.”
  • an extended gRNA will, e.g., bind two or more Cas9 proteins and bind a target nucleic acid at two or more distinct regions, as described herein.
  • the gRNA comprises a nucleotide sequence that complements a target site, which mediates binding of the nuclease/RNA complex to said target site, providing the sequence specificity of the nuclease:RNA complex.
  • the RNA- programmable nuclease is the (CRISPR-associated system) Cas9 endonuclease, for example Cas9 (Csnl) from Streptococcus pyogenes (see, e.g., “Complete genome sequence of an Ml strain of Streptococcus pyogenes Ferretti J.J. etal.., Proc. Natl. Acad. Sci. U.S.A.
  • the napR/DNAbp nucleases (e.g., Cas9) use RNA:DNA hybridization to target DNA cleavage sites, these proteins are able to be targeted, in principle, to any sequence specified by the guide RNA.
  • Methods of using napR/DNAbp nucleases, such as Cas9, for site-specific cleavage (e.g., to modify a genome) are known in the art (see e.g., Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013); Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013); Hwang, W.Y.
  • napR/DNAbp-programming nucleic acid molecule or equivalently “guide sequence” refers the one or more nucleic acid molecules which associate with and direct or otherwise program a napR/DNAbp protein to localize to a specific target nucleotide sequence (e.g ., a gene locus of a genome) that is complementary to the one or more nucleic acid molecules (or a portion or region thereof) associated with the protein, thereby causing the napR/DNAbp protein to bind to the nucleotide sequence at the specific target site.
  • a specific target nucleotide sequence e.g ., a gene locus of a genome
  • a non limiting example is a guide RNA of a Cas protein of a CRISPR-Cas genome editing system.
  • a nuclear localization signal or sequence is an amino acid sequence that tags, designates, or otherwise marks a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface. Different nuclear localized proteins may share the same NLS. An NLS has the opposite function of a nuclear export signal (NES), which targets proteins out of the nucleus. Thus, a single nuclear localization signal can direct the entity with which it is associated to the nucleus of a cell.
  • sequences can be of any size and composition, for example more than 25, 25, 15, 12, 10, 8, 7, 6, 5, or 4 amino acids, but will preferably comprise at least a four to eight amino acid sequence known to function as a nuclear localization signal (NLS).
  • nucleotide modification domain or “modification domain” embraces any protein, enzyme, or polypeptide (or variant thereof) which is capable of modifying or replacing or exchanging a DNA or RNA molecule (e.g. a DNA or RNA nucleobase). Nucleotide modification domains may be naturally occurring, or may be engineered.
  • a nucleotide modification domain can include one or more DNA repair enzymes, for example, and an enzyme or protein involved in homology-dependnent recombinational repair (HR), non-homologous end-joining repair (NHEJ), microhomology end-joining repair (MMEJ), mismatch repair (MMR), direct reversal repair, or other known DNA repair pathway.
  • a nucleotide modification domain can have one or more types of enzymatic activities, including, but not limited to, endonuclease activity, polymerase activity, ligase activity, replication activity, and proofreading activity.
  • Nucleotide modification domains include DNA or RNA-modifying enzymes and/or DNA or RNA-displacing enzymes, such as base exchange enzymes (e.g., transglycosylases), which covalently modify nucleobases leading in some cases to mutagenic corrections by way of normal cellular DNA repair and replication processes.
  • Exemplary nucleotide modification domains include, but are not limited to, a transglycosylase, a nuclease, a nickase, a recombinase, a methyltransferase, a methylase, an acetylase, an acetyltransferase, a transcriptional activator, or a transcriptional repressor domain.
  • the nucleotide modification domain is a transglycosylase (e.g., a TGT).
  • a transglycosylase e.g., a TGT.
  • oligonucleotide and polynucleotide can be used interchangeably to refer to a polymer of nucleotides (e.g ., a string of at least three nucleotides).
  • phage-assisted continuous evolution refers to continuous evolution that employs phage as viral vectors.
  • PACE phage-assisted continuous evolution
  • PCT/US 2009/056194 filed September 8, 2009, published as WO 2010/028347 on March 11, 2010; International PCT Application, PCT/US2011/066747, filed December 22, 2011, published as WO 2012/088381 on June 28, 2012; U.S. Patent No. 9,023,594, issued May 5, 2015; U.S. Patent No. 9,771,574, issued September 26, 2017; U.S. Patent No. 9,394,537, issued July 19, 2016; International PCT Application, PCT/US2015/012022, filed January 20, 2015, published as WO 2015/134121 on September 11, 2015; U.S. Patent No. 10,179,911, issued January 15, 2019; U.S. Patent No.
  • phage-assisted non-continuous evolution refers to non-continuous evolution that employs phage as viral vectors.
  • PANCE phage-assisted non-continuous evolution
  • PANCE is a simplified technique for rapid in vivo directed evolution using serial flask transfers of evolving ‘selection phage’ (SP), which contain a gene of interest to be evolved, across fresh E. coli host cells, thereby allowing genes inside the host E. coli to be held constant while genes contained in the SP continuously evolve. Following phage growth, an aliquot of infected cells is used to transfect a subsequent flask containing host E. coli. This process is continued until the desired phenotype is evolved, for as many transfers as required. Serial flask transfers have long served as a widely-accessible approach for laboratory evolution of microbes, and, more recently, analogous approaches have been developed for bacteriophage evolution.
  • the PANCE system features lower stringency than the PACE system.
  • promoter is art-recognized and refers to a nucleic acid molecule with a sequence recognized by the cellular transcription machinery and able to initiate transcription of a downstream gene.
  • a promoter can be constitutively active, meaning that the promoter is always active in a given cellular context, or conditionally active, meaning that the promoter is only active in the presence of a specific condition.
  • conditional promoter may only be active in the presence of a specific protein that connects a protein associated with a regulatory element in the promoter to the basic transcriptional machinery, or only in the absence of an inhibitory molecule.
  • a subclass of conditionally active promoters are inducible promoters that require the presence of a small molecule “inducer” for activity.
  • inducible promoters include, but are not limited to, arabinose-inducible promoters, Tet-on promoters, and tamoxifen-inducible promoters.
  • inducible promoters include, but are not limited to, arabinose-inducible promoters, Tet-on promoters, and tamoxifen-inducible promoters.
  • constitutive, conditional, and inducible promoters are well known to the skilled artisan, and the skilled artisan will be able to ascertain a variety of such promoters useful in carrying out the instant disclosure, which is not limited in this respect.
  • the specification provides vectors with appropriate promoters for driving expression of the nucleic acid sequences encoding the base editor fusion proteins (or one or more individual components thereof).
  • phage refers to a vims that infects bacterial cells.
  • phages consist of an outer protein capsid enclosing genetic material.
  • the genetic material may be ssRNA, dsRNA, ssDNA, or dsDNA, in either linear or circular form.
  • Phages and phage vectors are well known to those of skill in the art and non-limiting examples of phages that are useful for carrying out the methods provided herein are l, T2, T4, T7, T12, R17, M13, MS2, G4, PI, P2, P4, Phi X174, N4, F6, and F29.
  • the phage utilized in the present disclosure is M13. Additional suitable phages and host cells will be apparent to those of skill in the art and the disclosure is not limited in this aspect.
  • additional suitable phages and host cells see Elizabeth Kutter and Alexander Sulakvelidze: Bacteriophages: Biology and Applications . CRC Press; 1st edition (December 2004), ISBN: 0849313368; Martha R. J. Clokie and Andrew M.
  • Kropinski Bacteriophages: Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions (Methods in Molecular Biology) Humana Press; 1st edition (December, 2008), ISBN: 1588296822; Martha R. J. Clokie and Andrew M.
  • protein refers to a polymer of amino acid residues linked together by peptide (amide) bonds.
  • the terms refer to a protein, peptide, or polypeptide of any size, structure, or function. Typically, a protein, peptide, or polypeptide will be at least three amino acids long.
  • a protein, peptide, or polypeptide may refer to an individual protein or a collection of proteins.
  • One or more of the amino acids in a protein, peptide, or polypeptide may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a famesyl group, an isofamesyl group, a fatty acid group, a linker for conjugation, functionalization, or other modification, etc.
  • a protein, peptide, or polypeptide may also be a single molecule or may be a multi-molecular complex.
  • a protein, peptide, or polypeptide may be just a fragment of a naturally occurring protein or peptide.
  • a protein, peptide, or polypeptide may be naturally occurring, engineered, or synthetic, or any combination thereof.
  • fusion protein refers to a hybrid polypeptide which comprises protein domains from at least two different proteins.
  • One protein may be located at the amino-terminal (N-terminal) portion of the fusion protein or at the carboxy-terminal (C- terminal) protein thus forming an “amino-terminal fusion protein” or a “carboxy-terminal fusion protein,” respectively.
  • a protein may comprise different domains, for example, a nucleic acid binding domain (e.g ., the gRNA binding domain of Cas9 that directs the binding of the protein to a target site) and a nucleic acid cleavage domain or a catalytic domain of a recombinase.
  • a protein is in a complex with, or is in association with, a nucleic acid, e.g., RNA.
  • a nucleic acid e.g., RNA.
  • Any of the proteins provided herein may be produced by any method known in the art.
  • the proteins provided herein may be produced via recombinant protein expression and purification, which is especially suited for fusion proteins comprising a peptide linker. Methods for recombinant protein expression and purification are well known, and include those described by Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)), the entire contents of which are incorporated herein by reference.
  • recombinant protein or nucleic acid molecule comprises an amino acid or nucleotide sequence that comprises at least one, at least two, at least three, at least four, at least five, at least six, or at least seven mutations as compared to any naturally occurring sequence.
  • the term “subject,” as used herein, refers to an individual organism, for example, an individual mammal.
  • the subject is a human.
  • the subject is a non-human mammal.
  • the subject is a non-human primate.
  • the subject is a rodent.
  • the subject is a sheep, a goat, a cattle, a cat, or a dog.
  • the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode.
  • the subject is a research animal.
  • the subject is an experimental organism.
  • the subject is a plant.
  • the subject is genetically engineered, e.g., a genetically engineered non-human subject. The subject may be of either sex and at any stage of development.
  • target site refers to a sequence within a nucleic acid molecule that is edited by a base editor (e.g., an nCas9-transglycosylase fusion protein provided herein).
  • the target site further refers to the sequence within a nucleic acid molecule to which a complex of the base editor and gRNA binds.
  • transglycosylase refers to an enzyme that catalyzes the substutition of one glycoside for another through a nucleophilic attack at the glycosidic bond. Transglycosylase catalysis often involves the formation of a glycosyl-enzyme intermediate. As used herein, transglycosylases may refer to enzymes capable of catalyzing the substitution of one nucleoside for another. Exemplary transglycosylases of the disclosure are capable of forming a glycosyl-enzyme intermediate. Exemplary transglycosylases of the disclosure include naturally-occuring or engineered transglycosylases, such as tRNA-transglycosylases (TGTs) and deazapurine-in-DNA, gene A proteins (DpdA).
  • TGTs tRNA-transglycosylases
  • DpdA gene A proteins
  • vector may refer to a nucleic acid that has been modified to encode a gene of interest, and that is able to enter into a host cell, mutate, and replicate within the host cell, and then transfer a replicated form of the vector into another host cell.
  • vector may refer to a nucleic acid that has been modified to encode the base editor.
  • suitable vectors include viral vectors, such as retroviral vectors or bacteriophages and filamentous phage, and conjugative plasmids.
  • viral particle refers to a viral genome, for example, a DNA or RNA genome, that is associated with a coat of a viral protein or proteins, and, in some cases, with an envelope of lipids.
  • a phage particle comprises a phage genome packaged into a protein encoded by the wild type phage genome.
  • viral vector refers to a nucleic acid comprising a viral genome that, when introduced into a suitable host cell, can be replicated and packaged into viral particles able to transfer the viral genome into another host cell.
  • viral vector extends to vectors comprising truncated or partial viral genomes.
  • a viral vector is provided that lacks a gene encoding a protein essential for the generation of infectious viral particles.
  • suitable host cells for example, host cells comprising the missing gene under the control of a conditional promoter, however, such truncated viral vectors can replicate and generate viral particles able to transfer the truncated viral genome into another host cell.
  • the viral vector is an adeno- associated virus (AAV) vector.
  • AAV adeno- associated virus
  • treatment refers to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease, disorder, or condition, or one or more symptoms thereof, as described herein.
  • treatment refers to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease, disorder, or condition, or one or more symptoms thereof, as described herein.
  • treatment may be administered after one or more symptoms have developed and/or after a disease has been diagnosed.
  • treatment may be administered in the absence of symptoms, e.g., to prevent or delay onset of a symptom or inhibit onset or progression of a disease.
  • treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example, to prevent or delay their prevention or recurrence.
  • variant refers to a protein having characteristics that deviate from what occurs in nature, e.g., a “variant” is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the wild type protein.
  • a variant nucleotide modification domain is a nucleotide modification domain comprising one or more changes in amino acid residues of a transglycosylase, as compared to the wild type amino acid sequences thereof. These changes include chemical modifications, including substitutions of different amino acid residues, as well as truncations. This term embraces functional fragments of the wild type amino acid sequence.
  • the level or degree of which the property is retained may be reduced relative to the wild type protein but is typically the same or similar in kind. Generally, variants are overall very similar, and in many regions, identical to the amino acid sequence of the protein described herein. A skilled artisan will appreciate how to make and use variants that maintain all, or at least some, of a functional ability or property.
  • the variant proteins may comprise, or alternatively consist of, an amino acid sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100%, identical to, for example, the amino acid sequence of a wild-type protein, or any protein provided herein ( e.g ., Cas9 protein, fusion protein, and fusion protein protein).
  • polypeptides encompassed by the disclosure are polypeptides encoded by polynucleotides which hybridize to the complement of a nucleic acid molecule encoding a protein such as a Cas9 protein under stringent hybridization conditions (e.g., hybridization to filter bound DNA in 6x Sodium chloride/S odium citrate (SSC) at about 45 degrees Celsius, followed by one or more washes in 0.2.times.SSC, 0.1% SDS at about 50-65 degrees Celsius), under highly stringent conditions (e.g., hybridization to filter bound DNA in 6x sodium chloride/S odium citrate (SSC) at about 45 degrees Celsius, followed by one or more washes in O.lxSSC, 0.2% SDS at about 68 degrees Celsius), or under other stringent hybridization conditions which are known to those of skill in the art (see, for example, Ausubel, F. M. et al, eds., 1989 Current Protocol in Molecular Biology, Green Publishing Associates, Inc., and John Wi
  • polypeptide having an amino acid sequence at least, for example, 95%
  • amino acid sequence of the subject polypeptide is identical to the query sequence except that the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid sequence.
  • the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid sequence.
  • up to 5% of the amino acid residues in the subject sequence may be inserted, deleted, or substituted with another amino acid.
  • These alterations of the reference sequence may occur at the amino- or carboxy-terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
  • any particular polypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to, for instance, the amino acid sequence of a protein such as a Cas9 protein, can be determined conventionally using known computer programs.
  • a preferred method for determining the best overall match between a query sequence (a sequence of the present disclosure) and a subject sequence can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990)).
  • the query and subject sequences are either both nucleotide sequences or both amino acid sequences.
  • the result of said global sequence alignment is expressed as percent identity.
  • the percent identity is corrected by calculating the number of residues of the query sequence that are N- and C- terminal of the subject sequence, which are not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. Whether a residue is matched/aligned is determined by results of the FASTDB sequence alignment.
  • This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score.
  • This final percent identity score is what is used for the purposes of the present disclosure. Only residues to the N- and C-termini of the subject sequence, which are not matched/aligned with the query sequence, are considered for the purposes of manually adjusting the percent identity score. That is, only query residue positions outside the farthest N- and C-terminal residues of the subject sequence.
  • wild type is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from mutant or variant forms.
  • the present disclosure provides thymine-to-guanine or “TGBE” (or adenine-to- cytosine or “ACBE”) base editors which comprise a napR/DNAbp, or more specifically, a napDNAbp (e.g., a nCas9 domain), fused to a nucleotide modification domain comprising a transglycosylase.
  • TGBE base editors are capable of converting a T:A nucleobase pair to a G:C nucleobase pair in a target nucleotide sequence of interest, e.g., the genome of a cell.
  • the disclosed base editors may comprise an engineered transglycosylase variant that catalyzes the conversion of a target thymine to a guanine via the disruption and re-formation of a deoxyribose-nucleosidic bond (i.e., a nucleobase exchange, or base exchange, reaction).
  • the TGBEs of the disclosure may comprise a transglycosylase variant that catalyzes the conversion of a target thymine to a guanine via a base exchange reaction, and whereby the base-paired adenine of the non-edited strand is subsequently converted to a cytosine by the cell’s replication and mismatch repair machinery.
  • transglycosylation strategy an enzyme-catalyzed substitution of a thymine for a guanine is performed at the deoxyribose-nucleobase glycosidic bond (see FIG. 2), thereby substituting one nucleoside (thymidine) for another (deoxyguanosine).
  • a transglycosylase enzyme recognizes a target thymine base within a target sequence to which a single guide RNA (sgRNA) has complementarity and hybridizes.
  • sgRNA single guide RNA
  • the transglycosylase (e.g ., through an active site aspartate residue) excises the thymine from the 1 ' position of the deoxyribose sugar and covalently bonds to the sugar, thus forming a covalent glycosyl intermediate (for instance, TGT-DNA in cases where the transglycosylase is a TGT) (see FIG. 3).
  • a free guanine replaces the active site transglycosylase residue in a nucleophilic (backside) attack, re forming a glycosidic bond.
  • a base exchange is achieved by the targeted use of a fusion protein comprising a napDNAbp domain (e.g., a Cas9 nickase (“nCas9”) domain), a transglycosylase domain, and optionally a linker connecting these two domains (see FIG. 1).
  • a napDNAbp domain e.g., a Cas9 nickase (“nCas9”) domain
  • nCas9 Cas9 nickase
  • the transglycosylase domains of the disclosed base editors may comprise variants of wild-type transglycosylase enzymes. These variants may comprise an amino acid sequence that is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the wild type enzyme.
  • the transglycosylase domains may comprise an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, or more than 30 amino acids that differ relative to the amino acid sequence of the wild type enzyme.
  • the disclosed transglycosylase domains contain stretches of about 50, about 75, about 100, about 125, about 150, about 175, about 200, about 300, about 400, about 500, or more than 500 consecutive amino acids in common with the wild type enzyme.
  • the transglycosylase domains comprise truncations at the N-terminus or C-terminus relative to the wild-type enzyme.
  • the transglycosylase is a a tRNA guanine transglycosylase (“TGT”), or a variant thereof.
  • the transglycosylase is a bacterial TGT, or a variant thereof. In certain embodiments, the transglycosylase is an E. coli TGT, Pyrococcus horikoshii TGT, Zymomonas mobilis TGT, or a variant thereof.
  • the transglycosylase is a deazapurine-in-DNA, gene A protein (DpdA), or a variant thereof.
  • the transglycosylase is an E. coli DpdA, or a variant thereof.
  • the transglycosylase is a Salmonella enterica serovar Montevideo DpdA, Streptomyces sp. FXJ7.023 DpdA, Nocardioidaceae bacterium Broad- 1 DpdA, Desulfurobacterium thermolithotrophum DpdA, Cyanothece sp. CCY0110 DpdA, E.
  • the instant specification provides for TGBE base editors which overcome a need in the art for the installation of targeted transversions into a target nucleotide sequence, e.g., a genome.
  • the instant specification provides TGBE base editors (e.g., fusion proteins comprising an nCas9 domain and a transglycosylase domain) which overcome a need in the art for installation of targeted trans versions, particularly T:A to G:C trans versions.
  • compositions comprising the TGBE base editors as described herein, e.g., fusion proteins comprising an nCas9 domain and a transglycosylase domain, and one or more guide RNAs, e.g., a single-guide RNA (“sgRNA”).
  • sgRNA single-guide RNA
  • the instant specification provides for nucleic acid molecules encoding and/or expressing the TGBE base editors as described herein, as well as expression vectors and constructs for expressing the TGBE base editors described herein and/or a gRNA, host cells comprising said nucleic acid molecules and expression vectors and optionally vectors encoding one or more gRNAs, host cells comprising said TGBE base editors and optionally one or more gRNAs, and methods for delivering and/or administering nucleic acid-based embodiments described herein.
  • the present disclosure provides for methods of creating the TGBE base editors described herein, as well as methods of using the TGBE base editors or nucleic acid molecules encoding the TGBE base editors in applications including editing a nucleic acid molecule, e.g., a genome.
  • methods of engineering the TGBE base editors provided herein involve a phage-assisted continuous evolution (PACE) system or non-continuous system (e.g., PANCE), which may be utilized to evolve one or more components of the base editor (e.g ., a transglycosylase domain).
  • PACE phage-assisted continuous evolution
  • PANCE non-continuous system
  • methods of making the base editors comprise recombinant protein expression methodologies and techniques known to those of skill in the art.
  • the specification also provides methods for editing a target nucleic acid molecule, e.g., a single nucleotide within a genome, with a base editing system described herein (e.g., in the form of an evolved base editor as described herein, or a vector or construct encoding a base editor).
  • a base editing system described herein e.g., in the form of an evolved base editor as described herein, or a vector or construct encoding a base editor.
  • Such methods involve transducing (e.g., via transfection) cells with a plurality of complexes each comprising a base editor (e.g., a fusion protein comprising a Cas9 nickase (nCas9) domain and a transglycosylase domain) and optionally a gRNA molecule.
  • a base editor e.g., a fusion protein comprising a Cas9 nickase (nCas9) domain and a transglycosylase domain
  • the gRNA is bound to the napDNAbp domain (e.g., nCas9 domain) of the fusion protein.
  • the methods involve the transfection of nucleic acid constructs (e.g., plasmids), each of which encode the components of a complex of a base editor and gRNA.
  • the methods involve transfection of a nucleic acid construct that encodes both a base editor and a gRNA.
  • the disclosed methods comprise contacting a double- stranded DNA sequence with a complex comprising a fusion protein disclosed herein and a guide RNA, wherein the double- stranded DNA comprises a target T:A nucleobase pair; thereby substituting the thymine (T) of the T:A pair with a guanine.
  • the disclosed methods may alternatively result in substitution of the thymine (T) of the T:A pair with a 7-deazaguanine derivative; such that the cell thereby subsequently substitutes the 7-deazaguanine derivative with a guanine during a subsequent round of replication.
  • Exemplary 7-deazaguanine derivatives that may be substituted in the disclosed methods include, but are not limited to, 7- amino-methyl-7-deazaguanine, 7-cyano-7-deazaguanine (or 7-cyano-7-carbaguanine), 7- amido-7-deazaguanine, 2'-deoxy-7-amino-methyl-7-deazaguanosine, queuosine, prequeuosine, archaeosine, glycosylated queuosine, and derivatives thereof.
  • a nucleic acid construct e.g., a plasmid
  • a nucleic acid construct that encodes the fusion protein is transfected into the cell separately from the nucleic acid construct that encodes the gRNA molecule.
  • these components are encoded in a single construct and transfected together.
  • the methods disclosed herein involve the introduction into cells of a complex comprising a fusion protein and gRNA molecule that has been expressed and cloned outside of these cells.
  • any fusion protein e.g., any of the fusion proteins described herein, may be introduced into the cell in any suitable way, either stably or transiently.
  • a fusion protein may be transfected into the cell.
  • the cell may be transduced or transfected with a nucleic acid construct that encodes a fusion protein.
  • a cell may be transduced (e.g., with a virus encoding a fusion protein) with a nucleic acid that encodes a fusion protein, or the translated fusion protein.
  • a cell may be transfected (e.g., with a plasmid encoding a fusion protein) with a nucleic acid that encodes a fusion protein, or the translated fusion protein.
  • Such transductions or transfections may be stable or transient.
  • cells expressing a fusion protein or containing a fusion protein may be transduced or transfected with one or more gRNA molecules, for example when the fusion protein comprises a Cas9 (e.g., nCas9) domain.
  • a plasmid expressing a fusion protein may be introduced into cells through electroporation, transient (e.g., lipofection), stable genome integration (e.g., piggybac), viral transduction, or other methods known to those of skill in the art.
  • transient e.g., lipofection
  • stable genome integration e.g., piggybac
  • viral transduction or other methods known to those of skill in the art.
  • the methods described herein result in cutting (or nicking) one strand of the double- stranded DNA, for example, the strand that includes the adenine (A) of the target T: A nucleobase pair opposite the strand containing the target thymine (T) that is being excised.
  • This nicking result serves to direct mismatch repair machinery to the non- edited strand, ensuring that the modified nucleotide is not interpreted as a lesion by the cell’s machinery, but rather as a template for subsequent replication at the target site.
  • This nick may be created by the use of an nCas9.
  • the target nucleotide sequence may comprise a target sequence (e.g., a point mutation) associated with a disease, disorder, or condition, such as congenital deafness, spastic paraplegia, nonsyndromic hearing loss, spinal muscular atrophy, or hypohidrotic ectodermal dysplasia.
  • the target sequence may comprise a G to T point mutation associated with a disease, disorder, or condition, and wherein the TGBE-mediated exchange of the mutant T base results in mismatch repair-mediated correction to a sequence that is not associated with a disease, disorder, or condition.
  • the target sequence may comprise a C to A point mutation associated with a disease, disorder, or condition, and wherein the TGBE-mediated exchange of the mutant T base that is paired with the mutant A base results in mismatch repair- mediated correction to a sequence that is not associated with a disease, disorder, or condition.
  • the target sequence may encode a protein, and the point mutation is in a codon and results in a change in the amino acid encoded by the mutant codon as compared to a wild-type codon.
  • the target sequence may also be at a splice site, and the point mutation results in a change in the splicing of an mRNA transcript as compared to the wild-type transcript.
  • the target may be at a non-coding sequence of a gene, such as a gene promoter or gene repressor, and the point mutation results in increased or decreased expression of the gene.
  • Exemplary target genes include GJB2, in which a G to T point mutation at residue 139 results in a congenital deafness phenotype; and SPG11, in which a C to A point mutation at residue 2877 results in a apastic paraplegia phenotype.
  • Additional target genes include OTOF (associated with nonsyndromic hearing loss), IGHMBP2 (associated with spinal muscular atrophy), and EDAR (associated with hypohidrotic ectodermal dysplasia), for which the disease phenotype is frequently caused by C:G to A:T point mutations.
  • C:G to A:T point mutations introduce premature stop codons (UAA, UAG, UGA), resulting in nonsense mutations in protein coding regions.
  • UAA premature stop codon
  • UAG UAG
  • UGA premature stop codons
  • exemplary TGBEs disclosed herein correct these disease alleles in somatic cells, reducing or removing morbidity.
  • exemplary TGBEs disclosed herein may install disease- suppressing alleles in somatic cells.
  • the base exchange of a mutant T results in correction of the nonsense mutation and restoration of the wild-type codon, which may result in the expression of a full-length, wild-type peptide sequence.
  • the application of the base editors to target genetic sequences may induce a change in the mRNA transcript, such as restoring the mRNA transcript to a wild-type state.
  • the methods described herein involve contacting any of the disclosed fusion proteins (or base editors) with a target nucleotide sequence in vitro, ex vivo, or in vivo.
  • the step of contacting occurs in a subject.
  • the subject has been diagnosed with a disease, disorder, or condition, such as, but not limited to, a disease, disorder, or condition associated with a point mutation in a gene that may be any gene.
  • the methods described herein involve contacting a fusion protein with a target gene sequence in vitro, ex vivo, or in vivo.
  • the gene is selected from the GJB2 gene, the IGHMBP2 gene, the OTOF gene, the EDAR gene, or the SPG11 gene.
  • the specification discloses a pharmaceutical composition comprising any one of the disclosed base editor fusion proteins. In one aspect, the specification discloses a pharmaceutical composition comprising any one of the disclosed complexes of a fusion protein and gRNA. In one aspect, the specification discloses a pharmaceutical composition comprising a polynucleotide encoding the fusion proteins disclosed herein and a polynucleotide encoding a gRNA, or a polynucleotide encoding both. In another aspect, the specification discloses a pharmaceutical composition comprising any one of the disclosed vectors.
  • the nucleotide modification domain is a transglycosylase that enzymatically exchanges a thymine nucleobase of a T:A nucleobase pair with a guanine.
  • the transglycosylase enzymatically exchanges a thymine nucleobase of a T:A nucleobase pair with a 7-deazaguanine derivative, which is subsequently converted by the cell’s DNA repair and replication machinery to a guanine.
  • the T:A nucleobase pair is ultimately converted to a G:C nucleobase pair.
  • the various domains of the transversion fusion proteins described herein may be obtained as a result of mutagenizing a reference base editor (or a component or domain thereof) by a directed evolution process, e.g., a continuous evolution method (e.g., PACE) or a non-continuous evolution method (e.g., PANCE or other discrete plate-based selections).
  • a directed evolution process e.g., a continuous evolution method (e.g., PACE) or a non-continuous evolution method (e.g., PANCE or other discrete plate-based selections).
  • the disclosure provides a base editor that has one or more amino acid variations introduced into its amino acid sequence relative to the amino acid sequence of the reference base editor.
  • the base editor may include variants in one or more components or domains of the base editor (e.g., variants introduced into a Cas9 domain, variants introduced into a transglycosylase domain, or variants introduced into both of these domains).
  • the nucleotide modification domain may be engineered in any way known to those of skill in the art.
  • the nucleotide modification domain may be evolved from a reference protein that is an RNA modifying enzyme (e.g., a tRNA guanine transglycosylase) and evolved using PACE, PANCE, or other plate-based evolution methods to obtain a DNA modifying version of the nucleotide modification domain, which can then be used in the fusion proteins described herein.
  • RNA modifying enzyme e.g., a tRNA guanine transglycosylase
  • the disclosed transglycosylase variants may be at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the reference enzyme.
  • the transglycosylase variant may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,
  • the transglycosylase variant comprises multiple amino acid stretches having about 99.9% identity, followed by one or more stretches having at least about 90% or at least about 95% identity, followed by streteches of having about 99.9% identity, to the corresponding amino acid sequence of the reference transglycosylase.
  • the base editors described herein comprise a nucleic acid programmable DNA binding (napDNAbp) domain.
  • the napDNAbp is associated with at least one guide nucleic acid (e.g ., guide RNA), which localizes the napDNAbp to a DNA sequence that comprises a DNA strand ( i.e ., a target strand) that is complementary to the guide nucleic acid, or a portion thereof (e.g., the protospacer of a guide RNA).
  • the guide nucleic-acid “programs” the napDNAbp domain to localize and bind to a complementary sequence of the target strand. Binding of the napDNAbp domain to a complementary sequence enables the nucleobase modification domain of the base editor to access and enzymatically deaminate a target thymine base in the target strand.
  • the napDNAbp can be a CRISPR (clustered regularly interspaced short palindromic repeat)-associated nuclease.
  • CRISPR is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids).
  • CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids.
  • CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
  • crRNA CRISPR RNA
  • type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (me) and a Cas9 protein.
  • the tracrRNA serves as a guide for ribonuclease 3- aided processing of pre-crRNA. Subsequently, Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3 '-5' exonucleolytically. In nature, DNA-binding and cleavage typically requires protein and both RNAs. However, single guide RNAs (“sgRNA”, or simply “gNRA”) can be engineered so as to incorporate aspects of both the crRNA and tracrRNA into a single RNA species.
  • sgRNA single guide RNAs
  • the binding mechanism of a napDNAbp - guide RNA complex includes the step of forming an R-loop whereby the napDNAbp induces the unwinding of a double-strand DNA target, thereby separating the strands in the region bound by the napDNAbp.
  • the guideRNA protospacer then hybridizes to the “target strand.” This displaces a “non-target strand” that is complementary to the target strand, which forms the single strand region of the R-loop.
  • the napDNAbp includes one or more nuclease activities, which cuts the DNA leaving various types of lesions (e.g ., a nick in one strand of the DNA).
  • the napDNAbp may comprises a nuclease activity that cuts the non-target strand at a first location, and / or cuts the target strand at a second location.
  • the target DNA can be cut to form a “double- stranded break” whereby both strands are cut.
  • the target DNA can be cut at only a single site, i.e., the DNA is “nicked” on one strand.
  • the base editors may comprise the canonical SpCas9, or any ortholog Cas9 protein, or any variant Cas9 protein — including any naturally occurring variant, mutant, or otherwise engineered version of Cas9 — that is known or which can be made or evolved through a directed evolution or otherwise mutagenic process.
  • the napDNAbp has a nickase activity, i.e., only cleave one strand of the target DNA sequence.
  • the napDNAbp has an inactive nuclease, e.g., are “dead” proteins.
  • Cas9 proteins that may be used are those having a smaller molecular weight than the canonical SpCas9 (e.g., for easier delivery) or having modified or rearranged primary amino acid sequence (e.g., the circular permutant forms).
  • the base editors described herein may also comprise Cas9 equivalents, including Casl2a/Cpfl and Casl2b proteins.
  • the napDNAbps used herein e.g., an SpCas9 or SpCas9 variant
  • the disclosure contemplates any Cas9, Cas9 variant, or Cas9 equivalent which has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.9% sequence identity to a reference Cas9 sequence, such as a reference SpCas9 canonical sequence (set forth in SEQ ID NO: 9), a reference SaCas9 canonical sequence (set forth in SEQ ID NO: 79), or a reference Cas9 equivalent (e.g., Casl2a/Cpfl).
  • a reference Cas9 sequence such as a reference SpCas9 canonical sequence (set forth in SEQ ID NO: 9), a reference SaCas9 canonical sequence (set forth in SEQ ID NO: 79), or a reference Cas9 equivalent (e.g., Casl
  • the napDNAbp directs cleavage of one or both strands at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the napDNAbp directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S.
  • D10A aspartate-to-alanine substitution
  • pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand).
  • Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A in reference to the canonical SpCas9 sequence, or to equivalent amino acid positions in other Cas9 variants or Cas9 equivalents.
  • Cas protein refers to a full-length Cas protein obtained from nature, a recombinant Cas protein having a sequences that differs from a naturally occurring Cas protein, or any fragment of a Cas protein that nevertheless retains all or a significant amount of the requisite basic functions needed for the disclosed methods, i.e., (i) possession of nucleic-acid programmable binding of the Cas protein to a target DNA, and (ii) ability to nick the target DNA sequence on one strand.
  • the Cas proteins contemplated herein embrace CRISPR Cas9 proteins, as well as Cas9 equivalents, variants (e.g., Cas9 nickase (nCas9) or nuclease inactive Cas9 (dCas9)) homologs, orthologs, or paralogs, whether naturally occurring or non-naturally occurring (e.g., engineered or recombinant), and may include a Cas9 equivalent from any type of CRISPR system (e.g., type II, V, VI), including Cpfl (a type-V CRISPR-Cas systems), C2cl (a type V CRISPR-Cas system), C2c2 (a type VI CRISPR-Cas system) and C2c3 (a type V CRISPR-Cas system).
  • Cpfl a type-V CRISPR-Cas systems
  • C2cl a type V CRISPR-Cas system
  • C2c2 a type VI CRISPR-Ca
  • C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector,” Science 2016; 353(6299), the contents of which are incorporated herein by reference.
  • Cas9 or “Cas9 domain” embraces any naturally occurring Cas9 from any organism, any naturally-occurring Cas9 equivalent or functional fragment thereof, any Cas9 homolog, ortholog, or paralog from any organism, and any mutant or variant of a Cas9, naturally-occurring or engineered.
  • the term Cas9 is not meant to be particularly limiting and may be referred to as a “Cas9 or equivalent.”
  • Exemplary Cas9 proteins are further described herein and/or are described in the art and are incorporated herein by reference. The present disclosure is unlimited with regard to the particular napDNAbp that is employed in the base editors of the disclosure.
  • Cas9 and Cas9 equivalents are provided as follows; however, these specific examples are not meant to be limiting.
  • the base editors of the present disclosure may use any suitable napDNAbp, including any suitable Cas9 or Cas9 equivalent.
  • the base editor constructs described herein may comprise the “canonical SpCas9” nuclease from S. pyogenes, which has been widely used as a tool for genome engineering.
  • This Cas9 protein is a large, multi-domain protein containing two distinct nuclease domains. Point mutations can be introduced into Cas9 to abolish one or both nuclease activities, resulting in a nickase Cas9 (nCas9) or dead Cas9 (dCas9), respectively, that still retains its ability to bind DNA in a sgRNA-programmed manner.
  • Cas9 or variant thereof can target that protein to virtually any DNA sequence simply by co-expression with an appropriate sgRNA.
  • the canonical SpCas9 protein refers to the wild type protein from Streptococcus pyogenes having the following amino acid sequence:
  • the base editors described herein may include canonical SpCas9, or any variant thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with a wild type Cas9 sequence provided above.
  • These variants may include SpCas9 variants containing one or more mutations, including any known mutation reported with the SwissProt Accession No. Q99ZW2 entry, which include:
  • the base editors described herein may include any of the above SpCas9 sequences, or any variant thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.
  • the Cas9 protein can be a wild type Cas9 ortholog from another bacterial species.
  • the following Cas9 orthologs can be used in connection with the base editor constructs described in this disclosure.
  • any variant Cas9 orthologs having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to any of the below orthologs may also be used with the disclosed base editors.
  • the base editors described herein may include any of the above Cas9 ortholog sequences, or any variants thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.
  • the napDNAbp may include any suitable homologs and/or orthologs or naturally occurring enzymes, such as Cas9.
  • Cas9 homologs and/or orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus .
  • the Cas moiety is configured (e.g, mutagenized, recombinantly engineered, or otherwise obtained from nature) as a nickase, i.e., capable of cleaving only a single strand of the target double-stranded nucleic acid.
  • Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference.
  • a Cas9 nuclease has an inactive (e.g., an inactivated) DNA cleavage domain, that is, the Cas9 is a nickase.
  • the Cas9 protein comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 3. In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of a Cas9 protein as provided by any one of the Cas9 orthologs in the above tables.
  • the disclosed base editors may comprise a catalytically inactive, or “dead,” napDNAbp domain.
  • exemplary catalytically inactive domains in the disclosed base editors are dead S. pyogenes Cas9 (dSpCas9) and S. pyogenes Cas9 nickase (SpCas9n).
  • the base editors described herein may include a dead Cas9, e.g., dead SpCas9, which has no nuclease activity due to one or more mutations that inactivate both nuclease domains of SpCas9, namely the RuvC domain (which cleaves the non-protospacer DNA strand) and HNH domain (which cleaves the protospacer DNA strand).
  • the nuclease inactivation may be due to one or mutations that result in one or more substitutions and/or deletions in the amino acid sequence of the encoded protein, or any variants thereof having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.
  • the base editors described herein may include a dead Cas9, e.g., dead SpCas9, which has no nuclease activity due to one or more mutations that inactivate both nuclease domains of SpCas9, namely the RuvC domain (which cleaves the non-protospacer DNA strand) and HNH domain (which cleaves the protospacer DNA strand).
  • the D10A and N580A mutations in the wild-type S. aureus Cas9 amino acid sequence may be used to form a dSaCas9.
  • the napDNAbp domain of the base editors provided herein comprises a dSaCas9 that has D10A and N580A mutations relative to the wild-type SaCas9 sequence (SEQ ID NO: 79).
  • dCas9 refers to a nuclease-inactive Cas9 or nuclease-dead Cas9, or a functional fragment thereof, and embraces any naturally occurring dCas9 from any organism, any naturally-occurring dCas9 equivalent or functional fragment thereof, any dCas9 homolog, ortholog, or paralog from any organism, and any mutant or variant of a dCas9, naturally-occurring or engineered.
  • dCas9 is not meant to be particularly limiting and may be referred to as a “dCas9 or equivalent.”
  • Exemplary dCas9 proteins and method for making dCas9 proteins are further described herein and/or are described in the art and are incorporated herein by reference.
  • dCas9 corresponds to, or comprises in part or in whole, a Cas9 amino acid sequence having one or more mutations that inactivate the Cas9 nuclease activity.
  • Cas9 variants having mutations other than D10A and H840A are provided which may result in the full or partial inactivate of the endogenous Cas9 nuclease activity (e.g ., nCas9 or dCas9, respectively).
  • Such mutations include other amino acid substitutions at DIO and H820, or other substitutions within the nuclease domains of Cas9 (e.g., substitutions in the HNH nuclease subdomain and/or the RuvCl subdomain) with reference to a wild type sequence such as Cas9 from Streptococcus pyogenes (NCBI Reference Sequence: NC_017053.1).
  • variants or homologues of Cas9 are provided which are at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to NCBI Reference Sequence: NC_017053.1.
  • variants of dCas9 are provided having amino acid sequences which are shorter, or longer than NC_017053.1 by about 5 amino acids, by about 10 amino acids, by about 15 amino acids, by about 20 amino acids, by about 25 amino acids, by about 30 amino acids, by about 40 amino acids, by about 50 amino acids, by about 75 amino acids, by about 100 amino acids or more.
  • the napDNAbp domain of any of the disclosed base editors comprises a dead S. pyogenes Cas9 (dSpCas9).
  • the napDNAbp domain of any of the disclosed based editors is comprises at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 93.
  • the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 93.
  • the dead Cas9 may be based on the canonical SpCas9 sequence of Q99ZW2 and may have the following sequence, which comprises D10A and an H810A substitutions (underlined and bolded) in, or a variant of SEQ ID NO: 93, having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto:
  • the disclosed base editors may comprise a napDNAbp domain that comprises a nickase.
  • the base editors described herein comprise a Cas9 nickase.
  • the term “Cas9 nickase” of “nCas9” refers to a variant of Cas9 which is capable of introducing a single-strand break in a double strand DNA molecule target.
  • the Cas9 nickase comprises only a single functioning nuclease domain.
  • the wild type Cas9 (e.g., the canonical SpCas9) comprises two separate nuclease domains, namely, the RuvC domain (which cleaves the non-protospacer DNA strand) and HNH domain (which cleaves the protospacer DNA strand).
  • the Cas9 nickase comprises a mutation in the RuvC domain which inactivates the RuvC nuclease activity.
  • nickase mutations in the RuvC domain could include D10X, H983X, D986X, or E762X, wherein X is any amino acid other than the wild type amino acid.
  • the nickase could be D10A, of H983A, or D986A, or E762A, or a combination thereof.
  • the napDNAbp domain of any of the disclosed base editors comprises an S. pyogenes Cas9 nickase (SpCas9n).
  • the napDNAbp domain of any of the disclosed based editors is comprises at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 99.
  • the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 99.
  • the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 99.
  • the napDNAbp domain of any of the disclosed base editors comprises an S.
  • the napDNAbp domain of any of the disclosed based editors is comprises at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 99.
  • the napDNAbp domain of any of the disclosed base editors comprises the amino acid sequence of SEQ ID NO: 99.
  • the Cas9 nickase can having a mutation in the RuvC nuclease domain and have one of the following amino acid sequences, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.
  • the Cas9 nickase comprises a mutation in the HNH domain which inactivates the HNH nuclease activity.
  • mutations in histidine (H) 840 or asparagine (R) 863 have been reported as loss-of-function mutations of the HNH nuclease domain and the creation of a functional Cas9 nickase (e.g., Nishimasu el al, “Crystal structure of Cas9 in complex with guide RNA and target DNA,” Cell 156(5), 935-949, which is incorporated herein by reference).
  • nickase mutations in the HNH domain could include H840X and R863X, wherein X is any amino acid other than the wild type amino acid.
  • the nickase could be H840A or R863A or a combination thereof.
  • the Cas9 nickase can have a mutation in the HNH nuclease domain and have one of the following amino acid sequences, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.
  • the N-terminal methionine is removed from a Cas9 nickase, or from any Cas9 variant, ortholog, or equivalent disclosed or contemplated herein.
  • methionine-minus Cas9 nickases include the following sequences, or a variant thereof having an amino acid sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity thereto.
  • the napDNAbp domains used in the base editors described herein may also include other Cas9 variants that area at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference Cas9 protein, including any wild type Cas9, or mutant Cas9 (e.g., a dead Cas9 or Cas9 nickase), or circular permutant Cas9, or other variant of Cas9 disclosed herein or known in the art.
  • a Cas9 variant may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 21, 24, 25, 26, 27, 28, 29, 30,
  • the Cas9 variant comprises a fragment of a reference Cas9 (e.g., a gRNA binding domain or a DNA-cleavage domain), such that the fragment is at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to the corresponding fragment of wild type Cas9.
  • a reference Cas9 e.g., a gRNA binding domain or a DNA-cleavage domain
  • the fragment is at least 30%, at least 35%, 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% identical, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% of the amino acid length of a corresponding wild type Cas9 (e.g., SEQ ID NO: 9).
  • a corresponding wild type Cas9 e.g., SEQ ID NO: 9
  • the disclosure also may utilize Cas9 fragments which retain their functionality, and which are fragments of any Cas9 protein disclosed herein.
  • the Cas9 fragment is at least 100 amino acids in length.
  • the fragment is at least 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, or at least 1300 amino acids in length.
  • the base editors disclosed herein may comprise one of the Cas9 variants described as follows, or a Cas9 variant thereof having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference Cas9 variants.
  • the base editors described herein can include any Cas9 equivalent.
  • Cas9 equivalent is a broad term that encompasses any napDNAbp protein that serves the same function as Cas9 in the present base editors despite that its amino acid primary sequence and/or its three-dimensional structure may be different and/or unrelated from an evolutionary standpoint.
  • Cas9 equivalents include any Cas9 ortholog, homolog, mutant, or variant described or embraced herein that are evolutionarily related
  • the Cas9 equivalents also embrace proteins that may have evolved through convergent evolution processes to have the same or similar function as Cas9, but which do not necessarily have any similarity with regard to amino acid sequence and/or three dimensional structure.
  • the base editors described here embrace any Cas9 equivalent that would provide the same or similar function as Cas9 despite that the Cas9 equivalent may be based on a protein that arose through convergent evolution.
  • CasX is a Cas9 equivalent that reportedly has the same function as Cas9 but which evolved through convergent evolution.
  • Cas9 is a bacterial enzyme that evolved in a wide variety of species. However, the Cas9 equivalents contemplated herein may also be obtained from archaea, which constitute a domain and kingdom of single-celled prokaryotic microbes different from bacteria.
  • Cas9 equivalents may refer to CasX or CasY, which have been described in, for example, Burstein et al, “New CRISPR-Cas systems from uncultivated microbes.” Cell Res. 2017 Feb 21. doi: 10.1038/cr.2017.21, the entire contents of which is hereby incorporated by reference.
  • genome-resolved metagenomics a number of CRISPR-Cas systems were identified, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in little- studied nanoarchaea as part of an active CRISPR-Cas system.
  • Cas9 refers to CasX, or a variant of CasX. In some embodiments, Cas9 refers to a CasY, or a variant of CasY. It should be appreciated that other RNA-guided DNA binding proteins may be used as a nucleic acid programmable DNA binding protein (napDNAbp), and are within the scope of this disclosure. Also see Liu et al, “CasX enzymes comprises a distinct family of RNA-guided genome editors,” Nature , 2019, Vol.566: 218-223. Any of these Cas9 equivalents are contemplated.
  • the Cas9 equivalent comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring CasX or CasY protein.
  • the napDNAbp is a naturally-occurring CasX or CasY protein.
  • the napDNAbp comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a wild-type Cas moiety or any Cas moiety provided herein.
  • the nucleic acid programmable DNA binding proteins include, without limitation, Cas9 (e.g ., dCas9 and nCas9), CasX, CasY, Cpfl, C2cl, C2c2, C2C3, Argonaute, Casl2a, and Casl2b.
  • Cas9 e.g ., dCas9 and nCas9
  • CasX CasY
  • Cpfl C2cl
  • C2c2, C2C3, Argonaute Casl2a
  • Casl2b e.g., dCas9 and nCas9
  • Cpfl is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif (TTN, TTTN, or YTN). Moreover, Cpfl cleaves DNA via a staggered DNA double-stranded break.
  • TTN T-rich protospacer-adjacent motif
  • TTTN TTTN
  • YTN T-rich protospacer-adjacent motif
  • the Cas protein may include any CRISPR associated protein, including but not limited to Casl2a, Casl2b, Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (sometimes referred to as Csnl and Csxl2), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2.
  • a nickase mutation e.g., a mutation corresponding to the D10A mutation of the wild type SpCas9 polypeptide of SEQ ID NO: 9).
  • the napDNAbp can be any of the following proteins: a Cas9, a Cpfl, a CasX, a CasY, a C2cl, a C2c2, a C2c3, a GeoCas9, a CjCas9, a Casl2a, a Casl2b, a Casl2g, a Casl2h, a Casl2i, a Casl3b, a Casl3c, a Casl3d, a Casl4, a Csn2, an xCas9, an SpCas9-NG, a circularly permuted Cas9, or an Argonaute (Ago), a Cas9-KKH, a SmacCas9, a Spy-macCas9, an SpCas9-VRQR, an SpCas9-NRRH, an SpaCas9-
  • the base editors contemplated herein can include a Cas9 protein that is of smaller molecular weight than the canonical SpCas9 sequence.
  • the smaller-sized Cas9 variants may facilitate delivery to cells, e.g., by an expression vector, nanoparticle, or other means of delivery.
  • the canonical SpCas9 protein is 1368 amino acids in length and has a predicted molecular weight of 158 kilodaltons.
  • small-sized Cas9 variant refers to any Cas9 variant — naturally occurring, engineered, or otherwise — that is less than at least 1300 amino acids, or at least less than 1290 amino acids, or than less than 1280 amino acids, or less than 1270 amino acid, or less than 1260 amino acid, or less than 1250 amino acids, or less than 1240 amino acids, or less than 1230 amino acids, or less than 1220 amino acids, or less than 1210 amino acids, or less than 1200 amino acids, or less than 1190 amino acids, or less than 1180 amino acids, or less than 1170 amino acids, or less than 1160 amino acids, or less than 1150 amino acids, or less than 1140 amino acids, or less than 1130 amino acids, or less than 1120 amino acids, or less than 1110 amino acids, or less than 1100 amino acids, or less than 1050 amino acids, or less than 1000 amino acids, or less than 950 amino acids, or less than 900 amino acids, or less than 850 amino acids, or less than 800 amino acids
  • the base editors disclosed herein may comprise one of the small-sized Cas9 variants described as follows, or a Cas9 variant thereof having at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% identical to any reference small-sized Cas9 protein.
  • Exemplary small-sized Cas9 variants include, but are not limited to, SaCas9 and LbCasl2a.
  • the base editors described herein may also comprise Casl2a/Cpfl (dCpfl) variants that may be used as a guide nucleotide sequence- programmable DNA-binding protein domain.
  • the Casl2a/Cpfl protein has a RuvC-like endonuclease domain that is similar to the RuvC domain of Cas9 but does not have a HNH endonuclease domain, and the N-terminal of Cpfl does not have the alpha-helical recognition lobe of Cas9.
  • Additional exemplary Cas9 equivalent protein sequences can include the following: ncipDNAbps that recognize non-canonical PAM sequences
  • the napDNAbp is a nucleic acid programmable DNA binding protein that does not require a canonical (NGG) PAM sequence.
  • the napDNAbp is an argonaute protein.
  • NgAgo is a ssDNA-guided endonuclease. NgAgo binds 5' phosphorylated ssDNA of ⁇ 24 nucleotides (gDNA) to guide it to its target site and will make DNA double-strand breaks at the gDNA site.
  • NgAgo-gDNA system does not require a protospacer-adjacent motif (PAM).
  • PAM protospacer-adjacent motif
  • the disclosure provides napDNAbp domains that comprise SpCas9 variants that recognize and work best with NRRH, NRCH, and NRTH PAMs. See PCT Application No. PCT/US2019/47996, incorporated by reference herein.
  • the disclosed base editors comprise a napDNAbp domain selected from SpCas9-NRRH, SpCas9-NRTH, and SpCas9-NRCH.
  • the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SpCas9-NRRH.
  • the disclosed base editors comprise a napDNAbp domain that comprises SpCas9-NRRH.
  • the SpCas9-NRRH has an amino acid sequence as presented in SEQ ID NO: 128 (underlined residues are mutated relative to SpCas9, as set forth in SEQ ID NO: 9).
  • the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SpCas9-NRCH.
  • the disclosed base editors comprise a napDNAbp domain that comprises SpCas9-NRCH.
  • the SpCas9-NRCH has an amino acid sequence as presented in SEQ ID NO: 129 (underligned residues are mutated relative to SpCas9).
  • the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SpCas9-NRTH.
  • the disclosed base editors comprise a napDNAbp domain that comprises SpCas9-NRTH.
  • the SpCas9-NRTH has an amino acid sequence as presented in SEQ ID NO: 130 (underligned residues are mutated relative to SpCas9).
  • the napDNAbp of any of the disclosed base editors comprises a Cas9 derived from a Streptococcus macacae, e.g. Streptococcus macacae NCTC 11558, or SmacCas9, or a variant thereof.
  • the napDNAbp comprises a hybrid variant of SmacCas9 that incorporates an SpCas9 domain with the SmacCas9 domain and is known as Spy-macCas9, or a variant thereof.
  • the napDNAbp comprises a hybrid variant of SmacCas9 that incorporates an increased nucleolytic variant of an SpCas9 (iSpy Cas9) domain and is known as iSpy-macCas9.
  • iSpy Cas9 Relative to Spymac-Cas9, iSpyMac-Cas9 contains two mutations, R221K and N394K, that were identified by deep mutational scans of Spy Cas9 that raise modification rates of the protein on most targets. See Jakimo el al, bioRxiv, A Cas9 with Complete PAM Recognition for Adenine Dinucleotides (Sep 2018), herein incorporated by reference. Jakimo et al.
  • the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to iSpyMac-Cas9.
  • the disclosed base editors comprise a napDNAbp domain that comprises iSpyMac-Cas9.
  • the iSpyMac-Cas9 has an amino acid sequence as presented in SEQ ID NO: 131 (R221K and N394K mutations are underlined).
  • the napDNAbp of any of the disclosed base editors is a prokaryotic homolog of an Argonaute protein.
  • Prokaryotic homologs of Argonaute proteins are known and have been described, for example, in Makarova K., el al, “Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements”, Biol Direct. 2009 Aug 25;4:29. doi: 10.1186/1745-6150-4-29, the entire contents of which is hereby incorporated by reference.
  • the napDNAbp is a Marinitoga piezophila Argunaute (MpAgo) protein.
  • the CRISPR-associated Marinitoga piezophila Argunaute (MpAgo) protein cleaves single- stranded target sequences using 5'-phosphorylated guides.
  • the 5' guides are used by all known Argonautes.
  • the crystal structure of an MpAgo-RNA complex shows a guide strand binding site comprising residues that block 5' phosphate interactions. This data suggests the evolution of an Argonaute subclass with noncanonical specificity for a 5'-hydroxylated guide. See, e.g., Kaya el al, “A bacterial Argonaute with noncanonical guide RNA specificity”,
  • the napDNAbp is a single effector of a microbial CRISPR-Cas system.
  • Single effectors of microbial CRISPR-Cas systems include, without limitation, Cas9, Cpfl, C2cl, C2c2, and C2c3.
  • microbial CRISPR-Cas systems are divided into Class 1 and Class 2 systems. Class 1 systems have multisubunit effector complexes, while Class 2 systems have a single protein effector. For example, Cas9 and Cpfl are Class 2 effectors.
  • C2cl Class 2 CRISPR-Cas systems
  • C2c2 Three distinct Class 2 CRISPR-Cas systems
  • C2c3 Three distinct Class 2 CRISPR-Cas systems
  • Shmakov el al “Discovery and Functional Characterization of Diverse Class 2 CRISPR Cas Systems”, Mol. Cell, 2015 Nov 5; 60(3): 385-397, the entire contents of which is hereby incorporated by reference.
  • Effectors of two of the systems, C2cl and C2c3 contain RuvC-like endonuclease domains related to Cpfl.
  • a third system, C2c2 contains an effector with two predicated HEPN RNase domains.
  • C2cl depends on both CRISPR RNA and tracrRNA for DNA cleavage.
  • Bacterial C2c2 has been shown to possess a unique RNase activity for CRISPR RNA maturation distinct from its RNA-activated single- stranded RNA degradation activity. These RNase functions are different from each other and from the CRISPR RNA-processing behavior of Cpfl.
  • C2c2 is a single-component programmable RNA-guided RNA- targeting CRISPR effector”, Science, 2016 Aug 5; 353(6299), the entire contents of which are hereby incorporated by reference.
  • the napDNAbp may be a C2cl, a C2c2, or a C2c3 protein. In some embodiments, the napDNAbp is a C2cl protein. In some embodiments, the napDNAbp is a C2c2 protein. In some embodiments, the napDNAbp is a C2c3 protein.
  • the napDNAbp comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring C2cl, C2c2, or C2c3 protein.
  • the napDNAbp is a naturally-occurring C2cl, C2c2, or C2c3 protein.
  • pyogenes require a canonical NGG PAM sequence to bind a particular nucleic acid region. This may limit the ability to edit desired bases within a genome.
  • the base editing base editors provided herein may need to be placed at a precise location, for example where a target base is placed within a 4 base region (e.g ., a “editing window” or a “target window”), which is approximately 15 bases upstream of the PAM. See Komor, A.C., et al, “Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage” Nature 533, 420-424 (2016), the entire contents of which are hereby incorporated by reference.
  • any of the base editors provided herein may contain a Cas9 domain that is capable of binding a nucleotide sequence that does not contain a canonical (e.g., NGG) PAM sequence.
  • Cas9 domains that bind to non-canonical PAM sequences have been described in the art and would be apparent to the skilled artisan.
  • Cas9 domains that bind non-canonical PAM sequences have been described in Kleinstiver, B. P., et al., “Engineered CRISPR-Cas9 nucleases with altered PAM specificities” Nature 523, 481-485 (2015); and Kleinstiver, B.
  • a napDNAbp domain with altered PAM specificity such as a domain with at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with wild type Francisella novicida Cpfl (SEQ ID NO: 132) (D917, E1006, and D1255), which has the following amino acid sequence:
  • An additional napDNAbp domain with altered PAM specificity such as a domain having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with wild type Geobacillus thermodenitrificans Cas9 (SEQ ID NO: 133), which has the following amino acid sequence:
  • the nucleic acid programmable DNA binding protein is a nucleic acid programmable DNA binding protein that does not require a canonical (NGG) PAM sequence.
  • the napDNAbp is an argonaute protein.
  • One example of such a nucleic acid programmable DNA binding protein is an Argonaute protein from Natronobacterium gregoryi (NgAgo).
  • NgAgo is a ssDNA-guided endonuclease.
  • NgAgo binds 5' phosphorylated ssDNA of ⁇ 24 nucleotides (gDNA) to guide it to its target site and will make DNA double-strand breaks at the gDNA site.
  • the NgAgo-gDNA system does not require a protospacer-adjacent motif (PAM).
  • NgAgo nuclease inactive NgAgo
  • the characterization and use of NgAgo have been described in Gao et al, Nat Biotechnol., 34(7): 768-73 (2016), PubMed PMID: 27136078; Swarts et al., Nature, 507(7491): 258-61 (2014); and Swarts et al., Nucleic Acids Res. 43(10) (2015): 5120-9, each of which is incorporated herein by reference.
  • the sequence of Natronobacterium gregoryi Argonaute is provided in SEQ ID NO: 134.
  • the disclosed base editors may comprise a napDNAbp domain having at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity with wild type Natronobacterium gregoryi Argonaute (SEQ ID NO: 134), which has the following amino acid sequence: MTVIDLDSTTTADELTSGHTYDISVTLTGVYDNTDEQHPRMSLAFEQDNGERRYITLWKNTTPKDVFTYDYATGSTYIFTNID YEVKDGYENLTATYQTTVENATAQEVGTTDEDETFAGGEPLDHHLDDALNETPDDAETESDSGHVMTSFASRDQLPEWTLHTY TLTATDGAKTDTEYARRTLAYTVRQELYTDHDAAPVATDGLMLLTPEPLGETPLDLDCGVRVEADETRTLDYTTAKDRLLARE LVEEGLKRSLWDDYLVRGIDEVLSKEPVLTCDEFDLHERYDLSVEVGHSGRAYLHINFRHRFVPKLTLADIDDDNI
  • the base editors disclosed herein may comprise a circular permutant of Cas9.
  • Circularly permuted Cas9 or “circular permutant” of Cas9 or “CP-Cas9” refers to any Cas9 protein, or variant thereof, that occurs or has been modify to engineered as a circular permutant variant, which means the N-terminus and the C-terminus of a Cas9 protein (e.g ., a wild type Cas9 protein) have been topically rearranged.
  • Such circularly permuted Cas9 proteins, or variants thereof retain the ability to bind DNA when complexed with a guide RNA (gRNA).
  • gRNA guide RNA
  • any of the Cas9 proteins described herein, including any variant, ortholog, or naturally occurring Cas9 or equivalent thereof, may be reconfigured as a circular permutant variant.
  • the circular permutants of Cas9 may have the following structure:
  • the present disclosure contemplates the following circular permutants of canonical S. pyogenes Cas9 (1368 amino acids of UniProtKB - Q99ZW2 (CAS9_STRP1) (numbering is based on the amino acid position in SEQ ID NO: 9)):
  • the circular permuant Cas9 has the following structure (based on S. pyogenes Cas9 (1368 amino acids of UniProtKB - Q99ZW2 (CAS9_STRP1) (numbering is based on the amino acid position in SEQ ID NO: 9):
  • the circular permuant Cas9 has the following structure (based on S. pyogenes Cas9 (1368 amino acids of UniProtKB - Q99ZW2 (CAS9_STRP1) (numbering is based on the amino acid position in SEQ ID NO: 9):
  • the circular permutant can be formed by linking a C-terminal fragment of a Cas9 to an N-terminal fragment of a Cas9, either directly or by using a linker, such as an amino acid linker.
  • the C-terminal fragment may correspond to the C-terminal 95% or more of the amino acids of a Cas9 (e.g., amino acids about 1300-1368), or the C-terminal 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%,
  • the N-terminal portion may correspond to the N-terminal 95% or more of the amino acids of a Cas9 (e.g., amino acids about 1-1300), or the N-terminal 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% or more of a Cas9 (e.g., of SEQ ID NO: 9).
  • a Cas9 e.g., amino acids about 1-1300
  • the N-terminal 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% or more of a Cas9 e.g., of SEQ ID NO: 9).
  • the circular permutant can be formed by linking a C-terminal fragment of a Cas9 to an N-terminal fragment of a Cas9, either directly or by using a linker, such as an amino acid linker.
  • the C-terminal fragment that is rearranged to the N-terminus includes or corresponds to the C-terminal 30% or less of the amino acids of a Cas9 (e.g., amino acids 1012-1368 of SEQ ID NO: 9).
  • the C-terminal fragment that is rearranged to the N-terminus includes or corresponds to the C-terminal 30%, 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%,
  • the C-terminal fragment that is rearranged to the N-terminus includes or corresponds to the C-terminal 410 residues or less of a Cas9 (e.g., the Cas9 of SEQ ID NO:
  • the C-terminal portion that is rearranged to the N-terminus includes or corresponds to the C-terminal 410, 400, 390, 380, 370, 360, 350, 340, 330, 320, 310, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140,
  • the C-terminal portion that is rearranged to the N- terminus includes or corresponds to the C-terminal 357, 341, 328, 120, or 69 residues of a Cas9 (e.g., the Cas9 of SEQ ID NO: 9).
  • circular permutant Cas9 variants may be defined as a topological rearrangement of a Cas9 primary structure based on the following method, which is based on S. pyogenes Cas9 of SEQ ID NO: 9: (a) selecting a circular permutant (CP) site corresponding to an internal amino acid residue of the Cas9 primary structure, which dissects the original protein into two halves: an N-terminal region and a C-terminal region; (b) modifying the Cas9 protein sequence (e.g., by genetic engineering techniques) by moving the original C-terminal region (comprising the CP site amino acid) to preceed the original N- terminal region, thereby forming a new N-terminus of the Cas9 protein that now begins with the CP site amino acid residue.
  • CP circular permutant
  • the CP site can be located in any domain of the Cas9 protein, including, for example, the helical-II domain, the RuvCIII domain, or the CTD domain.
  • the CP site may be located (relative the S. pyogenes Cas9 of SEQ ID NO: 9) at original amino acid residue 181, 199, 230, 270, 310, 1010, 1016, 1023, 1029, 1041, 1247, 1249, or 1282.
  • original amino acid 181, 199, 230, 270, 310, 1010, 1016, 1023, 1029, 1041, 1247, 1249, or 1282 would become the new N- terminal amino acid.
  • Nomenclature of these CP-Cas9 proteins may be referred to as Cas9- CP 181 , Cas9-CP 199 , Cas9-CP 230 , Cas9-CP 270 , Cas9-CP 310 , Cas9-CP 1010 , Cas9-CP 1016 , Cas9- CP 1023 , Cas9-CP 1029 , Cas9-CP 1041 , Cas9-CP 1247 , Cas9-CP 1249 , and Cas9-CP 1282 , respectively.
  • This description is not meant to be limited to making CP variants from SEQ ID NO: 9, but may be implemented to make CP variants in any Cas9 sequence, either at CP sites that correspond to these positions, or at other CP sites entireley. This description is not meant to limit the specific CP sites in any way. Virtually any CP site may be used to form a CP-Cas9 variant.
  • Exemplary CP-Cas9 amino acid sequences are provided below in which linker sequences are indicated by underlining and optional methionine (M) residues are indicated in bold. It should be appreciated that the disclosure provides CP-Cas9 sequences that do not include a linker sequence or that include different linker sequences. It should be appreciated that CP-Cas9 sequences may be based on Cas9 sequences other than that of SEQ ID NO: 9 and any examples provided herein are not meant to be limiting. Exemplary CP-Cas9 sequences are as follows:
  • Cas9 circular permutants that may be useful in the base editor constructs described herein.
  • Exemplary C-terminal fragments of Cas9 based on the Cas9 of SEQ ID NO: 9, which may be rearranged to an N-terminus of Cas9, are provided below. It should be appreciated that such C-terminal fragments of Cas9 are exemplary and are not meant to be limiting.
  • These exemplary CP-Cas9 fragments have the following sequences:
  • the base editors of the present disclosure may also comprise Cas9 variants with modified PAM specificities.
  • Some aspects of this disclosure provide Cas9 proteins that exhibit activity on a target sequence that does not comprise the canonical PAM (5'-NGG-3', where N is A, C, G, or T) at its 3 '-end.
  • the Cas9 protein exhibits activity on a target sequence comprising a 5'-NGG-3' PAM sequence at its 3 '-end.
  • the Cas9 protein exhibits activity on a target sequence comprising a 5 -NNG- 3' PAM sequence at its 3 '-end.
  • the Cas9 protein exhibits activity on a target sequence comprising a 5'-NNA-3' PAM sequence at its 3 '-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5'-NNC-3' PAM sequence at its 3 '-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 -NNT-3' PAM sequence at its 3'-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 -NGT-3' PAM sequence at its 3'-end.
  • the Cas9 protein exhibits activity on a target sequence comprising a 5 -NGA-3' PAM sequence at its 3'-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 -NGC-3' PAM sequence at its 3'-end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5'- NAA-3' PAM sequence at its 3 -end. In some embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 -NAC-3' PAM sequence at its 3 '-end.
  • the Cas9 protein exhibits activity on a target sequence comprising a 5 -NAT-3' PAM sequence at its 3 -end. In still other embodiments, the Cas9 protein exhibits activity on a target sequence comprising a 5 -NAG-3' PAM sequence at its 3 -end.
  • the disclosed base editors comprise a napDNAbp domain comprising a SpCas9-NG, which has a PAM that corresponds to NGN. In some embodiments, the disclosed base editors comprise a napDNAbp domain comprising a SpCas9-KKH, which has a PAM that corresponds to NNNRRT.
  • any of the amino acid mutations described herein, (e.g ., A262T) from a first amino acid residue (e.g., A) to a second amino acid residue (e.g., T) may also include mutations from the first amino acid residue to an amino acid residue that is similar to (e.g., conserved) the second amino acid residue.
  • mutation of an amino acid with a hydrophobic side chain may be a mutation to a second amino acid with a different hydrophobic side chain (e.g., alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan).
  • alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan may be a mutation to a second amino acid with a different hydrophobic side chain (e.g., alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan).
  • a mutation of an alanine to a threonine may also be a mutation from an alanine to an amino acid that is similar in size and chemical properties to a threonine, for example, serine.
  • mutation of an amino acid with a positively charged side chain e.g., arginine, histidine, or lysine
  • mutation of a second amino acid with a different positively charged side chain e.g., arginine, histidine, or lysine.
  • mutation of an amino acid with a polar side chain may be a mutation to a second amino acid with a different polar side chain (e.g., serine, threonine, asparagine, or glutamine).
  • Additional similar amino acid pairs include, but are not limited to, the following: phenylalanine and tyrosine; asparagine and glutamine; methionine and cysteine; aspartic acid and glutamic acid; and arginine and lysine. The skilled artisan would recognize that such conservative amino acid substitutions will likely have minor effects on protein structure and are likely to be well tolerated without compromising function.
  • any amino of the amino acid mutations provided herein from one amino acid to a threonine may be an amino acid mutation to a serine.
  • any amino of the amino acid mutations provided herein from one amino acid to an arginine may be an amino acid mutation to a lysine.
  • any amino of the amino acid mutations provided herein from one amino acid to an isoleucine may be an amino acid mutation to an alanine, valine, methionine, or leucine.
  • any amino of the amino acid mutations provided herein from one amino acid to a lysine may be an amino acid mutation to an arginine.
  • any amino of the amino acid mutations provided herein from one amino acid to an aspartic acid may be an amino acid mutation to a glutamic acid or asparagine.
  • any amino of the amino acid mutations provided herein from one amino acid to a valine may be an amino acid mutation to an alanine, isoleucine, methionine, or leucine.
  • any amino of the amino acid mutations provided herein from one amino acid to a glycine may be an amino acid mutation to an alanine. It should be appreciated, however, that additional conserved amino acid residues would be recognized by the skilled artisan and any of the amino acid mutations to other conserved amino acid residues are also within the scope of this disclosure.
  • the Cas9 protein comprises a combination of mutations that exhibit activity on a target sequence comprising a 5 -NAA-3' PAM sequence at its 3 - end.
  • the combination of mutations are present in any one of the clones listed in Table 1.
  • the combination of mutations are conservative mutations of the clones listed in Table 1.
  • the Cas9 protein comprises the combination of mutations of any one of the Cas9 clones listed in Table 1.
  • the Cas9 protein comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 1. In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 1.
  • the Cas9 protein exhibits an increased activity on a target sequence that does not comprise the canonical PAM (5'-NGG-3') at its 3' end as compared to Streptococcus pyogenes Cas9 as provided by SEQ ID NO: 9.
  • the Cas9 protein exhibits an activity on a target sequence having a 3' end that is not directly adjacent to the canonical PAM sequence (5'-NGG-3') that is at least 5-fold increased as compared to the activity of Streptococcus pyogenes Cas9 as provided by SEQ ID NO: 9 on the same target sequence.
  • the Cas9 protein exhibits an activity on a target sequence that is not directly adjacent to the canonical PAM sequence (5'-NGG-3') that is at least 10- fold, at least 50-fold, at least 100-fold, at least 500-fold, at least 1,000-fold, at least 5,000- fold, at least 10,000-fold, at least 50,000-fold, at least 100,000-fold, at least 500,000-fold, or at least 1,000,000-fold increased as compared to the activity of Streptococcus pyogenes as provided by SEQ ID NO: 9 on the same target sequence.
  • the 3' end of the target sequence is directly adjacent to an AAA, GAA, CAA, or TAA sequence.
  • the Cas9 protein comprises a combination of mutations that exhibit activity on a target sequence comprising a 5 -NAC-3' PAM sequence at its 3 '-end. In some embodiments, the combination of mutations are present in any one of the clones listed in Table 2. In some embodiments, the combination of mutations are conservative mutations of the clones listed in Table 2. In some embodiments, the Cas9 protein comprises the combination of mutations of any one of the Cas9 clones listed in Table 2.
  • the Cas9 protein comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 2. In some embodiments, the Cas9 protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of a Cas9 protein as provided by any one of the variants of Table 2.
  • the Cas9 protein comprises a combination of mutations that exhibit activity on a target sequence comprising a 5'-NAT-3' PAM sequence at its 3 '-end.
  • the combination of mutations are present in any one of the clones listed in Table 3.
  • the combination of mutations are conservative mutations of the clones listed in Table 3.
  • the Cas9 protein comprises the combination of mutations of any one of the Cas9 clones listed in Table 3.
  • the above description of various napDNAbps which can be used in connection with the presently disclose base editors is not meant to be limiting in any way.
  • the base editors may comprise the canonical SpCas9, or any ortholog Cas9 protein, or any variant Cas9 protein — including any naturally occurring variant, mutant, or otherwise engineered version of Cas9 — that is known or which can be made or evolved through a directed evolutionary or otherwise mutagenic process.
  • the Cas9 or Cas9 varants have a nickase activity, i.e., only cleave of strand of the target DNA sequence.
  • the Cas9 or Cas9 variants have inactive nucleases, i.e., are “dead” Cas9 proteins.
  • Other variant Cas9 proteins that may be used are those having a smaller molecular weight than the canonical SpCas9 (e.g., for easier delivery) or having modified or rearranged primary amino acid structure (e.g., the circular permutant formats).
  • the base editors described herein may also comprise Cas9 equivalents, including Casl2a/Cpfl and Casl2b proteins which are the result of convergent evolution.
  • the napDNAbps used herein may also contain various modifications that alter/enhance their PAM specifities.
  • the application contemplates any Cas9, Cas9 variant, or Cas9 equivalent which has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.9% sequence identity to a reference Cas9 sequence, such as a references SpCas9 canonical sequences or a reference Cas9 equivalent (e.g., Casl2a/Cpfl).
  • a reference Cas9 sequence such as a references SpCas9 canonical sequences or a reference Cas9 equivalent (e.g., Casl2a/Cpfl).
  • the Cas9 variant having expanded PAM capabilities is SpCas9 (H840A) VRQR, or SpCas9-VRQR.
  • the disclosed base editors comprise a napDNAbp domain that has a sequence that is at least 90%, at least 95%, at least 98%, or at least 99% identical to SpCas9-VRQR.
  • the disclosed base editors comprise a napDNAbp domain that comprises SpCas9-VRQR.
  • the SpCas9- VRQR comprises the following amino acid sequence (with the V, R, Q, R substitutions relative to the SpCas9 (H840A) of SEQ ID NO: 145 show, in bold underline.
  • the Cas9 variant having expanded PAM capabilities is SpCas9 (H840A) VRER, having the following amino acid sequence (with the V, R, E, R substitutions relative to the SpCas9 (H840A) of SEQ ID NO: 146 are shown in bold underline.
  • the methionine residue in SpCas9 (H840) was removed for SpCas9 (H840A) VRER):
  • any available methods may be utilized to obtain or construct a variant or mutant Cas9 protein.
  • the term “mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue.
  • Mutations can include a variety of categories, such as single base polymorphisms, microduplication regions, indel, and inversions, and is not meant to be limiting in any way. Mutations can include “loss-of-function” mutations which is the normal result of a mutation that reduces or abolishes a protein activity.
  • Gain-of-function mutations are recessive, because in a heterozygote the second chromosome copy carries an unmutated version of the gene coding for a fully functional protein whose presence compensates for the effect of the mutation. Mutations also embrace “gain-of-function” mutations, which is one which confers an abnormal activity on a protein or cell that is otherwise not present in a normal condition. Many gain-of-function mutations are in regulatory sequences rather than in coding regions, and can therefore have a number of consequences. For example, a mutation might lead to one or more genes being expressed in the wrong tissues, these tissues gaining functions that they normally lack. Because of their nature, gain-of-function mutations are usually dominant.
  • Mutations can be introduced into a reference Cas9 protein using site-directed mutagenesis.
  • Older methods of site-directed mutagenesis known in the art rely on sub cloning of the sequence to be mutated into a vector, such as an M13 bacteriophage vector, that allows the isolation of single-stranded DNA template.
  • a mutagenic primer i.e ., a primer capable of annealing to the site to be mutated but bearing one or more mismatched nucleotides at the site to be mutated
  • a mutagenic primer i.e ., a primer capable of annealing to the site to be mutated but bearing one or more mismatched nucleotides at the site to be mutated
  • PCR-based site-directed mutagenesis has employed PCR methodologies, which have the advantage of not requiring a single-stranded template.
  • methods have been developed that do not require sub-cloning.
  • Several issues must be considered when PCR-based site-directed mutagenesis is performed. First, in these methods it is desirable to reduce the number of PCR cycles to prevent expansion of undesired mutations introduced by the polymerase. Second, a selection must be employed in order to reduce the number of non-mutated parental molecules persisting in the reaction. Third, an extended-length PCR method is preferred in order to allow the use of a single PCR primer set. And fourth, because of the non-template-dependent terminal extension activity of some thermostable polymerases it is often necessary to incorporate an end-polishing step into the procedure prior to blunt-end ligation of the PCR-generated mutant product.
  • the TGBE (and ACBE) base editors provided herein comprise a nucleotide modification domain comprising a transglycosylase domain (FIG. 1).
  • Any transglycosylase that is adapted to accept guanine nucleoside substrates are useful in the base editors and methods of editing disclosed herein.
  • Exemplary transglycosylases of the disclosure are capable of excising a thymine base, forming a glycosyl-enzyme intermediate with the apurinic deoxyribose, and accepting a free guanine base as substrate in a nucleophilic attack that displaces the enzyme and forms a new glycosidic bond with the deoxyribose.
  • the tranglycosylase may comprise a naturally-occuring or engineered transglycosylase, e.g., an engineered guanine transglycosylase.
  • a guanine transglycosylase is an enzyme that catalyzes the substitution of a queuine (abbreviated Q) (or precursor of queuine) nucleobase analog for a guanine nucleobase in a polynucleotide substrate (see FIG. 4). This reaction disrupts and then re-forms the glycosidic bond linking the guanine nucleobase to the anomeric carbon of the deoxyribose (or ribose) sugar. This reaction forms a queuosine (or prequeuosine) nucleoside.
  • TGT tRNA guanine transglycosylase
  • coli TGT involves a covalent TGT- RNA complex that is thermodynamically and kinetically stable, wherein the Asp264 residue of the enzyme is bound to the G position of the ribose ring.
  • Asp264 residue of the enzyme is bound to the G position of the ribose ring.
  • a 7-amino-methyl-7-deazaguanine (abbreviated preQi) replaces the aspartate active site residue, releasing the TGT.
  • PreQi is converted to Q.
  • TGT When preQi is absent, TGT is also capable of using 7-cyano-7-deazaguanine (preQo) as the second nucleobase substrate for this reaction.
  • PreQo is a common precursor of queuosine (Q) and archaeosine (G + ).
  • TGT is also sometimes referred to as queuine tRNA-ribosyltransferase.
  • TGT recognition is not critically dependent on a ribose backbone. Further, it is demonstrated in the Examples provided herein that wild-type TGT is capable of editing target guanines in non-UGU sequences in DNA hairpins (see FIGs. 6A-6B).
  • the preQi intermediate may be converted to a glycosylated queuosine product (glycosyl-Q) (see FIG. 4).
  • a separate transglycosylase the prokaryotic DpdA protein, is expressed from “gene A” located in a -20 kb “dpd” (deazapurine-in-DNA) gene cluster that also contains preQo synthesis and DNA metabolism genes.
  • dpd dieazapurine-in-DNA
  • Novel genomic island modifies DNA with 7-deazaguanine derivatives, PNAS, 113(1 l):E1452-9 (2016). This gene cluster is found in genomic islands.
  • the DpdA enzyme catalyzes the exchange of preQo (or 7-amido- 7-deazaguanine (ADG)) for guanine in bacterial and bacteriophage genomic DNA.
  • DpdA shows significant similarity to the TGT enzyme, as the key aspartate residues that catalyze the base exchange (Asp 102 and Asp280 of Zymomonas mobilis TGT and Asp95 and Asp249 of Pyrococcus horikoshii TGT), as well as the zinc binding site (CXCXXCX22H motif (SEQ ID NO: 29)), are conserved in DpdAs.
  • Prokaryotic DpdA is capable of recognizing and exchanging a deoxyguanine nucleobase in a DNA substrate with preQo.
  • the product of this base exchange reaction dPreQo nucleoside (i.e., 7-deazaguanine derivative nucleoside), were recently discovered in bacterial DNA.
  • the transglycosylases useful in the present disclosure may be modified from wild- type reference proteins, which include TGT and DpdA, to recognize and excise a target thymine base in DNA as a first nucleobase substrate.
  • wild-type and evolved variant transglycosylases are capable of inserting guanine into DNA ( i.e ., as a second nucleobase substrate) because this step represents the chemical reverse of the first recognition step of the native guanine base excision reaction.
  • evolved TGT and DpdA variants that recognize and excise a thymine base in DNA are provided in the present disclosure.
  • Wild-type reference transglycosylases may be those from E. coli, S. Montevideo , bacteriophage (such as E. coli phage 9g), yeast, mouse, human, or another organism, including other bacteria and bacteriophages.
  • Modified transglycosylases include variants with at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to a wild-type transglycosylase.
  • modified transglycosylases may be obtained by altering or evolving a reference protein using a continuous evolution process (e.g., PACE) or non-continuous evolution process (e.g., PANCE or discrete plate-based selections) described herein so that the transglycosylase is effective on a thymine base of a nucleic acid target (e.g., a DNA target).
  • a continuous evolution process e.g., PACE
  • non-continuous evolution process e.g., PANCE or discrete plate-based selections
  • the following mechanism is proposed for disclosed TGT and DpdA variants that recognize a thymine first nucleobase subsrate (without wishing to be bound by any particular theory).
  • the TGT (or DpdA) variant excises the thymine from position (i.e., the anomeric carbon) of the deoxyribose sugar and covalently bonds to the sugar, thus forming a covalent glycosyl- enzyme intermediate (for instance, TGT-DNA in cases where the transglycosylase is a TGT) (see FIG. 3).
  • This intermediate may be formed at an active site aspartate residue of the TGT (or DpdA) variant. Subsequently, a free guanine excises the active site residue in a nucleophilic attack, and forms a new glycosidic bond with the anomeric carbon of the deoxyribose.
  • the disclosed TGT and DpdA variants uses free deazaguanine derivatives, such as PreQo or PreQi, to excise the thymine and form a 2'-deoxy-7-cyano-7-deazaguanosine (dPreQo) or 2'-deoxy-7-amino-methyl-7-deazaguanosine (dPreQi) product.
  • dPreQo 2'-deoxy-7-cyano-7-deazaguanosine
  • dPreQi 2'-deoxy-7-amino-methyl-7-deazaguanosine
  • the cell’s mismatch repair machinery converts the dPreQo or dPreQi to a guanosine, thereby completing the T-to-G change.
  • Deazaguanines and their derivatives are not normally found in eukaryotic cells.
  • this reaction is expected to proceed through a guanine nucleobase substrate in eukaryotes, and not through a deazaguanine derivative. As such, in mammalian cells, this reaction is expected to proceed through a guanine nucleobase substrate.
  • transglycosylase domains that can be fused to napDNAbp domains according to embodiments of this disclosure are provided below.
  • the transglycosylase domain is a bacterial TGT, or a variant thereof.
  • the transglycsylase domain is a bacterial queuine tRNA-ribosyltransferase.
  • Exemplary transglycosylase domains include, but are not limited to, E. coli TGT, Pyrococcus horikoshii TGT, Zymomonas mobilis TGT, E. coli DpdA, Salmonella enterica serovar Montevideo DpdA, Streptomyces sp.
  • transglycosylase domains include variants with at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity to the following wild-type enzymes:
  • MKIVFGIV S QDLLIKINFPILIN QLRNKKITWKNETWVDS GGY QIALYNLKIS V KD VLEKYKT YN AY AFFS LDIPS IF S PLDRKNFE YFE YLYTKME YIERIIP VIHLYPTRE V DE AIDF Y S Q YTD YIAF GGIIAS S KLKILIYTFPW Y Y YIRKY VKRLH VLGMS AP YFLQIF DTANSMDTTTYTKTASYREIFWFDGTRRYVGDRKERTLTKEEEEKLFEFLDKTNFPF EYDFSNVKILKTMNAWILKYNNWNIKNKYTIYAEKLRKMGLDSLVTEIIQNYKIANE LKKEKQQNKKKN S IELEE (SEQ ID NO: 7)
  • the base editors disclosed herein further comprise one or more additional elements, e.g., linkers and localization sequences such as nuclear localization sequences (NLSs), nuclear export sequences, and other protein domains.
  • additional elements e.g., linkers and localization sequences such as nuclear localization sequences (NLSs), nuclear export sequences, and other protein domains.
  • the base editors disclosed herein further comprise a nuclear localization sequence.
  • the base editors disclosed herein further comprise one or more, preferably, at least two nuclear localization signals.
  • the base editors comprise at least two NLSs.
  • the NLSs can be the same NLSs, or they can be different NLSs.
  • the NLSs may be expressed as part of a fusion protein with the other portions of the base editors.
  • one or more of the NLSs are bipartite NLSs (“bpNLS”).
  • the disclosed fusion proteins comprise two bipartite NLSs.
  • the disclosed fusion proteins comprise more than two bipartite NLSs.
  • the location of the NLS fusion can be at the N-terminus, the C-terminus, or within a sequence of a base editor (e.g., inserted between the napDNAbp domain (e.g., Cas9) and a nucleotide modification domain (e.g., a transglycosylase)).
  • a base editor e.g., inserted between the napDNAbp domain (e.g., Cas9) and a nucleotide modification domain (e.g., a transglycosylase)).
  • the NLSs may be any known NLS in the art.
  • the NLSs may also be any NLSs for nuclear localization discovered in the future.
  • the NLSs also may be any naturally-occurring NLS, or any non-naturally occurring NLS (e.g., an NLS with one or more desired mutations).
  • NLS nuclear localization sequence
  • the term “nuclear localization sequence” or “NLS” refers to an amino acid sequence that promotes import of a protein into the cell nucleus, for example, by nuclear transport. Nuclear localization sequences are known in the art and would be apparent to the skilled artisan.
  • an NLS comprises the amino acid sequence PKKKRKV (SEQ ID NO: 51), MDSLLMNRRKFLY QFKNVRWAKGRRETYLC (SEQ ID NO: 52),
  • the NLS comprises the amino acid sequence:
  • NLS KRP A AIKKAGQ AKKKK (SEQ ID NO: 54), PAAKRVKLD (SEQ ID NO: 55), RQRRNELKRS F (SEQ ID NO: 56), or
  • a representative nuclear localization signal is a peptide sequence that directs the protein to the nucleus of the cell in which the sequence is expressed.
  • a nuclear localization signal is predominantly basic, can be positioned almost anywhere in a protein's amino acid sequence, generally comprises a short sequence of four amino acids (Autieri & Agrawal, (1998) J. Biol. Chem. 273: 14731-37, incorporated herein by reference) to eight amino acids, and is typically rich in lysine and arginine residues (Magin et al, (2000) Virology 274: 11-16, incorporated herein by reference). Nuclear localization signals often comprise proline residues.
  • nuclear localization signals have been identified and have been used to effect transport of biological molecules from the cytoplasm to the nucleus of a cell. See, e.g., Tinland et al., (1992) Proc. Natl. Acad. Sci. U.S.A. 89:7442-46; Moede et al., (1999) FEBS Lett. 461:229-34, which is incorporated herein by reference. Translocation is currently thought to involve nuclear pore proteins.
  • NLSs can be classified in three general groups: (i) a monopartite NLS exemplified by the SV40 large T antigen NLS (PKKKRKV (SEQ ID NO: 51)); (ii) a bipartite motif consisting of two basic domains separated by a variable number of spacer amino acids and exemplified by the Xenopus nucleoplasmin NLS (KRXXXXXXXXXKKKL (SEQ ID NO: 50)); and (iii) noncanonical sequences such as M9 of the hnRNP Al protein, the influenza virus nucleoprotein NLS, and the yeast Gal4 protein NLS (Dingwall and Laskey, Trends Biochem Sci. 1991 Dec;16(12):478-81).
  • Nuclear localization signals appear at various points in the amino acid sequences of proteins. NLSs have been identified at the N-terminus, the C-terminus, and in the central region of proteins. Thus, the specification provides base editors that may be modified with one or more NLSs at the C-terminus, the N-terminus, as well as at in internal region of the base editor. The residues of a longer sequence that do not function as component NLS residues should be selected so as not to interfere, for example tonically or sterically, with the nuclear localization signal itself. Therefore, although there are no strict limits on the composition of an NLS -comprising sequence, in practice, such a sequence can be functionally limited in length and composition.
  • the present disclosure contemplates any suitable means by which to modify a fusion protein (or base editor) to include one or more NLSs.
  • the fusion proteins can be engineered to express a fusion protein protein that is translationally fused at its N-terminus or its C-terminus (or both) to one or more NLSs, i.e., to form a fusion protein-NLS fusion construct.
  • the fusion protein-encoding nucleotide sequence can be genetically modified to incorporate a reading frame that encodes one or more NLSs in an internal region of the encoded fusion protein.
  • the NLSs may include various amino acid linkers or spacer regions encoded between the fusion protein and the N- terminally, C-terminally, or internally- attached NLS amino acid sequence.
  • the present disclosure also provides for nucleotide constructs, vectors, and host cells for expressing fusion proteins that comprise a fusion protein and one or more NLSs.
  • the fusion proteins described herein may also comprise nuclear localization signals which are linked to a fusion protein through one or more linkers, e.g., polymeric, amino acid, polysaccharide, chemical, or nucleic acid linker element.
  • linkers e.g., polymeric, amino acid, polysaccharide, chemical, or nucleic acid linker element.
  • the NLS is linked to a fusion protein using an XTEN linker, as set forth in SEQ ID NO: 11.
  • linkers within the contemplated scope of the disclosure are not intented to have any limitations and can be any suitable type of molecule (e.g., polymer, amino acid, polysaccharide, nucleic acid, lipid, or any synthetic chemical linker domain) and be joined to the fusion protein by any suitable strategy that effectuates forming a bond (e.g., covalent linkage, hydrogen bonding) between the fusion protein and the one or more NLSs.
  • suitable type of molecule e.g., polymer, amino acid, polysaccharide, nucleic acid, lipid, or any synthetic chemical linker domain
  • the fusion proteins described herein also may include one or more additional elements.
  • an additional element may comprise an effector of base repair, such as an inhibitor of base repair.
  • the fusion proteins described herein may comprise one or more heterologous protein domains (e.g., about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains in addition to the fusion protein components).
  • a fusion protein may comprise any additional protein sequence, and optionally a linker sequence between any two domains.
  • Other exemplary features that may be present are localization sequences, such as cytoplasmic localization sequences, export sequences, such as nuclear export sequences, or other localization sequences, as well as sequence tags.
  • Examples of protein domains that may be fused to a fusion protein or component thereof include, without limitation, epitope tags and reporter gene sequences.
  • epitope tags include histidine (His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx) tags.
  • reporter genes include, but are not limited to, glutathione-5-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT), beta-galactosidase, beta- glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP).
  • GST glutathione-5-transferase
  • HRP horseradish peroxidase
  • CAT chloramphenicol acetyltransferase
  • beta-galactosidase beta-galactosidase
  • beta-glucuronidase beta-galactosidase
  • luciferase green fluorescent protein
  • GFP green fluorescent protein
  • HcRed HcRed
  • DsRed cyan fluorescent protein
  • YFP
  • a fusion protein may be fused to a gene sequence encoding a protein or a fragment of a protein that binds DNA molecules or binds other cellular molecules, including, but not limited to, maltose binding protein (MBP), S-tag, Lex A DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex virus (HSV) BP16 protein fusions. Additional domains that may form part of a fusion protein are described in US Patent Publication No. 2011-0059502, published March 10, 2011, which is incorporated herein by reference in its entirety.
  • a reporter gene which includes, but is not limited to, glutathione-5-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP), may be introduced into a cell to encode a gene product which serves as a marker by which to measure the alteration or modification of expression of the gene product.
  • the gene product is luciferase.
  • the expression of the gene product is decreased.
  • tags that are useful for solubilization, purification, or detection of the fusion proteins.
  • Suitable protein tags include, but are not limited to, biotin carboxylase carrier protein (BCCP) tags, myc- tags, calmodulin-tags, FLAG-tags, hemagglutinin (HA)-tags, bgh-PolyA tags, polyhistidine tags, and also referred to as histidine tags or His-tags, maltose binding protein (MBP)-tags, nus-tags, glutathione-S-transferase (GST)-tags, green fluorescent protein (GFP)-tags, thioredoxin-tags, S-tags, Softags (e.g., Softag 1, Softag 3), strep-tags , biotin ligase tags, FlAsH tags, V5 tags, and SBP-tags.
  • BCCP biotin carboxylase carrier protein
  • MBP maltose binding protein
  • GST glutathione-S-
  • the fusion protein comprises one or more His tags.
  • Exemplary fusion proteins comprise sequences that are at least least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% identical to the following amino acid sequences (for the purposes of clarity, the nCas9 domain is underlined; the XTEN linker is shown in italics ; and NLS is shown in underlined italics ):
  • VKLNREDLLRKORTFDN GS IPHOIHLGELHAILRROEDFYPFLKDNREKIEKILTFRIPY
  • Linkers may be used to link any of the domains of the fusion protein (e.g ., a napDNAbp domain covalently linked to a nucleotide modification domain which is covalently linked to an NLS domain).
  • linker refers to a chemical group or a molecule linking two molecules or domains, e.g., a napDNAbp binding domain and a transglycosylase domain.
  • a linker joins an nCas9 domain and nucleobase modification domain (e.g., a transglycosylase).
  • the linker is positioned between, or flanked by, two groups, molecules, or other domains and connected to each one via a covalent bond, thus connecting the two.
  • the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein).
  • the linker is an organic molecule, group, polymer, functional group, polysaccharide, or a synthetic chemical domain.
  • Chemical domains include, but are not limited to, disulfide, hydrazone, thiol, amide, ester, carbon-carbon bond, carbon-heteroatom bond, urea, carbamate, and azo moieties.
  • the linker may comprise a peptide or a non-peptide moiety.
  • the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60- 70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length.
  • the linker is a single atom in length. Longer or shorter linkers are also contemplated.
  • the linker may be as simple as a covalent bond, or it may be a multi-atom linker or polymeric linker many atoms in length.
  • the linker is a polpeptide or based on amino acids. In other embodiments, the linker is not peptide-like.
  • the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.). In certain embodiments, the linker is a carbon-nitrogen bond of an amide linkage.
  • the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or hetero aliphatic linker.
  • the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, polyether, etc.).
  • the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid.
  • the linker comprises an aminoalkanoic acid (e.g., glycine, ethanoic acid, alanine, beta-alanine, 3-aminopropanoic acid, 4-aminobutanoic acid, 5-pentanoic acid, etc.).
  • the linker comprises a monomer, dimer, or polymer of aminohexanoic acid (Ahx). In certain embodiments, the linker is based on a carbocyclic domain (e.g., cyclopentane, cyclohexane). In other embodiments, the linker comprises a polyethylene glycol domain (PEG). In other embodiments, the linker comprises amino acids. In certain embodiments, the linker comprises a peptide. In certain embodiments, the linker comprises an aryl or heteroaryl domain. In certain embodiments, the linker is based on a phenyl ring.
  • Ahx aminohexanoic acid
  • the linker may included funtionalized domains to facilitate attachment of a nucleophile (e.g., thiol, amino) from the peptide to the linker.
  • a nucleophile e.g., thiol, amino
  • Any electrophile may be used as part of the linker.
  • Exemplary electrophiles include, but are not limited to, activated esters, activated amides, Michael acceptors, alkyl halides, aryl halides, acyl halides, and isothiocyanates.
  • the linker comprises the amino acid sequence (GGGGS) n (SEQ ID NO: 35), (G) spacious(SEQ ID NO: 36), (EAAAK) procur (SEQ ID NO: 37), (GGS) compassion (SEQ ID NO: 38), (SGGS) n (SEQ ID NO: 39), (XP) n (SEQ ID NO: 40), or any combination thereof, wherein n is independently an integer between 1 and 30, and wherein X is any amino acid.
  • the linker comprises the amino acid sequence (GGS) n (SEQ ID NO: 41), wherein n is 1, 3, or 7.
  • the linker comprises the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 48).
  • the linker comprises the amino acid sequence SGGSSGGSSGS ETPGT S ES ATPES SGGSSGGS (SEQ ID NO: 11), also known as an XTEN linker.
  • the linker comprises the amino acid sequence SGGSGGSGGS (SEQ ID NO: 12).
  • the linker comprises the amino acid sequence SGGS (SEQ ID NO: 14).
  • the linker comprises any of the amino acid sequences
  • the fusion protein comprises the structure [transglycosylase domain] -[optional linker]-[dCas9 or Cas9 nickase domain], or [dCas9 or Cas9 nickase domain] -[optional linker]-[transglycosylase domain].
  • the target nucleotide sequence is a DNA sequence in a genome, e.g., a eukaryotic genome.
  • the target nucleotide sequence is in a mammalian (e.g. a human) genome.
  • the target nucleotide sequence is in a human genome.
  • the target nucleotide sequence is in the genome of a rodent, such as a mouse or rat.
  • the target nucleotide sequence is in the genome of a domesticated animal, such as a horse, cat, dog, or rabbit.
  • any of the fusion proteins provided herein are capable of modifying a specific nucleobase without generating a significant proportion of indels.
  • An “indel”, as used herein, refers to the insertion or deletion of a nucleobase within a nucleic acid. Such insertions or deletions can lead to frame shift mutations within a coding region of a gene.
  • any of the fusion proteins provided herein are capable of generating a greater proportion of intended modifications (e.g., point mutations) versus indels.
  • the fusion proteins provided herein are capable of generating a ratio of intended point mutations to indels that is greater than 1:1. In some embodiments, the fusion proteins provided herein are capable of generating a ratio of intended point mutations to indels that is at least 1.5:1, at least 2:1, at least 2.5:1, at least 3:1, at least 3.5:1, at least 4:1, at least 4.5:1, at least 5:1, at least 5.5:1, at least 6:1, at least 6.5:1, at least 7:1, at least 7.5:1, at least 8:1, at least 10:1, at least 12:1, at least 15:1, at least 20:1, at least 25:1, at least 30:1, at least 40:1, at least 50:1, at least 100:1, at least 200:1, at least 300:1, at least 400:1, at least 500:1, at least 600:1, at least 700:1, at least 800:1, at least 900:1, or at least 1000:1, or more.
  • the number of intended mutations and indels may be determined using any suitable method.
  • sequencing reads are scanned for exact matches to two 10-bp sequences that flank both sides of a window in which indels might occur. If no exact matches are located, the read is excluded from analysis. If the length of this indel window exactly matches the reference sequence the read is classified as not containing an indel. If the indel window is two or more bases longer or shorter than the reference sequence, then the sequencing read is classified as an insertion or deletion, respectively.
  • the fusion proteins provided herein are capable of limiting formation of indels in a region of a nucleic acid.
  • the region is at a nucleotide targeted by a fusion protein or a region within 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20 or 25 nucleotides of a nucleotide targeted by a fusion protein.
  • any of the fusion proteins provided herein are capable of limiting the formation of indels at a region of a nucleic acid to less than 1%, less than 1.5%, less than 2%, less than 2.5%, less than 3%, less than 3.5%, less than 4%, less than 4.5%, less than 5%, less than 6%, less than 7%, less than 8%, less than 9%, less than 10%, less than 12%, less than 15%, or less than 20%.
  • the number of indels formed at a nucleic acid region may depend on the amount of time a nucleic acid (e.g ., a nucleic acid within the genome of a cell) is exposed to a fusion protein. In some embodiments, an number or proportion of indels is determined after at least 1 hour, at least 2 hours, at least 6 hours, at least 12 hours, at least 24 hours, at least 36 hours, at least 48 hours, at least 3 days, at least 4 days, at least 5 days, at least 7 days, at least 10 days, or at least 14 days of exposing a nucleic acid (e.g., a nucleic acid within the genome of a cell) to a fusion protein.
  • a nucleic acid e.g., a nucleic acid within the genome of a cell
  • the method results in less than 5%, or less than 10%, indel formation in the nucleic acid. In some embodiments, the method results in less than 20% indel formation in the nucleic acid. In other embodiments, the method results in less than 35% indel formation in the nucleic acid.
  • the first nucleobase is a thymine (of the target T: A nucleobase pair). In some embodiments, the second nucleobase is a guanine (e.g., the T is converted to G). In some embodiments, the third nucleobase is a adenine (of the target T: A base pair), and the fourth nucleobase is a cytosine.
  • the method results in less than 20%, 19%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 8%, 6%, 4%, 2%, 1%, 0.5%, 0.2%, or less than 0.1% indel formation.
  • at least 5% of the intended base pairs in a population of cells or in tissues in vivo are edited.
  • at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% of the intended base pairs in a population of cells or in a tissue in vivo are edited.
  • an intended mutation such as a point mutation
  • a nucleic acid e.g., a nucleic acid within a genome of a subject
  • an intended mutation is a mutation that is generated by a specific fusion protein bound to a gRNA, specifically designed to generate the intended mutation.
  • the intended mutation is a mutation associated with a disease, disorder, or condition.
  • the intended mutation is an adenine (A) to cytosine (C) point mutation associated with a disease, disorder, or condition. In some embodiments, the intended mutation is a thymine (T) to guanine (G) point mutation associated with a disease, disorder, or condition. In some embodiments, the intended mutation is an adenine (A) to cytosine (C) point mutation within the coding region of a gene. In some embodiments, the intended mutation is a thymine (T) to guanine (G) point mutation within the coding region of a gene.
  • the intended mutation is a point mutation that generates a stop codon, for example, a premature stop codon within the coding region of a gene. In some embodiments, the intended mutation is a mutation that eliminates a stop codon. In some embodiments, the intended mutation is a mutation that changes a codon to encode a different amino acid. In some embodiments, the intended mutation is a mutation that alters the splicing of a gene. In some embodiments, the intended mutation is a mutation that alters the regulatory sequence of a gene (e.g ., a gene promotor or gene repressor).
  • any of the fusion proteins provided herein are capable of generating a ratio of intended mutations to unintended mutations (e.g., intended point m utati o n s : u n i n t c n dcd point mutations) that is greater than 1:1.
  • any of the fusion proteins provided herein are capable of generating a ratio of intended mutations to unintended mutations (e.g., intended point m utati o n s : u n i n t c n dcd point mutations) that is at least 1.5:1, at least 2:1, at least 2.5:1, at least 3:1, at least 3.5:1, at least 4:1, at least 4.5:1, at least 5:1, at least 5.5:1, at least 6:1, at least 6.5:1, at least 7:1, at least 7.5:1, at least 8:1, at least 10:1, at least 12:1, at least 15:1, at least 20:1, at least 25:1, at least 30:1, at least 40:1, at least 50:1, at least 100:1, at least 150:1, at least 200:1, at least 250:1, at least 500:1, or at least 1000:1, or more.
  • intended point m utati o n s u n i n t c n dcd point mutations
  • Some embodiments of the disclosure are based on the recognition that the formation of indels in a region of a nucleic acid may be limited by nicking the non-edited strand opposite to the strand in which edits are introduced.
  • This nick serves to direct mismatch repair machinery to the non-edited strand, ensuring that the chemically modified nucleobase is not interpreted as a lesion by the machinery (but rather as a template).
  • This nick may be created by the use of an nCas9.
  • the methods provided in this disclosure comprise cutting (or nicking) the non-edited strand of the double-stranded DNA, for example, wherein the one strand comprises the T of the target T:A nucleobase pair.
  • Guide sequences e.s guide RNAs
  • the present disclosure further provides guide RNAs for use in accordance with the disclosed methods of editing.
  • the disclosure provides guide RNAs that are designed to recognize target sequences.
  • Such gRNAs may be designed to have guide sequences (or “spacers”) having complementarity to a protospacer within the target sequence.
  • Guide RNAs are also provided for use with one or more of the disclosed fusion proteins, e.g., in the disclosed methods of editing a nucleic acid molecule.
  • Such gRNAs may be designed to have guide sequences having complementarity to a protospacer within a target sequence to be edited, and to have backbone sequences that interact specifically with the napDNAbp domains of any of the disclosed base editors, such as Cas9 nickase domains of the disclosed fusion proteins.
  • the TGBEs may be complexed, bound, or otherwise associated with (e.g., via any type of covalent or non-covalent bond) one or more guide sequences.
  • the guide sequence becomes associated or bound to the fusion protein and directs its localization to a specific target sequence having complementarity to the guide sequence or a portion thereof.
  • a guide sequence will depend upon the nucleotide sequence of a genomic target site of interest (i.e ., the desired site to be edited) and the type of napDNAbp (e.g., type of Cas protein) present in the fusion protein, among other factors, such as PAM sequence locations, percent G/C content in the target sequence, the degree of microhomology regions, secondary structures, etc.
  • a genomic target site of interest i.e ., the desired site to be edited
  • type of napDNAbp e.g., type of Cas protein
  • a guide sequence is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of the napDNAbp (e.g., a Cas9, Cas9 homolog, or Cas9 variant) to the target sequence.
  • the degree of complementarity between a guide sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm is about or more than about 50%, 60%, 75%, 80%,
  • Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith- Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net).
  • any suitable algorithm for aligning sequences non-limiting example of which include the Smith- Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.gen
  • a guide sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length.
  • each gRNA comprises a guide sequence of at least 10 contiguous nucleotides (e.g ., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 contiguous nucleotides) that is complementary to a target sequence.
  • a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length.
  • the ability of a guide sequence to direct sequence- specific binding of a fusion protein to a target sequence may be assessed by any suitable assay.
  • the components of a fusion protein, including the guide sequence to be tested may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of a fusion protein disclosed herein, followed by an assessment of preferential cleavage within the target sequence.
  • cleavage of a target polynucleotide sequence may be evaluated in situ by providing the target sequence, components of a fusion protein, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions.
  • Other assays are possible, and will occur to those skilled in the art.
  • a guide sequence may be selected to target any target sequence.
  • the target sequence is a sequence within a genome of a cell.
  • Exemplary target sequences include those that are unique in the target genome.
  • a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNNNXGG (SEQ ID NO: 58) where NNNNNNNNNNXGG (N is A, G, T, or C; and X can be anything) (SEQ ID NO: 59) has a single occurrence in the genome.
  • a unique target sequence in a genome may include an S.
  • pyogenes Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNNNXGG (SEQ ID NO: 60), where NNNNNNNNNXGG (N is A, G, T, or C; and X can be anything) (SEQ ID NO: 61) has a single occurrence in the genome. For the S.
  • thermophilus CRISPR1 Cas9 a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNNNXXAGAAW (SEQ ID NO: 62), where NNNNNNNNNNXXAGAAW (N is A, G, T, or C; X can be anything; and W is A or T) (SEQ ID NO: 63) has a single occurrence in the genome.
  • a unique target sequence in a genome may include an S.
  • thermophilus CRISPR 1 Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXXAGAAW (SEQ ID NO: 64), where NNNNNNNNNXXAGAAW (N is A, G, T, or C; X can be anything; and W is A or T) (SEQ ID NO: 65) has a single occurrence in the genome. For the S.
  • a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNNNNNXGGXG (SEQ ID NO: 66), where NNNNNNNNNNXGGXG (N is A, G, T, or C; and X can be anything) (SEQ ID NO: 67) has a single occurrence in the genome.
  • a unique target sequence in a genome may include an S.
  • MMMMMMMMMNNNNNNNNNNNNNXGGXG (SEQ ID NO: 68), where NNNNNNNNNXGGXG (N is A, G, T, or C; and X can be anything) (SEQ ID NO: 69) has a single occurrence in the genome.
  • N is A, G, T, or C; and X can be anything
  • SEQ ID NO: 69 has a single occurrence in the genome.
  • M may be A, G, T, or C, and need not be considered in identifying a sequence as unique.
  • a guide sequence is selected to reduce the degree of secondary structure within the guide sequence.
  • Secondary structure may be determined by any suitable polynucleotide folding algorithm. Some programs are based on calculating the minimal Gibbs free energy. An example of one such algorithm is mFold, as described by Zuker & Stiegler ⁇ Nucleic Acids Res. 9 (1981), 133-148). Another example folding algorithm is the online Webserver RNAfold, developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see, e.g., A. R. Gruber el al, 2008, Cell 106(1): 23-24; and PA Carr & GM Church, 2009, Nature Biotechnology 27(12): 1151- 62).
  • the guide sequence is linked to a tracr mate sequence which in turn hybridizes to a tracr sequence.
  • a tracr mate sequence includes any sequence that has sufficient complementarity with a tracr sequence to promote one or more of: (1) excision of a guide sequence flanked by tracr mate sequences in a cell containing the corresponding tracr sequence; and (2) formation of a complex at a target sequence, wherein the complex comprises the tracr mate sequence hybridized to the tracr sequence.
  • degree of complementarity is with reference to the optimal alignment of the tracr mate sequence and tracr sequence, along the length of the shorter of the two sequences.
  • Optimal alignment may be determined by any suitable alignment algorithm, and may further account for secondary structures, such as self-complementarity within either the tracr sequence or tracr mate sequence.
  • the degree of complementarity between the tracr sequence and tracr mate sequence along the length of the shorter of the two when optimally aligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97.5%, 99%, or higher.
  • the tracr sequence is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length.
  • the tracr sequence and tracr mate sequence are contained within a single transcript, such that hybridization between the two produces a transcript having a secondary structure, such as a hairpin.
  • Preferred loop forming sequences for use in hairpin structures are four nucleotides in length, and most preferably have the sequence GAAA. However, longer or shorter loop sequences may be used, as may alternative sequences.
  • the sequences preferably include a nucleotide triplet (for example, AAA), and an additional nucleotide (for example C or G). Examples of loop forming sequences include CAAA and AAAG.
  • the transcript or transcribed polynucleotide sequence has at least two or more hairpins. In certain embodiments, the transcript has two, three, four or five hairpins. In a further embodiment of the disclosure, the transcript has at most five hairpins.
  • the single transcript further includes a transcription termination sequence; preferably this is a polyT sequence, for example, six T nucleotides.
  • a transcription termination sequence preferably this is a polyT sequence, for example, six T nucleotides.
  • a polyT sequence for example, six T nucleotides.
  • single polynucleotides comprising a guide sequence, a tracr mate sequence, and a tracr sequence are as follows (listed 5' to 3'), where “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator:
  • sequences (1) to (3) are used in combination with Cas9 from S. thermophilus CRISPR1.
  • sequences (4) to (6) are used in combination with Cas9 from S. pyogenes.
  • the tracr sequence is a separate transcript from a transcript comprising the tracr mate sequence.
  • a guide RNA typically comprises a tracrRNA framework allowing for Cas9 binding, and a guide sequence, which confers sequence specificity to the Cas9:nucleic acid editing enzyme/domain fusion protein.
  • the guide RNAs for use in accordance with the disclosed methods of editing comprise a backbone structure that is recognized by an S. pyogenes Cas9 protein or domain, such as an SpCas9 domain of the disclosed base editors.
  • the backbone structure recognized by an SpCas9 protein may comprise the sequence 5'-[guide sequence]- guuuuagagcuagaaauagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaaguggcaccgagucggugcuuu uu-3' (SEQ ID NO: 53), wherein the guide sequence comprises a sequence that is complementary to the protospacer of the target sequence. See U.S. Publication No. 2015/0166981, published June 18, 2015, the disclosure of which is incorporated by reference herein.
  • the guide sequence is typically 20 nucleotides long.
  • the guide RNAs for use in accordance with the disclosed methods of editing comprise a backbone structure that is recognized by an S. aureus Cas9 protein.
  • the backbone structure recognized by an SaCas9 protein may comprise the sequence 5 '-[guide sequence] - guuuuaguacucuguaaugaaaauuacagaaucuacuaaaacaaggcaaaaugccguguuuaucucgucaacuuguugg cgagauuuuuuuuu-3' (SEQ ID NO: 147).
  • suitable guide RNAs for targeting Cas9:nucleic acid editing enzyme/domain fusion proteins to specific genomic target sites will be apparent to those of skill in the art based on the instant disclosure.
  • Such suitable guide RNA sequences typically comprise guide sequences that are complementary to a nucleic sequence within 50 nucleotides upstream or downstream of the target nucleotide to be edited.
  • Some exemplary guide RNA sequences suitable for targeting any of the provided fusion proteins to specific target sequences are provided herein. Additional guide sequences are are well known in the art and may be used with the fusion proteins described herein.
  • the disclosure further relates in various aspects to methods of making the disclosed fusion proteins by various modes of manipulation that include, but are not limited to, codon optimization of one or more domains of the fusion proteins (e.g ., of a transglycosylase) to achieve greater expression levels in a cell, and the use of nuclear localization sequences (NLSs), preferably at least two NLSs, e.g., two bipartite NLSs, to increase the localization of the expressed fusion proteins into a cell nucleus.
  • NLSs nuclear localization sequences
  • the fusion proteins contemplated herein can include modifications that result in increased expression, for example, through codon optimization.
  • the fusion proteins (or a component thereof) is codon optimized for expression in particular cells, such as eukaryotic cells (e.g. mammalian cells or human cells).
  • eukaryotic cells e.g. mammalian cells or human cells.
  • the eukaryotic cells may be those of or derived from a particular organism, such as a mammal, including, but not limited to, human, mouse, rat, rabbit, dog, or non human primate.
  • codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon (e.g., about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence.
  • codon bias differs in codon usage between organisms
  • mRNA messenger RNA
  • tRNA transfer RNA
  • Codon usage tables are readily available, for example, at the “Codon Usage Database,” and these tables can be adapted in a number of ways. See Nakamura, Y., el al. “Codon usage tabulated from the international DNA sequence databases: status for the year 2000” Nucl. Acids Res. 28:292 (2000).
  • Computer algorithms for codon optimizing a particular sequence for expression in a particular host cell are also available, such as Gene Forge (Aptagen; Jacobus, PA), are also available.
  • one or more codons in a sequence encoding a CRISPR enzyme correspond to the most frequently used codon for a particular amino acid.
  • nucleic acid constructs are codon-optimized for expression in HEK293T cells.
  • nucleic acid constructs are codon-optimized for expression in mammalian cells.
  • nucleic acid constructs are codon-optimized for expression in human cells.
  • Directed evolution methods e.g., PACE or PANCE
  • Various embodiments of the disclosure relate to providing directed evolution methods and systems (e.g., appropriate vectors, cells, phage, flow vessels, etc.) for engineering of the base editors or base editor domains of the present disclosure.
  • the disclosure provides vector systems for the disclosed directed evolution methods to engineer any of the disclosed fusion protein or fusion protein domains (e.g., the transglycosylase domains of any of the disclosed fusion proteins).
  • the directed evolution vector systems and methods provided herein allow for a gene of interest (e.g., a fusion protein- or transglycosylasr-encoding gene) in a viral vector to be evolved over multiple generations of viral life cycles in a flow of host cells to acquire a desired function or activity.
  • a gene of interest e.g., a fusion protein- or transglycosylasr-encoding gene
  • the gene under selection is encoded on the M13 bacteriophage genome. Its activity is linked to M13 propagation by controlling expression of gene III so that only active variants produce infectious progeny phage. Phage are continuously propagated and mutagenized, but mutations accumulate only in the phage genome, not the host or its selection circuit, because fresh host cells are continually flowed into (and out of) the growth vessel, effectively resetting the selection background.
  • PACE enables the rapid continuous evolution of biomolecules through many generations of mutation, selection, and replication per day.
  • host E. coli cells continuously dilute a population of bacteriophage (selection phage, SP) containing the gene of interest.
  • the gene of interest replaces gene III on the SP, which is required for progeny phage infectivity.
  • SP containing desired gene variants trigger host-cell gene III expression from an accessory plasmid (AP).
  • AP accessory plasmid
  • Host-cell DNA plasmids encode a genetic circuit that links the desired activity of the protein encoded in the SP to the expression of gene III on the AP.
  • SP variants containing desired gene variants can propagate, while phage encoding inactive variants do not generate infectious progeny and are rapidly diluted out of the culture vessel (or lagoon).
  • An arabinose-inducible mutagenesis plasmid (MP) controls the phage mutation rate.
  • the viral vector or the phage is a filamentous phage, for example, an M13 phage, such as an M13 selection phage as described in more detail elsewhere herein.
  • the gene required for the production of infectious viral particles is the M13 gene III (gill).
  • the viral vector infects mammalian cells.
  • the viral vector is a retroviral vector.
  • the viral vector is a vesicular stomatitis virus (VSV) vector.
  • VSV vesicular stomatitis virus
  • the generation of infectious VSV particles requires the envelope protein VSV-G, a viral glycoprotein that mediates phosphatidylserine attachment and cell entry.
  • VSV can infect a broad spectrum of host cells, including mammalian and insect cells. VSV is therefore a highly suitable vector for continuous evolution in human, mouse, or insect host cells.
  • other retroviral vectors that can be pseudotyped with VSV-G envelope protein are equally suitable for continuous evolution processes as described herein.
  • Murine Leukemia Vims vectors, or Lentiviral vectors can efficiently be packaged with VSV- G envelope protein as a substitute for the vims’s native envelope protein.
  • VSV-G packagable vectors are adapted for use in a continuous evolution system in that the native envelope (env) protein (e.g., VSV-G in VSVS vectors, or env in MLV vectors) is deleted from the viral genome, and a gene of interest is inserted into the viral genome under the control of a promoter that is active in the desired host cells.
  • env native envelope
  • the host cells express the VSV-G protein, another env protein suitable for vector pseudotyping, or the viral vector’s native env protein, under the control of a promoter the activity of which is dependent on an activity of a product encoded by the gene of interest, so that a viral vector with a mutation leading to increased activity of the gene of interest will be packaged with higher efficiency than a vector with baseline or a loss-of-function mutation.
  • mammalian host cells are subjected to infection by a continuously evolving population of viral vectors, for example, VSV vectors comprising a gene of interest and lacking the VSV-G encoding gene, wherein the host cells comprise a gene encoding the VSV-G protein under the control of a conditional promoter.
  • viral vectors for example, VSV vectors comprising a gene of interest and lacking the VSV-G encoding gene, wherein the host cells comprise a gene encoding the VSV-G protein under the control of a conditional promoter.
  • retrovirus-bases system could be a two-vector system (the viral vector and an expression construct comprising a gene encoding the envelope protein), or, alternatively, a helper virus can be employed, for example, a VSV helper vims.
  • a helper virus typically comprises a truncated viral genome deficient of structural elements required to package the genome into viral particles, but including viral genes encoding proteins required for viral genome processing in the host cell, and for the generation of viral particles.
  • the viral vector-based system could be a three-vector system (the viral vector, the expression construct comprising the envelope protein driven by a conditional promoter, and the helper vims comprising viral functions required for viral genome propagation but not the envelope protein).
  • expression of the five genes of the VSV genome from a helper vims or expression constmct in the host cells allows for production of infectious viral particles carrying a gene of interest, indicating that unbalanced gene expression permits viral replication at a reduced rate, suggesting that reduced expression of VSV-G would indeed serve as a limiting step in efficient viral production.
  • helper virus One advantage of using a helper virus is that the viral vector can be deficient in genes encoding proteins or other functions provided by the helper virus, and can, accordingly, carry a longer gene of interest.
  • the helper virus does not express an envelope protein, because expression of a viral envelope protein is known to reduce the infectability of host cells by some viral vectors via receptor interference.
  • Viral vectors for example retroviral vectors, suitable for continuous evolution processes, their respective envelope proteins, and helper viruses for such vectors, are well known to those of skill in the art.
  • helper viruses for continuous evolution procedures as described herein, see Coffin et al, Retroviruses, CSHL Press 1997, ISBN0-87969-571-4, incorporated herein in its entirety.
  • the incubating of the host cells is for a time sufficient for at least 10, at least 20, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least, 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1250, at least 1500, at least 1750, at least 2000, at least 2500, at least 3000, at least 4000, at least 5000, at least 7500, at least 10000, or more consecutive viral life cycles.
  • the viral vector is an M13 phage, and the length of a single viral life cycle is about 10-20 minutes.
  • a viral vector/host cell combination is chosen in which the life cycle of the viral vector is significantly shorter than the average time between cell divisions of the host cell.
  • Average cell division times and viral vector life cycle times are well known in the art for many cell types and vectors, allowing those of skill in the art to ascertain such host cell/vector combinations.
  • host cells are being removed from the population of host cells contacted with the viral vector at a rate that results in the average time of a host cell remaining in the host cell population before being removed to be shorter than the average time between cell divisions of the host cells, but to be longer than the average life cycle of the viral vector employed.
  • the host cells on average, do not have sufficient time to proliferate during their time in the host cell population while the viral vectors do have sufficient time to infect a host cell, replicate in the host cell, and generate new viral particles during the time a host cell remains in the cell population.
  • the average time a host cell remains in the host cell population is about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 70, about 80, about 90, about 100, about 120, about 150, or about 180 minutes.
  • the average time a host cell remains in the host cell population depends on how fast the host cells divide and how long infection (or conjugation) requires.
  • the flow rate should be faster than the average time required for cell division, but slow enough to allow viral (or conjugative) propagation.
  • the former will vary, for example, with the media type, and can be delayed by adding cell division inhibitor antibiotics (FtsZ inhibitors in E. coli, etc.). Since the limiting step in continuous evolution is production of the protein required for gene transfer from cell to cell, the flow rate at which the vector washes out will depend on the current activity of the gene(s) of interest. In some embodiments, titratable production of the protein required for the generation of infectious particles, as described herein, can mitigate this problem.
  • an indicator of phage infection allows computer-controlled optimization of the flow rate for the current activity level in real-time.
  • the fresh host cells comprise the accessory plasmid required for selection of viral vectors, for example, the accessory plasmid comprising the gene required for the generation of infectious phage particles that is lacking from the phages being evolved.
  • the host cells are generated by contacting an uninfected host cell with the relevant vectors, for example, the accessory plasmid and, optionally, a mutagenesis plasmid, and growing an amount of host cells sufficient for the replenishment of the host cell population in a continuous evolution experiment.
  • Methods for the introduction of plasmids and other gene constructs into host cells are well known to those of skill in the art and the disclosure is not limited in this respect.
  • such methods include, but are not limited to, electroporation and heat-shock of competent cells.
  • the accessory plasmid comprises a selection marker, for example, an antibiotic resistance marker, and the fresh host cells are grown in the presence of the respective antibiotic to ensure the presence of the plasmid in the host cells.
  • a selection marker for example, an antibiotic resistance marker
  • different markers are typically used. Such selection markers and their use in cell culture are known to those of skill in the art, and the disclosure is not limited in this respect.
  • a first accessory plasmid comprises gene III
  • a second accessory plasmid comprises a T7 RNAP gene deactivated by a G to T mutation, which results in an early stop codon.
  • a third acessory plasmid may comprise a nucleotide encoding a dCas9 fused at the N terminus to the C-terminal half of a fast-splicing intein.
  • An exemplary phage plasmid may comprise a nucleotide encoding a transglycosylase fused at the C terminus to the N-terminal half of the fast-splicing intein.
  • the full-length fusion protein is reconstituted from the two intein components.
  • the full-length base editor may be reconstituted from the two intein components. Sucessful replication of phage progeny would require the base editor to perform T to G transversion mutations in the T7 RNAP gene, allowing sucessful translation of full-length T7 RNAP and subsequent transcription of gene III.
  • the nucleotide encoding a guide RNA targeting dCas9 to the appropriate sequence of T7RNAP may be located on any of these acessory plasmids. For instance, it may be located on the first accessory plasmid, i.e. the same accessory plasmid on which gene III is located.
  • This accessory plasmid design emulates the PACE circuit of cytosine base editors, as disclosed in Thuronyi el al, Continuous evolution of base editors with expanded target compatibility and improved activity, Nat Biotechnol. 2019 Jul 22, International Application No. PCT/US2019/37216, filed June 14, 2019, and International Patent Publication WO 2019/023680, published January 31, 2019, each of which are incorporated herein by reference.
  • the selection marker is a spectinomycin antibiotic resistance marker.
  • Cells are transformed with a selection plasmid containing an inactivated spectinomycin resistance gene with a mutation at an active site that requires A:T to C:G editing to correct. Cells that fail to install the correct transversion mutation in the spectinomycin resistance gene will die, while cells that make the correction will survive.
  • E. coli cells expressing an sgRNA targeting the active site mutation in the spectinomycin resistance gene and a nucleotide modification domain-dCas9 fusion protein are plated onto 2xYT agar with 256 pg/mL of spectinomycin.
  • the selection marker is a chloramphenicol antibiotic resistance marker.
  • E. coli cells expressing an sgRNA targeting the active site mutation in the chloramphenicol resistance gene and a nucleotide modification domain-dCas9 fusion protein are plated onto 2xYT agar with 256 pg/mL of chloramphenicol. Surviving colonies (measured through CFUs) were sequenced to find consensus mutations in the fusion proteins expressed in the evolved survivors.
  • the selection marker is a carbenicillin antibiotic resistance marker.
  • Cells are transformed with a selection plasmid containing an inactivated carbenicillin resistance gene with a mutation at an active site that requires A:T to C:G editing to correct. Cells that fail to install the correct transversion mutation in the spectinomycin resistance gene will die, while cells that make the correction will survive.
  • E. coli cells expressing an sgRNA targeting the active site mutation in the carbenecillin resistance gene and a nucleotide modification domain-dCas9 fusion protein are plated onto 2xYT agar with 256 pg/mL of carbenicillin. Surviving colonies (measured through CFUs) were sequenced to find consensus mutations in the fusion proteins expressed in the evolved survivors.
  • the host cell population in a continuous evolution experiment is replenished with fresh host cells growing in a parallel, continuous culture.
  • the cell density of the host cells in the host cell population contacted with the viral vector and the density of the fresh host cell population is substantially the same.
  • the cells being removed from the cell population contacted with the viral vector comprise cells that are infected with the viral vector and uninfected cells.
  • cells are being removed from the cell populations continuously, for example, by effecting a continuous outflow of the cells from the population.
  • cells are removed semi-continuously or intermittently from the population.
  • the replenishment of fresh cells will match the mode of removal of cells from the cell population, for example, if cells are continuously removed, fresh cells will be continuously introduced.
  • the modes of replenishment and removal may be mismatched, for example, a cell population may be continuously replenished with fresh cells, and cells may be removed semi-continuously or in batches.
  • the rate of fresh host cell replenishment and/or the rate of host cell removal is adjusted based on quantifying the host cells in the cell population.
  • the turbidity of culture media comprising the host cell population is monitored and, if the turbidity falls below a threshold level, the ratio of host cell inflow to host cell outflow is adjusted to effect an increase in the number of host cells in the population, as manifested by increased cell culture turbidity. In other embodiments, if the turbidity rises above a threshold level, the ratio of host cell inflow to host cell outflow is adjusted to produce a decrease in the number of host cells in the population, as manifested by decreased cell culture turbidity.
  • Maintaining the density of host cells in the host cell population within a specific density range ensures that enough host cells are available as hosts for the evolving viral vector population, and avoids the depletion of nutrients at the cost of viral packaging and the accumulation of cell-originated toxins from overcrowding the culture.
  • the cell density in the host cell population and/or the fresh host cell density in the inflow is about 10 2 cells/ml to about 10 12 cells/ml.
  • the host cell density is about 10 2 cells/ml, about 10 3 cells/ml, about 10 4 cells/ml, about 10 5 cells/ml, about 5 ⁇ 10 5 cells/ml, about 10 6 cells/ml, about 5 ⁇ 10 6 cells/ml, about 10 7 cells/ml, about 5 ⁇ 10 7 cells/ml, about 10 8 cells/ml, about 5 ⁇ 10 8 cells/ml, about 10 9 cells/ml, about 5 ⁇ 10 9 cells/ml, about 10 10 cells/ml, or about 5 ⁇ 10 10 cells/ml.
  • the host cell density is more than about 10 10 cells/ml.
  • the host cell population is contacted with a mutagen.
  • the cell population contacted with the viral vector e.g ., the phage
  • the mutagen is continuously exposed to the mutagen at a concentration that allows for an increased mutation rate of the gene of interest, but is not significantly toxic for the host cells during their exposure to the mutagen while in the host cell population.
  • the host cell population is contacted with the mutagen intermittently, creating phases of increased mutagenesis, and accordingly, of increased viral vector diversification.
  • the host cells are exposed to a concentration of mutagen sufficient to generate an increased rate of mutagenesis in the gene of interest for about 10%, about 20%, about 50%, or about 75% of the time.
  • the host cells comprise a mutagenesis expression construct, for example, in the case of bacterial host cells, a mutagenesis plasmid.
  • the mutagenesis plasmid comprises a gene expression cassette encoding a mutagenesis- promoting gene product, for example, a proofreading-impaired DNA polymerase.
  • the mutagenesis plasmid including a gene involved in the SOS stress response, ( e.g ., UmuC, UmuD', and/or RecA).
  • the mutagenesis- promoting gene is under the control of an inducible promoter.
  • Suitable inducible promoters are well known to those of skill in the art and include, for example, arabinose-inducible promoters, tetracycline or doxycyclin-inducible promoters, and tamoxifen-inducible promoters.
  • the host cell population is contacted with an inducer of the inducible promoter in an amount sufficient to produce an increased rate of mutagenesis.
  • a bacterial host cell population is provided in which the host cells comprise a mutagenesis plasmid in which a dnaQ926, UmuC, UmuD', and RecA expression cassette is controlled by an arabinose-inducible promoter.
  • the population of host cells is contacted with the inducer, for example, arabinose in an amount sufficient to induce an increased rate of mutation.
  • diversifying the viral vector population is achieved by providing a flow of host cells that does not select for gain-of-function mutations in the gene of interest for replication, mutagenesis, and propagation of the population of viral vectors.
  • the host cells are host cells that express all genes required for the generation of infectious viral particles, for example, bacterial cells that express a complete helper phage, and, thus, do not impose selective pressure on the gene of interest.
  • the host cells comprise an accessory plasmid comprising a conditional promoter with a baseline activity sufficient to support viral vector propagation even in the absence of significant gain-of-function mutations of the gene of interest.
  • phage vectors for phage-assisted continuous evolution are provided.
  • a selection phage is provided that comprises a phage genome deficient in at least one gene required for the generation of infectious phage particles and a gene of interest to be evolved.
  • phage vectors for phage-assisted continuous evolution are provided.
  • a selection phage is provided that comprises a phage genome deficient in at least one gene required for the generation of infectious phage particles and a gene of interest to be evolved.
  • the selection phage comprises an M13 phage genome deficient in a gene required for the generation of infectious M13 phage particles, for example, a full-length gill.
  • the selection phage comprises a phage genome providing ah other phage functions required for the phage life cycle except the gene required for generation of infectious phage particles.
  • an M13 selection phage is provided that comprises a gl, gll, gIV, gV, gVI, gVII, gVIII, glX, and a gX gene, but not a full-length gill.
  • the 3'- fragment of gill comprises the last 180 bp, the last 150 bp, the last 125 bp, the last 100 bp, the last 50 bp, or the last 25 bp of gill. In some embodiments, the 3'- fragment of gill comprises the last 180 bp of gill.
  • M13 selection phage comprises a gene of interest in the phage genome, for example, inserted downstream of the gVIII 3 '-terminator and upstream of the gIII-3 '-promoter.
  • an M13 selection phage is provided that comprises a multiple cloning site for cloning a gene of interest into the phage genome, for example, a multiple cloning site (MCS) inserted downstream of the gVIII 3 '-terminator and upstream of the gill- 3 '-promoter.
  • MCS multiple cloning site
  • a vector system for continuous evolution procedures comprising of a viral vector, for example, a selection phage, and a matching accessory plasmid.
  • a vector system for phage-based continuous directed evolution comprises (a) a selection phage comprising a gene of interest to be evolved, wherein the phage genome is deficient in a gene required to generate infectious phage; and (b) an accessory plasmid comprising the gene required to generate infectious phage particle under the control of a conditional promoter, wherein the conditional promoter is activated by a function of a gene product encoded by the gene of interest.
  • the selection phage is an M 13 phage as described herein.
  • the selection phage comprises an M13 genome including all genes required for the generation of phage particles, for example, gl, gll, gIV, gV, gVI, gVII, gVIII, glX, and gX gene, but not a full-length gill gene.
  • the selection phage genome comprises an FI or an M 13 origin of replication.
  • the selection phage genome comprises a 3 '-fragment of gill gene.
  • the selection phage comprises a multiple cloning site upstream of the gill 3 '-promoter and downstream of the gVIII 3 '-terminator.
  • Some embodiments of this disclosure provide a method of non-continuous evolution of a gene of interest.
  • the method of non-continuous evolution is PANCE.
  • the method of non-continuous evolution is an antibiotic or plate-based selection method.
  • the cells are re-transformed with the mutagenesis plasmid regularly to ensure the plasmid has not been inactivated.
  • An aliquot of a desired concentration, often 2 mL, is then transferred to a smaller flask, supplemeted with inducing agent arabinose (Ara) for the mutagenesis plasmid, and infected with the selection phage (SP).
  • a drift plasmid can also be provided that enables phage to propagate without passing the selection.
  • Expression is under the control of an inducible promoter and can be turned on with 50 ng/mL of anhydrotetracycline. This culture is incubated at 37 °C for 8-12 h to facilitate phage growth, which is confirmed by determination of the phage titer. Following phage growth, an aliquot of infected cells is used to transfect a subsequent flask containing host E. coli. This process is continued until the desired phenotype is evolved for as many transfers as required, while increasing the stringency in stepwise fashion by decreasing the incubation time or titer of phage with which the bacteria is infected. Reference is made to Suzuki T. et al, Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase, Nat Chem Biol. 13(12): 1261-1266 (2017), incorporated herein in its entirety.
  • negative selection is applied during a non-continuous evolution method as described herein, by penalizing undesired activities. In some embodiments, this is achieved by causing the undesired activity to interfere with pill production.
  • expression of an antisense RNA complementary to the gill RBS and/or start codon is one way of applying negative selection, while expressing a protease ( e.g ., TEV) and engineering the protease recognition sites into pill is another.
  • Vectors may be designed to clone and/or express the fusion proteins as disclosed herein.
  • Vectors may also be designed to transfect the fusion proteins and gRNAs of the disclosure into one or more cells, e.g., a target diseased eukaryotic cell for treatment with the fusion protein systems and methods disclosed herein.
  • Vectors can be designed for expression of fusion protein transcripts (e.g ., nucleic acid transcripts, proteins, or enzymes) in prokaryotic or eukaryotic cells.
  • fusion protein transcripts can be expressed in bacterial cells, such as Escherichia coli, insect cells (using baculovirus expression vectors), yeast cells, or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods In Enzymology 185, Academic Press. San Diego, Calif. (1990).
  • expression vectors encoding one or more fusion proteins described herein can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
  • Vectors for rational mutagenesis methods such as PACE may be introduced and propagated in a prokaryotic cells.
  • a prokaryote is used to amplify copies of a vector to be introduced into a eukaryotic cell or as an intermediate vector in the production of a vector to be introduced into a eukaryotic cell (e.g., amplifying a plasmid as part of a viral vector packaging system).
  • a prokaryote is used to amplify copies of a vector and express one or more nucleic acids, such as to provide a source of one or more proteins for delivery to a host cell or host organism. Expression of proteins in prokaryotes is most often carried out in Escherichia coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins.
  • Fusion expression vectors also may be used to express the fusion proteins of the disclosure. Such vectors generally add a number of amino acids to a protein encoded therein, such as to the amino terminus of the recombinant protein. Such fusion vectors may serve one or more purposes, such as: (i) to increase expression of a recombinant protein; (ii) to increase the solubility of a recombinant protein; and (iii) to aid in the purification of a recombinant protein by acting as a ligand in affinity purification.
  • a proteolytic cleavage site is introduced at the junction of the fusion domain and the recombinant protein to enable separation of the recombinant protein from the fusion domain subsequent to purification of the fusion protein.
  • enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
  • Exemplary fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith and Johnson, 1988.
  • GST glutathione S-transferase
  • a vector is a yeast expression vector for expressing the fusion proteins described herein.
  • yeast expression vectors for expression in yeast Saccharomyces cerivisae include pYepSecl (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa (Kuijan and Herskowitz, 1982.
  • a vector drives protein expression in insect cells using baculovims expression vectors.
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith, et al, 1983. Mol. Cell. Biol. 3: 2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170: 31-39).
  • a vector is capable of driving expression of one or more sequences in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, 1987.
  • the expression vector's control functions are typically provided by one or more regulatory elements.
  • promoters are derived from polyoma, adenovirus 2, cytomegalovirus, simian vims 40, and others disclosed herein and known in the art.
  • suitable expression systems for both prokaryotic and eukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al, Molecular Cloning: A Faboratory Manual.
  • the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid).
  • tissue-specific regulatory elements are known in the art.
  • suitable tissue-specific promoters include the albumin promoter (liver- specific; Pinkert, et al., 1987. Genes Dev. 1: 268-277), lymphoid- specific promoters (Calame and Eaton, 1988. Adv. Immunol.
  • promoters of T cell receptors Winoto and Baltimore, 1989. EMBO J. 8: 729-733 and immunoglobulins (Baneiji, et al., 1983. Cell 33: 729-740; Queen and Baltimore, 1983. Cell 33: 741-748), neuron- specific promoters (e.g., the neurofilament promoter; Byme and Ruddle, 1989. Proc. Natl. Acad. Sci. USA 86: 5473-5477), pancreas-specific promoters (Edlund, et al., 1985. Science 230: 912-916), and mammary gland- specific promoters (e.g., milk whey promoter, U.S. Pat.
  • mammary gland- specific promoters e.g., milk whey promoter, U.S. Pat.
  • the method is a method for editing a nucleobase of a nucleic acid (e.g ., a base pair of a double- stranded DNA sequence).
  • the method comprises contacting a target region of a nucleic acid (e.g., a double- stranded transglycosylase domain) and a guide nucleic acid (e.g., gRNA), wherein the target region comprises a targeted nucleobase pair.
  • strand separation of said target region is induced, a first nucleobase of said target nucleobase pair in a single strand of the target region is converted to a second nucleobase, and no more than one strand of said target region is cut (or nicked), wherein a third nucleobase complementary to the first nucleobase base is replaced by a fourth nucleobase complementary to the second nucleobase.
  • the first nucleobase is a thymine (of the target T:A nucleobase pair).
  • the second nucleobase is a guanine (i.e., the T is converted to G).
  • the third nucleobase is a adenine (of the target T:A base pair), and the fourth nucleobase is a cytosine, thereby generating an intended edited base pair (e.g., T:A pair to a G:C pair).
  • At least 5% of the intended base pairs are edited. In some embodiments, at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% of the intended base pairs are edited.
  • the ratio of intended products to unintended products in the target nucleotide is at least 2:1, 5:1, 10:1, 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, 100:1, or 200:1, or more. In some embodiments, the ratio of intended point mutation to indel formation is greater than 1:1, 10:1, 50:1, 100:1, 500:1, or 1000:1, or more.
  • the cut single strand (nicked strand) is hybridized to the guide nucleic acid. In some embodiments, the cut single strand is opposite to the strand comprising the first nucleobase. In some embodiments, the fusion protein comprises nickase activity.
  • the intended edited base pair is upstream of a PAM site. In some embodiments, the intended edited base pair is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides upstream of the PAM site. In some embodiments, the intended edited base pair is downstream of a PAM site. In some embodiments, the intended edited base pair is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides downstream stream of the PAM site. In some embodiments, the target region comprises a target window, wherein the target window comprises the target nucleobase pair. In some embodiments, the target window comprises 1-10 nucleotides.
  • the target window is 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, or 1 nucleotides in length. In some embodiments, the target window is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides in length.
  • the intended edited base pair is within the target window. In some embodiments, the target window comprises the intended edited base pair. In some embodiments, the method is performed using any of the fusion proteins provided herein.
  • a target window is a editing window. In some embodiments, the target window is an editing window of 2-20 nucleotides, preferably 2-10 or 2-8 nucleotides.
  • the disclosure provides editing methods comprising contacting a DNA, or RNA molecule with any of the fusion proteins provided herein, and with at least one guide nucleic acid (e.g., guide RNA), wherein the guide nucleic acid, (e.g., guide RNA) is about 15-100 nucleotides long and comprises a sequence of at least 10 contiguous nucleotides that is complementary to a target sequence.
  • the 3' end of the target sequence is immediately adjacent to a canonical PAM sequence (NGG).
  • the 3' end of the target sequence is not immediately adjacent to a canonical PAM sequence (NGG).
  • the 3' end of the target sequence is immediately adjacent to an AGC, GAG, TTT, GTG, or CAA sequence.
  • the target nucleic acid sequence comprises a sequence associated with a disease, disorder, or condition. In some embodiments, the target nucleic acid sequence comprises a point mutation associated with a disease, disorder, or condition.
  • the activity of the fusion protein results in a correction of the point mutation.
  • the target nucleic acid sequence comprises a G T point mutation associated with a disease, disorder, or condition, and wherein the conversion of the mutant T to a G results in a sequence that is not associated with a disease, disorder, or condition.
  • the target sequence may comprise a C A point mutation associated with a disease, disorder, or condition, and wherein the conversion of the mutant A to a C results in a sequence that is not associated with a disease, disorder, or condition.
  • the target nucleic acid sequence encodes a protein
  • the point mutation is in a codon and results in a change in the amino acid encoded by the mutant codon as compared to the wild- type codon.
  • the transversion of the mutant T (or mutant A) results in a change of the amino acid encoded by the mutant codon.
  • the transversion of the mutant T (or mutant A) results in the codon encoding the wild-type amino acid.
  • the contacting is in vivo in a subject.
  • the subject has or has been diagnosed with a disease, disorder, or condition.
  • the disease, disorder, or condition is congenital deafness, spastic paraplegia, nonsyndromic hearing loss, spinal muscular atrophy, or hypohidrotic ectodermal dysplasia.
  • the base editors are used to introduce a point mutation into a nucleic acid by exchanging a target T nucleobase for a guanin nucleobase.
  • the transglycosylation and exchange of the target nucleobase results in the correction of a genetic defect, e.g., in the correction of a point mutation that leads to a loss of function in a gene product.
  • the genetic defect is associated with a disease, disorder, or condition, e.g., a lysosomal storage disorder or a metabolic disease, such as, for example, type I diabetes.
  • the methods provided herein are used to introduce a deactivating point mutation into a gene or allele that encodes a gene product that is associated with a disease, disorder, or condition.
  • methods are provided herein that employ a DNA editing fusion protein to introduce a deactivating point mutation into an oncogene (e.g., in the treatment of a proliferative disease).
  • a deactivating mutation may, in some embodiments, generate a premature stop codon in a coding sequence, which results in the expression of a truncated gene product, e.g., a truncated protein lacking the function of the full-length protein.
  • the methods provided herein are intended to restore the function of a dysfunctional gene via genome editing.
  • the fusion protein proteins provided herein can be validated for gene editing-based human therapeutics in vitro, e.g., by correcting a disease-associated mutation in human cell culture. It will be understood by the skilled artisan that the fusion proteins provided herein, e.g., the fusion proteins comprising a nucleic acid programmable DNA binding protein (e.g., Cas9) and a nucleotide modification domain can be used to correct any single point T to G or A to C mutation. Transglycosylase- mediated exchange of the mutant T that is base-paired with the mutant A, followed by a round of replication, corrects the mutation.
  • a nucleic acid programmable DNA binding protein e.g., Cas9
  • the present disclosure provides methods for the treatment of a subject diagnosed with a disease associated with or caused by a point mutation that can be corrected by a DNA editing fusion protein provided herein.
  • a method comprises administering to a subject having such a disease, e.g., a cancer associated with a point mutation as described above, an effective amount of a transglycosylase fusion protein and a gRNA that forms a complex with the fusion protein, that corrects the point mutation or introduces a deactivating mutation into a disease- associated gene.
  • a method comprises administering to a subject having such a disease, e.g., a cancer associated with a point mutation as described above, an effective amount of a transglycosylase fusion protein-gRNA complex that corrects the point mutation or introduces a deactivating mutation into a disease-associated gene.
  • methods comprising administering to a subject one or more vectors that contains a nucleotide sequence that expresses the fusion protein and gRNA that forms a complex with the fusion protein.
  • the disease is a proliferative disease.
  • the disease is a genetic disease.
  • the disease is a neoplastic disease.
  • the disease is a metabolic disease.
  • Other diseases that can be treated by correcting a point mutation or introducing a deactivating mutation into a disease-associated gene will be known to those of skill in the art, and the disclosure is not limited in this respect.
  • the instant disclosure provides methods for the treatment of additional diseases or disorders, e.g., diseases or disorders that are associated or caused by a point mutation that can be corrected by transglycosylase-mediated gene editing.
  • Exemplary suitable diseases and disorders include, without limitation: Non-Bruton type Agammaglobulinemia, Hypomyelinating Leukodystrophy, 21 -hydroxylase deficiency, familial Breast-ovarian cancer, Immunodeficiency with basal ganglia calcification, Congenital myasthenic syndrome, Shprintzen-Goldberg syndrome, Peroxisome biogenesis disorder, Nephronophthisis, autosomal recessive early-onset, digenic, PINK1/DJ1 Parkinson disease, Cerebral visual impairment and intellectual disability,
  • Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart Immunodeficiency, Leber congenital amaurosis, Amyotrophic lateral sclerosis type 10, Motor neuron disease, Malignant melanoma of skin, Local cortical dysplasia type II, papillary Renal cell carcinoma, Glioblastoma, Colorectal Neoplasms, Uterine cervical neoplasms, sporadic Papillary renal cell carcinoma, Malignant neoplasm of body of uterus, Kidney Carcinoma, Neoplasm of the breast, Glioblastoma, Smith-Kingsmore syndrome, Homocysteinemia due to MTHPR deficiency, type 2A2A Charcot-Marie-Tooth disease, Bartter syndrome type 3, Cataract, multiple types, Gastrointestinal stroma tumor, Paragangliomas, Pheochromocytoma, Hereditary cancer-predisposing syndrome, Paragangliomas, Hereditary cancer-pre
  • Thrombocythemia somatic, Hematologic neoplasm, Early infantile epileptic encephalopathy, Mental retardation, autosomal recessive, Familial porphyria cutanea tarda, MYH-associated polyposis, Hereditary cancer-predisposing syndrome, MUTYH- associated polyposis, Hereditary cancer-predisposing syndrome, Methylmalonic acidemia with homocystinuria, Methylmalonic aciduria and homocystinuria, cblC type, digenic, Muscle eye brain disease, Congenital Muscular Dystrophy, alpha-dystroglycan related, Limb-Girdle Muscular Dystrophy, Recessive, Muscle eye brain disease, Congenital muscular dystrophy- dystroglycanopathy with brain and eye anomalies, type A3, Adenocarcinoma of the colon, Congenital primary aphakia, Hepatic failure, early-onset, and
  • Ovarian Serous Cystadenocarcinoma Malignant neoplasm of body of uterus, RAS Inhibitor response, Malignant lymphoma, non-Hodgkin, Medulloblastoma, Malignant melanoma of skin, Multiple myeloma, Acute myeloid leukemia, Myelodysplastic syndrome, Cutaneous melanoma, Transitional cell carcinoma of the bladder, Neoplasm, Colorectal Neoplasms, Adenocarcinoma of stomach, Cutaneous melanoma, Malignant melanoma of skin, Multiple myeloma, Acute myeloid leukemia, Noonan syndrome, Myelodysplastic syndrome,
  • Hereditary nephrotic syndrome Nephrotic syndrome, idiopathic, steroid-resistant, Pituitary hormone deficiency, combined, Glutamine deficiency, congenital, Prostate cancer, hereditary, Junctional epidermolysis bullosa gravis of Herlitz, Hyperparathyroidism, Factor H deficiency, Basal laminar drusen, CFHR5 deficiency, Factor XIII subunit B deficiency, Primary autosomal recessive microcephaly 5, Macular dystrophy, Leber congenital amaurosis, Retinitis pigmentosa, Leber congenital amaurosis, Macular dystrophy, Acute myeloid leukemia with maturation, Microcephaly, primary, autosomal recessive, Hypokalemic periodic paralysis, Left ventricular noncompaction, Familial hypertrophic cardiomyopathy, Left ventricular noncompaction, Familial restrictive cardiomyopathy, Cardiovascular phenotype, Renal
  • Lung adenocarcinoma Cutaneous melanoma, Hepatocellular carcinoma, Transitional cell carcinoma of the bladder, Colorectal Neoplasms, Adrenocortical carcinoma, Malignant neoplasm of body of uterus, Adenocarcinoma of prostate, Nemaline myopathy, Spinocerebellar ataxia, autosomal recessive, Perrault syndrome, Hydrops, lactic acidosis, and sideroblastic anemia, Perrault syndrome, Bardet-Biedl syndrome, Bardet-Biedl syndrome, Failure of tooth eruption, primary, Gray platelet syndrome, Pretibial epidermolysis bullosa, Epidermolysis bullosa pruriginosa, autosomal dominant, Recessive dystrophic epidermolysis bullosa, Microcephaly, progressive, with seizures and cerebral and cerebellar atrophy, Epileptic encephalopathy, Nephrotic syndrome, type 5, with or without ocular abnormalities, Muscular dys
  • Neoplasms Multiple myeloma, Squamous cell carcinoma of the head and neck, Lung adenocarcinoma, Non-small cell lung cancer, Squamous cell lung carcinoma, Colorectal Neoplasms, Non small cell lung cancer, Rasopathy, Neoplasm of the breast, Neoplasm, Carcinoma of colon, Noonan syndrome, Cataract and cardiomyopathy, Myotonia congenital, Congenital myotonia, autosomal recessive form, Premature ovarian failure, Cortical dysplasia-focal epilepsy syndrome, Rolandic epilepsy, Pitt-Hopkins-like syndrome, Rolandic epilepsy, Long QT syndrome, Congenital long QT syndrome, Short QT syndrome, Cardiovascular phenotype, Long QT syndrome, Glaucoma, open angle, F, Glycogen storage disease of heart, lethal congenital, Familial hypertrophic cardiomyopathy, Primary familial hypertrophic cardiomyopathy, Holoprosencephaly, Currarino
  • LAMM labyrinthine aplasia microtia and microdontia
  • LAMM labyrinthine aplasia microtia and microdontia
  • LAMM labyrinthine aplasia microtia and microdontia
  • SLM labyrinthine aplasia microtia and microdontia
  • SLM labyrinthine aplasia microtia and microdontia
  • IB Usher syndrome
  • MY07A-Related Disorders polycystic liver disease with or without kidney cysts
  • Tremor hereditary essential
  • Mitochondrial complex I deficiency Mitochondrial diseases, Tyrosinase-negative oculocutaneous albinism, Tyrosinase-negative oculocutaneous albinism, Oculocutaneous albinism type IB, Albinism, ocular, with sensorineural deafness, Skin/hair/eye pigmentation, variation
  • APOA4* l/APOA4*2 Hyperalphalipoproteinemia, Coronary heart disease, Apolipoprotein A-I (Baltimore), Immunodeficiency, Kabuki syndrome, Wiedemann-Steiner syndrome, Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay, Glucose-6- phosphate transport defect, Acute intermittent porphyria, Congenital myasthenic syndrome, Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia, Microphthalmia, isolated, Gaze palsy, familial horizontal, with progressive scoliosis, Megalencephalic leukoencephalopathy with subcortical cysts 2a, Deficiency of isobutyryl- CoA dehydrogenase, Cone dystrophy, Retinal cone dystrophy, Megalencephaly- polymicrogyria-polydactyly-hydrocephalus syndrome, Tumoral
  • Alzheimer disease type 3, Alzheimer disease, type 3, Pick's disease, Alzheimer disease, type 3, Frontotemporal dementia, Pick's disease, Acne inversa, familial, Coenzyme Q10 deficiency, primary, Methylmalonate semialdehyde dehydrogenase deficiency, Niemann-Pick disease type C2, Niemann-Pick disease, type C, Leukoencephalopathy with vanishing white matter, Carcinoma of colon, Endometrial carcinoma, Hereditary nonpolyposis colorectal cancer type 7, Lynch syndrome, MLH3-Related Lynch Syndrome, Nevus comedonicus, Proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome, Cone-rod dystrophy, Congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies, type A2, Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B2, Limb-girdle muscular dystrophy-dystrogly
  • Marfan lipodystrophy syndrome Cardiovascular phenotype, Marfan syndrome, Thoracic aortic aneurysm and aortic dissection, Thoracic aortic Aneurysm and dissection (TAAD), Cardiovascular phenotype, Stiff skin syndrome, Marfan syndrome, Thoracic aortic aneurysm and aortic dissection, Thoracic aortic Aneurysm and dissection (TAAD), Marfan Syndrome/Loeys-Dietz Syndrome/Familial Thoracic Aortic Aneurysms and Dissections, Cardiovascular phenotype, Seckel syndrome, Aromatase deficiency, Lethal congenital contracture syndrome, Intellectual developmental disorder with cardiac arrhythmia, Primary ciliary dyskinesia, Craniosynostosis, Parkinson disease, age at onset, susceptibility to, Parkinson disease, Parkinson disease, autosomal recessive early-onset, Hyperchlorhidrosis, isolated, Nemaline myopathy,
  • Bile acid synthesis defect congenital, Generalized epilepsy with febrile seizures plus, type 9, Warfarin response, warfarin response - Dosage, Warfarin response, Familial renal glucosuria, Glycogen storage disease IXb, Behcet's syndrome, Cylindromatosis, familial, Townes-Brocks syndrome, Joubert syndrome, Hamamy syndrome, Multicentric osteolysis, nodulosis and arthropathy, Bardet-Biedl syndrome, Retinitis pigmentosa, Nephrotic syndrome, type 12, Familial hypokalemia-hypomagnesemia, Spondyloepimetaphyseal dysplasia, Faden-Alkuraya type, Polymicrogyria, bilateral frontoparietal, Lissencephaly, with microcephaly, Retinitis pigmentosa, Poikiloderma with neutropenia, Brachioskeletogenital syndrome, Mitochondrial DNA depletion syndrome, Lamella
  • Neoplasm of brain Neoplasm of the breast
  • Glioblastoma Hepatocellular carcinoma
  • Hereditary cancer- predisposing syndrome Pancreatic adenocarcinoma
  • Transitional cell carcinoma of the bladder Brainstem glioma, Carcinoma of esophagus, Colorectal Neoplasms,
  • Adenocarcinoma of stomach Ovarian Serous Cystadenocarcinoma, Adenocarcinoma of prostate, Uterine Carcinosarcoma, Liver cancer, Chronic lymphocytic leukemia, Multiple myeloma, Squamous cell carcinoma of the head and neck, Lung adenocarcinoma, Li- Fraumeni syndrome, Neoplasm of brain, Neoplasm of the breast, Glioblastoma, Hepatocellular carcinoma, Pancreatic adenocarcinoma, Transitional cell carcinoma of the bladder, Carcinoma of esophagus, Colorectal Neoplasms, Uterine cervical neoplasms, Adenocarcinoma of stomach, Ovarian Serous Cystadenocarcinoma, Malignant neoplasm of body of uterus, Uterine Carcinosarcoma, Li-Fraumeni syndrome, Liver cancer,
  • Hepatocellular carcinoma Hereditary cancer-predisposing syndrome, Liver cancer,
  • Malignant melanoma of skin Multiple myeloma, Squamous cell carcinoma of the head and neck, Lung adenocarcinoma, Breast cancer, somatic, Squamous cell lung carcinoma, Neoplasm of brain, Neoplasm of the breast, Hepatocellular carcinoma, Breast adenocarcinoma, Hereditary cancer-predisposing syndrome, Pancreatic adenocarcinoma, Transitional cell carcinoma of the bladder, Carcinoma of esophagus, Colorectal Neoplasms, Adenoid cystic carcinoma, Adenocarcinoma of stomach, Ovarian Serous Cystadenocarcinoma, Malignant neoplasm of body of uterus, Uterine Carcinosarcoma, Carcinoma of pancreas, Dyskeratosis congenita, autosomal recessive, Leber congenital amaurosis, Cone-rod dystrophy, Autosomal recessive congenital ichthyosis
  • Congenital cataract, Klippel-feil syndrome, autosomal recessive, with nemaline myopathy and facial dysmorphism Hermansky-Pudlak syndrome, Cataract, congenital nuclear, autosomal recessive, Cataract, multiple types, Familial cancer of breast, Hereditary cancer- predisposing syndrome, Hereditary cancer-predisposing syndrome, Familial cancer of breast, Prostate cancer, somatic, Hereditary cancer-predisposing syndrome, Osteosarcoma, Neurofibromatosis, type 2, Epilepsy, familial focal, with variable foci, Rolandic epilepsy, Parkinson disease, Sorsby fundus dystrophy, Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss, Microcytic anemia, Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease, Waardenburg syndrome type 4C, Parkinson disease
  • Pathogenic T to G or A to C mutations may be corrected using the methods and compositions provided herein, for example, by mutating the T to an A, and/or the A to a T, thereby restoring gene function.
  • Guide RNAs (gRNA) sequences which encode RNA that can direct a napDNAbp, or any of the fusion proteins provided herein, to a target site gRNA sequences may be cloned into an expression vector, such as Addgene pFYF1320 (which targets EGFP), to encode a gRNA that targets a napDNAbp, or any of the fusion proteins provided herein, to a target site in order to correct a disease-related mutation.
  • Pharmaceutical compositions such as Addgene pFYF1320 (which targets EGFP), to encode a gRNA that targets a napDNAbp, or any of the fusion proteins provided herein, to a target site in order to correct a disease-related mutation.
  • compositions comprising any of the fusion proteins or the fusion protein-gRNA complexes described herein.
  • pharmaceutical composition refers to a composition formulated for pharmaceutical use.
  • the pharmaceutical composition further comprises a pharmaceutically acceptable carrier.
  • the pharmaceutical composition comprises additional agents (e.g ., for specific delivery, for targeted delivery, increasing half-life, or other therapeutic compounds).
  • any of the fusion proteins, gRNAs, and/or complexes described herein are provided as part of a pharmaceutical composition.
  • the pharmaceutical composition comprises any of the fusion proteins provided herein.
  • the pharmaceutical composition comprises any of the complexes provided herein.
  • pharmaceutical composition comprises a gRNA, a napDNAbp fusion protein, and a pharmaceutically acceptable excipient.
  • pharmaceutical composition comprises a gRNA, a transglycosylase-nCas9 fusion protein, and a pharmaceutically acceptable excipient.
  • Pharmaceutical compositions may optionally comprise one or more additional therapeutically active substances.
  • compositions provided herein are administered to a subject, for example, to a human subject, in order to effect a targeted genomic modification within the subject.
  • cells are obtained from the subject and contacted with a any of the pharmaceutical compositions provided herein.
  • cells removed from a subject and contacted ex vivo with a pharmaceutical composition are re-introduced into the subject, optionally after the desired genomic modification has been effected or detected in the cells.
  • compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with merely ordinary, if any, experimentation.
  • Subjects to which administration of the pharmaceutical compositions is contemplated include, but are not limited to, humans and/or other primates; mammals, domesticated animals, pets, and commercially relevant mammals such as cattle, pigs, horses, sheep, cats, dogs, mice, and/or rats; and/or birds, including commercially relevant birds such as chickens, ducks, geese, and/or turkeys.
  • Formulations of the pharmaceutical compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology. In general, such preparatory methods include the step of bringing the active ingredient(s) into association with an excipient and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.
  • compositions may additionally comprise a pharmaceutically acceptable excipient, which, as used herein, includes any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
  • a pharmaceutically acceptable excipient includes any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired.
  • Remington s The Science and Practice of Pharmacy, 21 st Edition, A. R. Gennaro (Lippincott, Williams & Wilkins, Baltimore, MD, 2006; incorporated in its entirety herein by reference) discloses various excipient
  • the term “pharmaceutically acceptable carrier” means a pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g ., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body).
  • a pharmaceutically acceptable carrier is “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g ., physiologically compatible, sterile, physiologic pH, etc.).
  • materials which can serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as com starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as ethyl
  • wetting agents coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservative and antioxidants may also be present in the formulation.
  • excipient carrier
  • pharmaceutically acceptable carrier or the like are used interchangeably herein.
  • the pharmaceutical composition is formulated for delivery to a subject, e.g., for gene editing.
  • Suitable routes of administrating the pharmaceutical composition described herein include, without limitation: topical, subcutaneous, transdermal, intradermal, intralesional, intraarticular, intraperitoneal, intravesical, transmucosal, gingival, intradental, intracochlear, transtympanic, intraorgan, epidural, intrathecal, intramuscular, intravenous, intravascular, intraosseus, periocular, intratumoral, intracerebral, and intracerebroventricular administration.
  • the pharmaceutical composition described herein is administered locally to a diseased site.
  • the pharmaceutical composition described herein is administered to a subject by injection, by means of a catheter, by means of a suppository, or by means of an implant, the implant being of a porous, non-porous, or gelatinous material, including a membrane, such as a sialastic membrane, or a fiber.
  • the pharmaceutical composition is formulated in accordance with routine procedures as a composition adapted for intravenous or subcutaneous administration to a subject, e.g., a human.
  • pharmaceutical composition for administration by injection are solutions in sterile isotonic aqueous buffer.
  • the pharmaceutical can also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection.
  • a solubilizing agent such as lignocaine to ease pain at the site of the injection.
  • the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent.
  • the pharmaceutical is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline.
  • an ampoule of sterile water for injection or saline can be provided so that the ingredients can be mixed prior to administration.
  • the pharmaceutical composition can be contained within a lipid particle or vesicle, such as a liposome or microcrystal, which is also suitable for parenteral administration.
  • the particles can be of any suitable structure, such as unilamellar or plurilamellar, so long as compositions are contained therein.
  • Compounds can be entrapped in “stabilized plasmid- lipid particles” (SPLP) containing the fusogenic lipid dioleoylphosphatidylethanolamine (DOPE), low levels (5-10 mol%) of cationic lipid, and stabilized by a polyethyleneglycol (PEG) coating (Zhang Y. P. et al, Gene Ther. 1999, 6:1438-47).
  • SPLP stabilized plasmid- lipid particles
  • lipids such as N-[l-(2,3-dioleoyloxi)propyl]-N,N,N-trimethyl-amoniummethylsulfate, or “DOTAP,” are particularly preferred for such particles and vesicles.
  • DOTAP N-[l-(2,3-dioleoyloxi)propyl]-N,N,N-trimethyl-amoniummethylsulfate
  • the preparation of such lipid particles is well known. See, e.g., U.S. Patent Nos. 4,880,635; 4,906,477; 4,911,928; 4,917,951; 4,920,016; 4,921,757; and 9,526,784, each of which is incorporated herein by reference.
  • the pharmaceutical composition described herein may be administered or packaged as a unit dose, for example.
  • unit dose when used in reference to a pharmaceutical composition of the present disclosure refers to physically discrete units suitable as unitary dosage for the subject, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent; i.e., carrier, or vehicle.
  • the pharmaceutical composition can be provided as a pharmaceutical kit comprising (a) a container containing a compound of the disclosure in lyophilized form and (b) a second container containing a pharmaceutically acceptable diluent (e.g., sterile water) for injection.
  • a pharmaceutically acceptable diluent e.g., sterile water
  • the pharmaceutically acceptable diluent can be used for reconstitution or dilution of the lyophilized compound of the disclosure.
  • Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.
  • an article of manufacture containing materials useful for the treatment of the diseases described above is included.
  • the article of manufacture comprises a container and a label.
  • Suitable containers include, for example, bottles, vials, syringes, and test tubes.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition that is effective for treating a disease described herein and may have a sterile access port.
  • the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle.
  • the active agent in the composition is a compound of the disclosure.
  • the label on or associated with the container indicates that the composition is used for treating the disease of choice.
  • the article of manufacture may further comprise a second container comprising a pharmaceutically acceptable buffer, such as phosphate-buffered saline, Ringer’s solution, or dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.
  • the disclosure provides methods comprising delivering any of the fusion proteins, gRNAs, and/or complexes described herein.
  • the disclosure provides methods comprising delivery of one or more vectors as described herein, one or more transcripts thereof, and/or one or proteins transcribed therefrom, to a host cell.
  • the disclosure further provides cells produced by such methods, and organisms (such as animals, plants, or fungi) comprising or produced from such cells.
  • a fusion protein as described herein in combination with (and optionally complexed with) a guide sequence is delivered to a cell.
  • Non-viral vector delivery systems include ribonucleoprotein (RNP) complexes, DNA plasmids, RNA (e.g., a transcript of a vector described herein), naked nucleic acid, and nucleic acid complexed with a delivery vehicle, such as a liposome.
  • RNP ribonucleoprotein
  • Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell.
  • the method of delivery and vector provided herein is an RNP complex.
  • RNP delivery of fusion proteins markedly increases the DNA specificity of base editing.
  • RNP delivery of fusion proteins leads to decoupling of on- and off-target editing.
  • Methods of non-viral delivery of nucleic acids include RNP complexes, lipofection, nucleofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipidmucleic acid conjugates, naked DNA, artificial virions, and agent- enhanced uptake of DNA.
  • Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g., TransfectamTM and LipofectinTM).
  • Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Feigner, WO 1991/17424; WO 1991/16024. Delivery can be to cells (e.g., in vitro or ex vivo administration) or target tissues (e.g., in vivo administration).
  • lipidmucleic acid complexes including targeted liposomes such as immunolipid complexes
  • crystal Science 270:404-410 (1995); Blaese et al., Cancer Gene Ther. 2:291-297 (1995); Behr et al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos.
  • RNA or DNA viral based systems for the delivery of nucleic acids take advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus.
  • Viral vectors can be administered directly to patients ⁇ in vivo ) or they can be used to treat cells in vitro , and the modified cells may optionally be administered to patients ⁇ ex vivo).
  • Conventional viral based systems could include retroviral, lentivirus, adenoviral, adeno-associated and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues.
  • Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression.
  • Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia vims (GaLV), Simian Immuno deficiency vims (SIV), human immuno deficiency vims (HIV), and combinations thereof (see, e.g., Buchscher et al, J. Virol. 66:2731-2739 (1992); Johann et al., J. Virol. 66:1635-1640 (1992); Sommnerfelt et al., Virol. 176:58-59 (1990); Wilson et al., J. Virol. 63:2374-2378 (1989); Miller etal, J. Virol. 65:2220-2224 (1991);
  • Adenoviral based systems may be used.
  • Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system.
  • Adeno-associated vims (“AAV”) vectors may also be used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al, Virology 160:38-47 (1987); U.S. Pat. No.
  • Packaging cells are typically used to form vims particles that are capable of infecting a host cell. Such cells include 293 cells, which package adenovirus, and y2 cells or PA317 cells, which package retrovirus.
  • Viral vectors used in gene therapy are usually generated by producing a cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the polynucleotide(s) to be expressed. The missing viral functions are typically supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome which are required for packaging and integration into the host genome.
  • Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences.
  • the cell line may also be infected with adenovirus as a helper.
  • the helper vims promotes replication of the AAV vector and expression of AAV genes from the helper plasmid.
  • the helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovims is more sensitive than AAV. Additional methods for the delivery of nucleic acids to cells are known to those skilled in the art.
  • the disclosed expression constructs may be engineered for delivery in one or more rAAV vectors.
  • An rAAV as related to any of the methods and compositions provided herein may be of any serotype including any derivative or pseudotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 2/1, 2/5, 2/8, 2/9, 3/1, 3/5, 3/8, or 3/9).
  • An rAAV may comprise a genetic load (i.e ., a recombinant nucleic acid vector that expresses a gene of interest, such as a whole or split fusion protein that is carried by the rAAV into a cell) that is to be delivered to a cell.
  • an rAAV may be chimeric.
  • the serotype of an rAAV refers to the serotype of the capsid proteins of the recombinant virus.
  • Non-limiting examples of derivatives and pseudotypes include rAAV2/l, rAAV2/5, rAAV2/8, rAAV2/9, AAV2-AAV3 hybrid, AAVrh.lO, AAVhu.14, AAV3a/3b, AAVrh32.33, AAV-HSC15, AAV-HSC17, AAVhu.37, AAVrh.8, CHt-P6, AAV2.5, AAV6.2, AAV2i8, AAV-HSC15/17, AAVM41, AAV9.45, AAV6(Y445F/Y731F), AAV2.5T, AAV-HAE1/2, AAV clone 32/83, AAVShHIO, AAV2 (Y->F), AAV8 (Y733F), AAV2.1
  • a non-limiting example of derivatives and pseudotypes that have chimeric VP1 proteins is rAAV2/5-lVPlu, which has the genome of AAV2, capsid backbone of AAV5 and VPlu of AAV1.
  • Other non-limiting example of derivatives and pseudotypes that have chimeric VP1 proteins are rAAV2/5-8VPlu, rAAV2/9-lVPlu, and rAAV2/9-8VPlu.
  • AAV derivatives/pseudotypes, and methods of producing such derivatives/pseudotypes are known in the art (see, e.g., Mol Ther. 2012 Apr;20(4):699-708. doi: 10.1038/mt.2011.287. Epub 2012 Jan 24.
  • the AAV vector toolkit poised at the clinical crossroads. Asokan Al, Schaffer DV, Samulski RJ.).
  • Methods for producing and using pseudotyped rAAV vectors are known in the art (see, e.g., Duan et al, J. Virol., 75:7662- 7671, 2001; Halbert et al, J. Virol., 74:1524-1532, 2000; Zolotukhin et al, Methods, 28:158- 167, 2002; and Auricchio et al., Hum. Molec. Genet., 10:3075-3081, 2001).
  • Methods of making or packaging rAAV particles are known in the art and reagents are commercially available (see, e.g., Zolotukhin et al. Production and purification of serotype 1, 2, and 5 recombinant adeno-associated viral vectors. Methods 28 (2002) 158-167; and U.S. Patent Publication Numbers US20070015238 and US20120322861, which are incorporated herein by reference; and plasmids and kits available from ATCC and Cell Biolabs, Inc.).
  • a plasmid comprising a gene of interest may be combined with one or more helper plasmids, e.g., that contain a rep gene (e.g., encoding Rep78, Rep68, Rep52 and Rep40) and a cap gene (encoding VP1, VP2, and VP3, including a modified VP2 region as described herein), and transfected into a recombinant cells such that the rAAV particle can be packaged and subsequently purified.
  • helper plasmids e.g., that contain a rep gene (e.g., encoding Rep78, Rep68, Rep52 and Rep40) and a cap gene (encoding VP1, VP2, and VP3, including a modified VP2 region as described herein)
  • the fusion proteins can be divided at a split site and provided as two halves of a whole/complete fusion protein.
  • the two halves can be delivered to cells (e.g., as expressed proteins or on separate expression vectors) and once in contact inside the cell, the two halves form the complete fusion protein through the self-splicing action of the inteins on each fusion protein half.
  • Split intein sequences can be engineered into each of the halves of the encoded fusion protein to facilitate their transplicing inside the cell and the concomitant restoration of the complete, functioning TGBE.
  • split intein-based methods overcome several barriers to in vivo delivery.
  • the DNA encoding fusion proteins is larger than the recombinant AAV (rAAV) packaging limit, and so requires different solutions.
  • One such solution is formulating the editor fused to split intein pairs that are packaged into two separate rAAV particles that, when co-delivered to a cell, reconstitute the functional editor protein.
  • rAAV recombinant AAV
  • the disclosure provides dual rAAV vectors and dual rAAV vector particles that comprise expression constructs that encode two halves of any of the disclosed fusion proteins, wherein the encoded fusion protein is divided between the two halves at a split site.
  • the two halves may be delivered to cells (e.g., as expressed proteins or on separate expression vectors) and once in contact inside the cell, the two halves form the complete fusion protein through the self-splicing action of the inteins on each fusion protein half.
  • Split intein sequences can be engineered into each of the halves of the encoded fusion protein to facilitate their transplicing inside the cell and the concomitant restoration of the complete, functioning TGBE.
  • the fusion proteins may be engineered as two half proteins (i.e ., an TGBE N-terminal half and a TGBE C-terminal half) by “splitting” the whole fusion protein as a “split site.”
  • the “split site” refers to the location of insertion of split intein sequences (i.e., the N intein and the C intein) between two adjacent amino acid residues in the fusion protein. More specifically, the “split site” refers to the location of dividing the whole fusion protein into two separate halves, wherein in each halve is fused at the split site to either the N intein or the C intein motifs.
  • the split site can be at any suitable location in the fusion protein fusion protein, but preferably the split site is located at a position that allows for the formation of two half proteins which are appropriately sized for delivery (e.g., by expression vector) and wherein the inteins, which are fused to each half protein at the split site termini, are available to sufficiently interact with one another when one half protein contacts the other half protein inside the cell.
  • any fusion protein e.g., any of the fusion proteins provided herein, may be introduced into the cell in any suitable way, either stably or transiently.
  • a fusion protein may be transfected into the cell.
  • the cell may be transduced or transfected with a nucleic acid construct that encodes a fusion protein.
  • a cell may be transduced (e.g., with a virus encoding a fusion protein), or transfected (e.g., with a plasmid encoding a fusion protein) with a nucleic acid that encodes a fusion protein, or the translated fusion protein.
  • transduction may be a stable or transient transduction.
  • cells expressing a fusion protein or containing a fusion protein may be transduced or transfected with one or more gRNA molecules, for example when the fusion protein comprises a Cas9 (e.g., nCas9) domain.
  • Cas9 e.g., nCas9
  • a plasmid expressing a fusion protein may be introduced into cells through electroporation, transient (e.g., lipofection) and stable genome integration (e.g., piggybac) and viral transduction or other methods known to those of skill in the art.
  • kits comprising a nucleic acid construct comprising nucleotide sequences encoding the fusion proteins, gRNAs, and/or complexes described herein. Some embodiments of this disclosure provide kits comprising a nucleic acid construct comprising a nucleotide sequence encoding a transglycosylase-napDNAbp fusion protein capable of recognizing and excising a thymine in a nucleic acid molecule. In some embodiments, the nucleotide sequence encodes any of the transglycosylases provided herein. In some embodiments, the nucleotide sequence comprises a heterologous promoter that drives expression of the fusion protein. The nucleotide sequence may further comprise a heterologous promoter that drives expression of the gRNA, or a heterologous promoter that drives expression of the fusion protein and the gRNA.
  • the kit further comprises an expression construct encoding a guide nucleic acid backbone, e.g., a guide RNA backbone, wherein the construct comprises a cloning site positioned to allow the cloning of a nucleic acid sequence identical or complementary to a target sequence into the guide nucleic acid, e.g., guide RNA backbone.
  • the disclosure further provides kits comprising a fusion protein as provided herein, a gRNA having complementarity to a target sequence, and one or more of the following: cofactor proteins, buffers, media, and target cells (e.g., human cells). Kits may comprise combinations of several or all of the aforementioned components.
  • cells comprising any of the fusion proteins or complexes provided herein.
  • the cells comprise nucleotide constructs that encodes any of the fusion proteins provided herein.
  • the cells comprise any of the nucleotides or vectors provided herein.
  • a host cell is transiently or non-transiently transfected with one or more vectors described herein.
  • a cell is transfected as it naturally occurs in a subject.
  • a cell that is transfected is taken from a subject.
  • the cell is derived from cells taken from a subject, such as a cell line. A wide variety of cell lines for tissue culture are known in the art.
  • Some embodiments of this disclosure provide cells comprising any of the transglycosylases, fusion proteins, or complexes provided herein.
  • the cells comprise a nucleotide that encodes any of the fusion proteins provided herein.
  • the cells comprise any of the nucleotides or vectors provided herein.
  • a host cell is transiently or non-transiently transfected with one or more vectors described herein.
  • a cell is transfected as it naturally occurs in a subject.
  • a cell that is transfected is taken from a subject.
  • the cell is derived from cells taken from a subject, such as a cell line.
  • cell lines for tissue culture are known in the art.
  • Examples of cell lines include, but are not limited to, C8161, CCRF-CEM, MOLT, mIMCD-3, NHDF, HeLa-S3, Huhl, Huh4, Huh7, HUVEC, HASMC, HEKn, HEKa, MiaPaCell, Panel, PC-3, TF1, CTLL- 2, C1R, Rat6, CV1, RPTE, A10, T24, J82, A375, ARH-77, Calul, SW480, SW620, SKOV3, SK-UT, CaCo2, P388D1, SEM-K2, WEHI-231, HB56, TIB55, Jurkat, J45.01, LRMB, Bcl-1, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E, MRC5, MEF, Hep G2, HeLa B, HeLa T4, COS, COS-1, COS-6, COS-M6A
  • a cell transfected with one or more vectors described herein is used to establish a new cell line comprising one or more vector-derived sequences.
  • a cell transiently transfected with the components of a CRISPR system as described herein (such as by transient transfection of one or more vectors, or transfection with RNA), and modified through the activity of a CRISPR complex, is used to establish a new cell line comprising cells containing the modification but lacking any other exogenous sequence.
  • cells transiently or non-transiently transfected with one or more vectors described herein, or cell lines derived from such cells are used in assessing one or more test compounds.
  • E. coli tRNA guanine transglycosylase (TGT) is capable of exchanging an unmodified guanine with a labeled guanine in a target DNA sequence. (See Nonekowski et al., J. Biol. Chem. 277:7178-7182 (2002).) Experiments were conducted to test whether E. coli TGT was capable of catalyzing a similar base exchange in a modified DNA hairpin substrate.
  • E. coli TGT was purified and isolated. TGT was combined into a reaction mix with tritiated guanine and DNA hairpins containing an altered trinucleotide sequence (“NGN”) that mimics the sequence of TGT enzyme’s native tRNA substrate (see FIG. 6A). (The minimal recognition sequence for TGT is “UGU” in tRNA.)
  • NNN trinucleotide sequence
  • UGU trinucleotide sequence
  • TGT successfully catalyzed the replacement of the target guanine with tritiated G across four different sequences (see FIG. 6B). TGT showed highest editing activity against the UGU and AGA target sequences, with the number of radiolabeled hairpin products exceedin 20,000 disintegrations per minute for both targets.
  • E. coli TGT was tethered to an nCas9 using an XTEN linker (SEQ ID NO: 11).
  • the fusion protein was introduced to E. coli cells.
  • mutations are targeted to residues in the active site and/or at the DNA binding interface.
  • variants of TGT are evolved using PACE systems to form a large library of TGT mutants. Mutants are cloned into a vector coding for an N-terminal fusion with a dCas9.
  • Mutants are subjected to selection based on ability to recognize and excise thymine in DNA, subsequently replacing this base with guanine, using a spectinomycin antibiotic resistance assay.
  • the E. coli selection strain is transformed with a) an accessory plasmid containing an TGT mutant-dCas9 fusion and targeting guide RNAs, and b) a selection plasmid containing an inactivated spectinomycin resistance gene with a mutation at the active site that requires T:A-to-G:C editing to correct (FIG. 5).
  • Cells harboring TGT mutants that restore antibiotic resistance are isolated and subjected to further rounds of mutation and selection under varying selection stringencies.
  • TGT variants that confer a survival advantage to E. coli cells containing the edited selection gene of > 100-fold are expressed within a fusion construct comprising a Cas9 nickase, wherein the nickase is tethered to the transglycosylase by a linker (e.g., an XTEN linker).
  • the resulting fusion protein is tested for base editing activity in human and murine cells.
  • Candidate TGBEs are characterized in human (HEK293T) and murine cell lines across > 30 endogenous genomic loci to assess editing efficiency, product purity, the size of the editing window, and sequence context preferences (FIG. 5). Directed evolution is continued until the resulting TGBEs perform at a level useful to the genome editing community (e.g., > 20% editing, > 50% product purity, ⁇ 5% indels, and an editing window of 2-8 nucleotides). Similar to studies reported with previous fusion proteins, off-target high throughput screening analysis is performed for candidate TGBEs at Cas9 nuclease off-target sites the HEK293 genomic locus identified by GUIDE-seq using the same sgRNAs.
  • GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nature Biotechnology 33, 187-197 (2015), incorporated herein in its entirety.
  • E. coli TGT ultimately proves unsuccessful, selections and evolutions are performed using other candidate guanine-generating enzymes that are capable of acting on DNA.
  • These enzymes include, but are not limited to, Salmonella enterica serovar Montevideo DpdA, Streptomyces sp. FXJ7.023 DpdA, Nocardioidaceae bacterium Broad- 1 DpdA, Desulfurobacterium thermolithotrophum DpdA, Cyanothece sp. CCY0110 DpdA, E.
  • the disclosure encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim.
  • any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim.
  • elements are presented as lists, e.g., in Markush group format, each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the disclosure, or embodiments of the disclosure, is/are referred to as comprising particular elements and/or features, certain embodiments of the disclosure or embodiments of the disclosure consist, or consist essentially of, such elements and/or features.

Abstract

La présente invention concerne des éditeurs de base satisfaisant un besoin dans l'état de la technique pour l'installation de transversions ciblées de thymine (T) en guanine (G), ou de manière correspondante, des transversions d'adénine (A) en cytosine (C). Les éditeurs de base comprennent un domaine de protéine de liaison à l'ADN programmable par un acide nucléique et un domaine de transglycosylase. Les éditeurs de bases peuvent être modifiés au moyen de systèmes d'évolution continu ou non continu. La présente invention concerne des variants d'éditeur de base thymine-à-guanine (ou adénine-à-cytosine) pouvant installer des mutations de transversion à base unique dans l'ADN. En outre, l'invention porte sur des procédés d'édition ciblée d'acides nucléiques. L'invention concerne en outre des compositions pharmaceutiques comprenant les éditeurs de bases de l'invention, et des vecteurs et des kits utiles pour la génération de ces éditeurs de bases. Selon certains autres modes de réalisation, l'invention concerne des cellules contenant ces vecteurs. L'invention concerne en outre des procédés comprenant la mise en contact d'une cellule avec les éditeurs de bases et des procédés comprenant l'administration des éditeurs de bases à un sujet.
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