WO2021226558A1 - Methods and compositions for simultaneous editing of both strands of a target double-stranded nucleotide sequence - Google Patents

Methods and compositions for simultaneous editing of both strands of a target double-stranded nucleotide sequence Download PDF

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WO2021226558A1
WO2021226558A1 PCT/US2021/031439 US2021031439W WO2021226558A1 WO 2021226558 A1 WO2021226558 A1 WO 2021226558A1 US 2021031439 W US2021031439 W US 2021031439W WO 2021226558 A1 WO2021226558 A1 WO 2021226558A1
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Prior art keywords
nucleotides
stranded dna
sequence
dna sequence
nucleobase pairs
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French (fr)
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WO2021226558A8 (en
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David R. Liu
Andrew Vito ANZALONE
Jonathan Ma LEVY
Xin Gao
Christopher J. PODRACKY
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Broad Institute Inc
Harvard University
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Broad Institute Inc
Harvard University
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Priority to BR112022022603A priority Critical patent/BR112022022603A2/pt
Priority to AU2021267940A priority patent/AU2021267940A1/en
Priority to JP2022567857A priority patent/JP2023525304A/ja
Priority to CN202180049194.2A priority patent/CN116096873A/zh
Priority to GB2218378.4A priority patent/GB2614813B/en
Priority to DE112021002672.0T priority patent/DE112021002672T5/de
Priority to MX2022014008A priority patent/MX2022014008A/es
Priority to EP21729144.2A priority patent/EP4146804A1/en
Priority to KR1020227042608A priority patent/KR20230019843A/ko
Application filed by Broad Institute Inc, Harvard University filed Critical Broad Institute Inc
Priority to IL297761A priority patent/IL297761A/en
Priority to CA3177481A priority patent/CA3177481A1/en
Publication of WO2021226558A1 publication Critical patent/WO2021226558A1/en
Publication of WO2021226558A8 publication Critical patent/WO2021226558A8/en
Priority to US18/053,269 priority patent/US11912985B2/en
Anticipated expiration legal-status Critical
Priority to US18/534,489 priority patent/US12031126B2/en
Priority to US18/961,081 priority patent/US20250215418A1/en
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    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
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    • C12N15/102—Mutagenizing nucleic acids
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    • C12N15/09—Recombinant DNA-technology
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1241—Nucleotidyltransferases (2.7.7)
    • C12N9/1276—RNA-directed DNA polymerase (2.7.7.49), i.e. reverse transcriptase or telomerase
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    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/07—Nucleotidyltransferases (2.7.7)
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2310/3519—Fusion with another nucleic acid

Definitions

  • each DNA synthesis template encodes a single-stranded DNA sequence comprising an edited portion.
  • Two single-stranded DNA sequences encoded may by complementary to one another and form a duplex that integrates into the target site to be edited.
  • the two single-stranded DNA sequences encoded may comprise a region of complementarity to one another.
  • the method then involves hybridizing the 3 ⁇ end of the free single-strand DNA to the reverse transcription template sequence, thereby priming the reverse transcriptase domain.
  • the method then involves polymerizing a strand of DNA from the 3 ⁇ end, thereby generating a single- strand DNA flap comprising the desired nucleotide change.
  • the method involves replacing an endogenous DNA strand adjacent the cut site with the single-strand DNA flap, thereby installing the desired nucleotide change in the double-stranded DNA sequence.
  • the desired nucleoid change can convert (1) a G:C basepair to a T:A basepair, (2) a G:C basepair to an A:T basepair, (3) a G:C basepair to C:G basepair, (4) a T:A basepair to a G:C basepair, (5) a T:A basepair to an A:T basepair, (6) a T:A basepair to a C:G basepair, (7) a C:G basepair to a G:C basepair, (8) a C:G basepair to a T:A basepair, (9) a C:G basepair to an A:T basepair, (10) an A:T basepair to a T:A basepair, (11) an A:T basepair to a G:C basepair, or (12) an A:T basepair to a C:G basepair.
  • the reverse transcriptase may comprise any one of the amino acid sequences of SEQ ID NOs: 89-100, 105-122, 128-129, 132, 139, 143, 149, 154, 159, 235, 454, 471, 516, 662, 700-716, 739-742, and 766.
  • FIG.1C provides a schematic of an exemplary process for introducing a single nucleotide change, and/or insertion, and/or deletion into a DNA molecule (e.g., a genome) using a fusion protein comprising a reverse transcriptase fused to a Cas9 protein in complex with an extended guide RNA molecule.
  • the guide RNA is extended at the 5 ⁇ end to include a reverse transcriptase template sequence.
  • the schematic shows how a reverse transcriptase (RT) fused to a Cas9 nickase, in a complex with a guide RNA (gRNA), binds the DNA target site and nicks the PAM- containing DNA strand adjacent to the target nucleotide.
  • RT reverse transcriptase
  • gRNA guide RNA
  • FIGs.1J-1K depict a variation of prime editing contemplated herein that replaces the napDNAbp (e.g., SpCas9 nickase) with any programmable nuclease domain, such as zinc finger nucleases (ZFN) or transcription activator-like effector nucleases (TALEN).
  • ZFN zinc finger nucleases
  • TALEN transcription activator-like effector nucleases
  • suitable nucleases do not necessarily need to be “programmed” by a nucleic acid targeting molecule (such as a guide RNA), but rather, may be programmed by defining the specificity of a DNA-binding domain, such as and in particular, a nuclease.
  • a prime editor comprising a fusion protein having a polymerase (e.g., reverse transcriptase) and a napDNAbp (e.g., SpCas9 nickase, e.g., a SpCas9 having a deactivating mutation in an HNH nuclease domain (e.g., H840A) or a deactivating mutation in a RuvC nuclease domain (D10A)) is complexed with a PEgRNA and DNA having a target DNA to be edited.
  • the PEgRNA comprises a spacer, gRNA core (aka gRNA scaffold or gRNA backbone) (which binds to the napDNAbp), and an extension arm.
  • FIG.3E provides the structure of another PEgRNA contemplated herein.
  • the PEgRNA comprises three main component elements ordered in the 5 ⁇ to 3 ⁇ direction, namely: a spacer, a gRNA core, and an extension arm at the 3 ⁇ end.
  • the extension arm may further be divided into the following structural elements in the 5 ⁇ to 3 ⁇ direction, namely: a primer binding site (A), an edit template (B), and a homology arm (C).
  • the orientation of the extension arm (3) can be in the natural 5 ⁇ -to-3 ⁇ direction, or synthesized in the opposite orientation in the 3 ⁇ -to-5 ⁇ direction (relative to the orientation of the PEgRNA molecule overall). It is also noted that one of ordinary skill in the art will be able to select an appropriate DNA polymerase, depending on the nature of the nucleic acid materials of the extension arm (i.e., DNA or RNA), for use in prime editing that may be implemented either as a fusion with the napDNAbp or as provided in trans as a separate moiety to synthesize the desired template-encoded 3 ⁇ single-strand DNA flap that includes the desired edit.
  • the top strand comprises the complement of the “protospacer” and the complement of the PAM sequence and is referred to as the “target strand” because it is the strand that is target by and anneals to the spacer of the PEgRNA.
  • the complementary lower strand is referred to as the “non- target strand” or the “PAM strand” or the “protospacer strand” since it contains the PAM sequence (e.g., NGG) and the protospacer.
  • the PEgRNA depicted would be complexed with a Cas9 or equivalent domain of a prime editor fusion protein. As shown in the schematic, the spacer of the PEgRNA anneals to the complementary region of the protospacer on the target strand.
  • FIG.9A shows a dual-FP reporter for flap-directed mutagenesis.
  • FIG.9B shows stop codon repair in HEK cells.
  • FIG.9C shows sequenced yeast clones after flap repair.
  • FIG.9D shows testing of different flap features in human cells.
  • FIG.10 demonstrates prime editing on plasmid substrates.
  • a dual-fluorescent reporter plasmid was constructed for yeast (S. cerevisiae) expression. Expression of this construct in yeast produces only GFP.
  • the in vitro prime editing reaction introduces a point mutation, and transforms the parent plasmid or an in vitro Cas9(H840A) nicked plasmid into yeast. The colonies are visualized by fluorescence imaging. Yeast dual-FP plasmid transformants are shown.
  • FIG.26B shows a schematic outlining various applications involving protein/peptide tagging, including (a) rendering proteins soluble or insoluble, (b) changing or tracking the cellular localization of a protein, (c) extending the half-life of a protein, (d) facilitating protein purification, and (e) facilitating the detection of proteins.
  • FIG.27 shows an overview of prime editing by installing a protective mutation in PRNP that prevents or halts the progression of prion disease.
  • FIG.28A is a schematic of PE-based insertion of sequences encoding RNA motifs.
  • FIG. 28B is a list (not exhaustive) of some example motifs that could potentially be inserted, and their functions.
  • FIG.29A is a depiction of a prime editor.
  • FIG.29B shows possible modifications to genomic, plasmid, or viral DNA directed by a PE.
  • FIG.29C shows an example scheme for insertion of a library of peptide loops into a specified protein (in this case GFP) via a library of PEgRNAs.
  • FIG.29D shows an example of possible programmable deletions of codons or N-, or C-terminal truncations of a protein using different PEgRNAs. Deletions would be predicted to occur with minimal generation of frameshift mutations.
  • FIG.30 shows a possible scheme for iterative insertion of codons in a continual evolution system, such as PACE.
  • dCas9 was complexed with PEgRNAs containing RT template of varying lengths, then added to DNA substrates along with the indicated components. Reactions were incubated at 37 °C for 1 hour, then analyzed by denaturing urea PAGE and visualized for Cy5 fluorescence.
  • FIG.38E shows primer extension assays performed as in FIG.38D using 3 ⁇ -extended PEgRNAs pre-complexed with dCas9 or Cas9 H840A nickase, and pre-nicked or non-nicked 5 ⁇ -Cy5- labeled dsDNA substrates.
  • FIG.42A shows total C•G-to-T•A editing efficiency at the same target nucleotides for PE2, PE3, BE2max, and BE4max at endogenous HEK3, FANCF, and EMX1 sites in HEK293T cells.
  • FIG.42B shows indel frequency from treatments in FIG.42A.
  • FIG.42C shows the editing efficiency of precise C•G-to-T•A edits (without bystander edits or indels) for PE2, PE3, BE2max, and BE4max at HEK3, FANCF, and EMX1.
  • precise PE combination edits of all possible combinations of C•G-to-T•A conversion at the three targeted nucleotides are also shown.
  • FIG.43E is a graph showing the installation of a G•C-to-T•A transversion mutation in DNMT1 of mouse primary cortical neurons using a dual split-intein PE3 lentivirus system, in which the N-terminal half is Cas9 (1-573) fused to N-intein and through a P2A self-cleaving peptide to GFP–KASH, and the C-terminal half is the C-intein fused to the remainder of PE2.
  • PE2 halves are expressed from a human synapsin promoter that is highly specific for mature neurons. Sorted values reflect editing or indels from GFP-positive nuclei, while unsorted values are from all nuclei.
  • PEgRNAs 1 through 5 contain a 15-nt linker sequence (linker A for PEgRNA 1, linker B for PEgRNAs 2 through 5) between the spacer and the PBS, a 5-nt PBS sequence, and RT templates of 7 nt (PEgRNAs 1 and 2), 8 nt (PEgRNA 3), 15 nt (PEgRNA 4), and 22 nt (PEgRNA 5).
  • PEgRNAs are those used in FIG.44E and 44F; full sequences are listed in Tables 2A-2C.
  • FIG.44B shows in vitro nicking assays of Cas9 H840A using 5 ⁇ -extended and 3 ⁇ - extended PEgRNAs.
  • FIGs.47A-47S show the evaluation of M-MLV RT variants for prime editing.
  • FIG.47A shows the abbreviations for prime editor variants used in this figure.
  • FIG.47B shows targeted insertion and deletion edits with PE1 at the HEK3 locus.
  • FIGs.47C-47H show a comparison of 18 prime editor constructs containing M-MLV RT variants for their ability to install a +2 G•C-to-C•G transversion edit at HEK3 as shown in FIG.47C, a 24-bp FLAG insertion at HEK3 as shown in FIG.
  • FIG.48C shows +5 G•C-to-T•A transversion editing and indels for RUNX1 as in FIG.48A. Values and error bars reflect the mean and s.d. of three independent biological replicates.
  • FIGs.49A-49B show the effects of PE2, PE2 R110S K103L, Cas9 H840A nickase, and dCas9 on cell viability.
  • HEK293T cells were transfected with plasmids encoding PE2, PE2 R110S K103L, Cas9 H840A nickase, or dCas9, together with a HEK3-targeting PEgRNA plasmid.
  • FIGs.53A-53E show FACS gating examples for GFP-positive cell sorting. Below are examples of original batch analysis files outlining the sorting strategy used for generating HEXA 1278+TATC and HBB E6V HEK293T cell lines.
  • FIG.56B shows the same as FIG.56A, but for FANCF.
  • FIG.56C shows the same as in FIG.56A but for HEK3.
  • FIG.56D shows the same as FIG.56A but for RNF2. Values and error bars reflect the mean and s.d. of three independent biological replicates.
  • FIGs.59A-59G show the protocol for cloning 3 ⁇ -extended PEgRNAs into mammalian U6 expression vectors by Golden Gate assembly.
  • FIG.59A shows the cloning overview.
  • FIG.59B shows ‘Step 1: Digest pU6-PEgRNA-GG-Vector plasmid (component 1)’.
  • FIG.59C shows ‘Steps 2 and 3: Order and anneal oligonucleotide parts (components 2, 3, and 4)’.
  • FIG.70A Step 1. Define the target sequence and the edit. Retrieve the sequence of the target DNA region ( ⁇ 200bp) centered around the location of the desired edit (point mutation, insertion, deletion, or combination thereof).
  • FIG.70B Step 2. Locate target PAMs. Identify PAMs in proximity to the edit location. Be sure to look for PAMs on both strands. While PAMs close to the edit position are preferred, it is possible to install edits using protospacers and PAMs that place the nick ⁇ 30 nt from the edit position.
  • FIG.70C Step 3. Locate the nick sites. For each PAM being considered, identify the corresponding nick site.
  • the data shows the editing efficiency of the PE2 construct with the current linker (noted as PE2 – white box) compared to various versions with the linker replaced with a sequence as indicated at the HEK3, EMX1, FANCF, RNF2 loci for representative PEgRNAs for transition, transversion, insertion, and deletion edits.
  • FIGs.91A-91B provide results from Example 7.
  • FIG.97B CRISPResso2 analysis of amplicon sequencing of anticipated junction, showing plasmid backbone and genomic DNA sequence bridged by the pegRNA-templated attP sequence.
  • FIGs.98A-98B show the results of targeted chromosomal translocation with quadruple-flap prime editing.
  • pegRNAs target two regions on different chromosomes. Complementary 3 ⁇ DNA flaps bridge the two chromosome sequences and direct the orientation of the translocation.
  • FIG.98B Targeted translocation between MYC and TIMM44 loci in HEK239T cells.
  • FIG.99 shows installation of Bxb1 attB and attP sites with dual-flap prime editing at IDS locus.
  • HEK293T cells were transfected with PE2 and different pairs of pegRNAs (e.g. in the first column pegRNA A1_a and pegRNA B2_a with templates for installing attP site in the forward direction). The efficiency was measured by HTS.
  • FIGs.100A-100B describe dual-flap-mediated duplication.
  • FIG.100A is a schematic showing dual-flap-mediated duplication at AAVS1 locus in 293T cells.
  • FIG.100B shows results of using dual-flap pegRNA with PE2 for inducing duplication of genetic sequences at AAVS1.
  • FIG.101 shows multi-flap induced new translocation MYC-CCR5.
  • MYC-CCR5 translocation was induced by quad-flap pegRNAs and PE2.
  • MYC-CCR5 translocation events were induced by quadruple-pegRNAs.
  • FIG. 102B shows multi-flap (quadruple-pegRNA) directed 2.7 kb inversion at the AAVS1 in HeLa cells.
  • FIG.103A-103B shows results of inversion efficiency measurement by HTS at CCR5 locus.
  • Cas9 orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus. Additional suitable Cas9 nucleases and sequences will be apparent to those of skill in the art based on this disclosure, and such 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.
  • tracrRNA trans- encoded small RNA
  • rnc 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 endonucleolytically cleaves a linear or circular dsDNA target complementary to the RNA.
  • the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3 ⁇ -5′ exonucleolytically.
  • 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.
  • Transcription terminator – the guide RNA or PEgRNA may comprise a transcriptional termination sequence at the 3 ⁇ of the molecule.
  • Homology arm refers to a portion of the extension arm that encodes a portion of the resulting reverse transcriptase-encoded single strand DNA flap that is to be integrated into the target DNA site by replacing the endogenous strand.
  • the portion of the single strand DNA flap encoded by the homology arm is complementary to the non-edited strand of the target DNA sequence, which facilitates the displacement of the endogenous strand and annealing of the single strand DNA flap in its place, thereby installing the edit. This component is further defined elsewhere.
  • the homology arm is part of the DNA synthesis template since it is by definition encoded by the polymerase of the prime editors described herein.
  • Host cell refers to a cell that can host, replicate, and express a vector described herein, e.g., a vector comprising a nucleic acid molecule encoding a fusion protein comprising a Cas9 or Cas9 equivalent and a reverse transcriptase.
  • intein refers to auto-processing polypeptide domains found in organisms from all domains of life.
  • the MS2 tagging technique is based on the natural interaction of the MS2 bacteriophage coat protein (“MCP” or “MS2cp”) with a stem-loop or hairpin structure present in the genome of the phage, i.e., the “MS2 hairpin.”
  • MCP MS2 bacteriophage coat protein
  • the MS2 tagging technique comprises introducing the MS2 hairpin into a desired RNA molecule involved in prime editing (e.g., a PEgRNA or a tPERT), which then constitutes a specific interactable binding target for an RNA-binding protein that recognizes and binds to that structure.
  • a PEgRNA or a tPERT e.g., a PEgRNA or a tPERT
  • the amino acid sequence of the MCP or MS2cp is: GSASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTI KVEVPKVATQTVGGEELPVAGWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIA ANSGIY (SEQ ID NO: 764).
  • NLS sequences are described in Plank et al., international PCT application, PCT/EP2000/011690, filed November 23, 2000, published as WO/2001/038547 on May 31, 2001, the contents of which are incorporated herein by reference for its disclosure of exemplary nuclear localization sequences.
  • a NLS comprises the amino acid sequence PKKKRKV (SEQ ID NO: 16) or MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO: 17).
  • Nucleic acid molecule refers to a polymer of nucleotides.
  • the terms “prime editing guide RNA” or “PEgRNA” or “extended guide RNA” refer to a specialized form of a guide RNA that has been modified to include one or more additional sequences for implementing the prime editing methods and compositions described herein.
  • the prime editing guide RNA comprise one or more “extended regions” of nucleic acid sequence.
  • the extended regions may comprise, but are not limited to, single-stranded RNA or DNA. Further, the extended regions may occur at the 3 ⁇ end of a traditional guide RNA. In other arrangements, the extended regions may occur at the 5 ⁇ end of a traditional guide RNA.
  • the extension arm (3) further comprises in the 3 ⁇ to 5 ⁇ direction a “primer binding site” (A), an “edit template” (B), and a “homology arm” (C).
  • the extension arm (3) may also comprise an optional modifier region at the 3 ⁇ and 5 ⁇ ends, which may be the same sequences or different sequences.
  • the PEgRNAs may also comprise a transcriptional terminator sequence at the 3 ⁇ end. These sequence elements of the PEgRNAs are further described and defined herein.
  • the polymerase of the prime editor can be an RNA-dependent DNA polymerase (such as, a reverse transcriptase).
  • the polymerase of the prime editor may be a DNA-dependent DNA polymerase.
  • the newly synthesized strand i.e., the replacement DNA strand containing the desired edit
  • the DNA polymerase e.g., reverse transcriptase
  • the DNA polymerase can be fused to the napDNAbp or alternatively can be provided in trans to the napDNAbp.
  • the napDNAbp and guide RNA are released.
  • Steps (f) and (g) relate to the resolution of the single strand DNA flap such that the desired nucleotide change becomes incorporated into the target locus.
  • This process can be driven towards the desired product formation by removing the corresponding 5 ⁇ endogenous DNA flap that forms once the 3 ⁇ single strand DNA flap invades and hybridizes to the endogenous DNA sequence.
  • the cells endogenous DNA repair and replication processes resolves the mismatched DNA to incorporate the nucleotide change(s) to form the desired altered product.
  • the process can also be driven towards product formation with “second strand nicking,” as exemplified in FIG.1F. This process may introduce at least one or more of the following genetic changes: transversions, transitions, deletions, and insertions.
  • multi-flap prime editing is a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a nucleic acid programmable DNA binding protein (“napDNAbp”) working in association with a polymerase (i.e., in the form of a fusion protein or otherwise provided in trans with the napDNAbp), wherein the prime editing system is programmed with a prime editing (PE) guide RNA (“PEgRNA”) that both specifies the target site and templates the synthesis of the desired edit in the form of a replacement DNA strand by way of an extension (either DNA or RNA) engineered onto a guide RNA (e.g., at the 5 ⁇ or 3 ⁇ end, or at an internal portion of a guide RNA).
  • PE prime editing
  • PEgRNA prime editing guide RNA
  • Prime editor refers to the herein described fusion constructs comprising a napDNAbp (e.g., Cas9 nickase) and a reverse transcriptase and is capable of carrying out prime editing on a target nucleotide sequence in the presence of a PEgRNA (or “extended guide RNA”).
  • the term “prime editor” may refer to the fusion protein or to the fusion protein complexed with a PEgRNA, and/or further complexed with a second-strand nicking sgRNA.
  • Primer binding site refers to the nucleotide sequence located on a PEgRNA as a component of the extension arm (typically at the 3 ⁇ end of the extension arm) and serves to bind to the primer sequence that is formed after Cas9 nicking of the target sequence by the prime editor.
  • the Cas9 nickase component of a prime editor nicks one strand of the target DNA sequence, a 3 ⁇ -ended ssDNA flap is formed, which serves a primer sequence that anneals to the primer binding site on the PEgRNA to prime reverse transcription.
  • the PAM sequence can be modified by introducing one or more mutations, including (a) D1135V, R1335Q, and T1337R “the VQR variant”, which alters the PAM specificity to NGAN or NGNG, (b) D1135E, R1335Q, and T1337R “the EQR variant”, which alters the PAM specificity to NGAG, and (c) D1135V, G1218R, R1335E, and T1337R “the VRER variant”, which alters the PAM specificity to NGCG.
  • serine recombinases of the resolvase-invertase group e.g., Tn3 and ⁇ resolvases and the Hin and Gin invertases
  • Tn3 and ⁇ resolvases and the Hin and Gin invertases have modular structures with autonomous catalytic and DNA-binding domains (See, e.g., Grindley et al., “Mechanism of site-specific recombination.” Ann Rev Biochem.2006; 75: 567–605, the entire contents of which are incorporated by reference).
  • M-MLV reverse transcriptase substantially lacking in RNase H activity has also been described. See, e.g., U.S. Pat. No.5,244,797.
  • the invention contemplates the use of any such reverse transcriptases, or variants or mutants thereof.
  • the invention contemplates the use of reverse transcriptases that are error-prone, i.e., that may be referred to as error-prone reverse transcriptases or reverse transcriptases that do not support high fidelity incorporation of nucleotides during polymerization.
  • Phage refers to a virus that infects bacterial cells. Typically, phages consist of an outer protein capsid enclosing genetic material. The genetic material can 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 PACE methods provided herein are ⁇ (Lysogen), T2, T4, T7, T12, R17, M13, MS2, G4, P1, P2, P4, Phi X174, N4, ⁇ 6, and ⁇ 29.
  • the second nick in certain embodiments, can be introduced between about 5-150 nucleotides on the unedited strand away from the site of the PEgRNA-induced nick, or between about 5-140, or between about 5-130, or between about 5-120, or between about 5-110, or between about 5-100, or between about 5-90, or between about 5-80, or between about 5-70, or between about 5-60, or between about 5-50, or between about 5-40, or between about 5-30, or between about 5-20, or between about 5-10.
  • the second nick is introduced between 14-116 nucleotides away from the PEgRNA-induced nick.
  • An exemplary split intein is the Ssp DnaE intein, which comprises two subunits, namely, DnaE-N and DnaE-C.
  • the two different subunits are encoded by separate genes, namely dnaE-n and dnaE-c, which encode the DnaE-N and DnaE-C subunits, respectively.
  • DnaE is a naturally occurring split intein in Synechocytis sp. PCC6803 and is capable of directing trans-splicing of two separate proteins, each comprising a fusion with either DnaE-N or DnaE-C.
  • the sgRNA serves to target the prime editor (or more generally, to target the napDNAbp component of the prime editor) to the desired genomic target site, while the tPERT is used by the polymerase (e.g., a reverse transcriptase) to write new DNA sequence into the target locus once the tPERT is recruited in trans to the prime editor by the interaction of binding domains located on the prime editor and on the tPERT.
  • the binding domains can include RNA- protein recruitment moieties, such as a MS2 aptamer located on the tPERT and an MS2cp protein fused to the prime editor.
  • Trans prime editor RNA template [0334]
  • a “trans prime editor RNA template (tPERT)” refers to a component used in trans prime editing or trans dual prime editing, a modified version of prime editing which operates by separating the PEgRNA into two distinct molecules: a guide RNA and a tPERT molecule.
  • the tPERT molecule is programmed to co-localize with the prime editor complex at a target DNA site, bringing the primer binding site and the DNA synthesis template to the prime editor in trans.
  • Transitions refer to the interchange of purine nucleobases (A ⁇ G) or the interchange of pyrimidine nucleobases (C ⁇ T). This class of interchanges involves nucleobases of similar shape.
  • the compositions and methods disclosed herein are capable of inducing one or more transitions in a target DNA molecule.
  • the compositions and methods disclosed herein are also capable of inducing both transitions and transversion in the same target DNA molecule. These changes involve A ⁇ G, G ⁇ A, C ⁇ T, or T ⁇ C.
  • transversions refer to the following base pair exchanges: A:T ⁇ G:C, G:G ⁇ A:T, C:G ⁇ T:A, or T:A ⁇ C:G.
  • the compositions and methods disclosed herein are capable of inducing one or more transitions in a target DNA molecule.
  • the compositions and methods disclosed herein are also capable of inducing both transitions and transversion in the same target DNA molecule, as well as other nucleotide changes, including deletions and insertions.
  • 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 recurrence.
  • HDR Homology directed repair
  • DSB double-stranded DNA break
  • the presently described multi-flap prime editing systems involve distinct constructs, systems, and methodologies that, in various embodiments, generate pairs or multiple pairs of 3 ⁇ flaps on different strands, which form duplexes comprising desired edits and which become incorporated into target nucleic acid molecules, e.g., at specific loci or edit sites in a genome.
  • the pairs or multiple pairs of 3 ⁇ flaps form duplexes because they comprise reverse complementary sequences which anneal to one another once generated by the prime editors described herein.
  • duplexes become incorporated into the target site by cell-driven mechanisms that naturally replace the endogenous duplex sequences located between adjacent nick sites.
  • the new duplex sequences may be introduced at one or more locations (e.g., at adjacent genomic loci or on two different chromosomal locations), and may comprise one or more sequences of interest, e.g., protein-encoding sequence, peptide-encoding sequence, or RNA-encoding sequence.
  • the guide nucleic-acid “programs” the napDNAbp (e.g., Cas9 or equivalent) to localize and bind to complementary sequence of the protospacer in the DNA.
  • the napDNAbp may be any Class 2 CRISPR-Cas system, including any type II, type V, or type VI CRISPR-Cas enzyme. Given the rapid development of CRISPR-Cas as a tool for genome editing, there have been constant developments in the nomenclature used to describe and/or identify CRISPR-Cas enzymes, such as Cas9 and Cas9 orthologs.
  • 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 DNA.
  • a nickase i.e., capable of cleaving only a single strand of the target double-stranded DNA.
  • Additional suitable Cas9 nucleases and sequences will be apparent to those of skill in the art based on this disclosure, and such 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.
  • 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 multi-flap prime editors described herein may include a dead Cas9, e.g., dead SpCas9, which has no nuclease activity due to one or more mutations that inactive both nuclease domains of Cas9, namely the RuvC domain (which cleaves the non-protospacer DNA strand) and HNH domain (which cleaves the protospacer DNA strand).
  • a dead Cas9 e.g., dead SpCas9
  • the RuvC domain which cleaves the non-protospacer DNA strand
  • HNH domain which cleaves the protospacer DNA strand
  • 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.
  • 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.
  • 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.
  • Cas9 variants Besides dead Cas9 and Cas9 nickase variants, the Cas9 proteins used herein may also include other “Cas9 variants” 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 protein, including any wild type Cas9, or mutant Cas9 (e.g., a dead Cas9 or Cas9 nickase), or fragment Cas9, or circular permutant Cas9, or other variant of Cas9 disclosed herein or known in the art.
  • Cas9 variants 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
  • 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 multi-flap prime 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 multi-flap prime 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 smaller-sized Cas9 variants can include enzymes categorized as type II enzymes of the Class 2 CRISPR-Cas systems.
  • the smaller-sized Cas9 variants can include enzymes categorized as type V enzymes of the Class 2 CRISPR-Cas systems.
  • the smaller-sized Cas9 variants can include enzymes categorized as type VI enzymes of the Class 2 CRISPR-Cas systems.
  • the Cas9 variants can include those categorized as type II, type V, or type VI enzymes of the Class 2 CRISPR- Cas system.
  • the multi-flap prime 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.
  • the multi-flap prime editors described herein can include any Cas9 equivalent.
  • the term “Cas9 equivalent” is a broad term that encompasses any napDNAbp protein that serves the same function as Cas9 in the present multi-flap prime 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 that do not necessarily have any similarity with regard to amino acid sequence and/or three-dimensional structure.
  • the multi-flapprime 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.
  • Cas9 refers to Cas12e, or a variant of Cas12e.
  • Cas9 refers to a Cas12d, or a variant of Cas12d. 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 Cas12e (CasX) or Cas12d (CasY) protein.
  • the napDNAbp is a naturally-occurring Cas12e (CasX) or Cas12d (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), Cas12e (CasX), Cas12d (CasY), Cas12a (Cpf1), Cas12b1 (C2c1), Cas13a (C2c2), Cas12c (C2c3), Argonaute, and Cas12b1.
  • Cas9 e.g., dCas9 and nCas9
  • Cpf1-family proteins Two enzymes from Acidaminococcus and Lachnospiraceae are shown to have efficient genome-editing activity in human cells.
  • Cpf1 proteins are known in the art and have been described previously, for example Yamano et al., “Crystal structure of Cpf1 in complex with guide RNA and target DNA.” Cell (165) 2016, p.949-962; the entire contents of which is hereby incorporated by reference.
  • the Cas protein may include any CRISPR associated protein, including but not limited to, Cas12a, Cas12b1, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof, and preferably comprising a nickase mutation
  • Exemplary Cas9 equivalent protein sequences can include the following: [0399]
  • the multi-flap prime editors described herein may also comprise Cas12a (Cpf1) (dCpf1) variants that may be used as a guide nucleotide sequence-programmable DNA-binding protein domain.
  • the Cas12a (Cpf1) 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 Cas12a (Cpf1) does not have the alfa-helical recognition lobe of Cas9.
  • the RuvC-like domain of Cas12a (Cpf1) is responsible for cleaving both DNA strands and inactivation of the RuvC-like domain inactivates Cas12a (Cpf1) nuclease activity.
  • the napDNAbp is a single effector of a microbial CRISPR-Cas system.
  • Single effectors of microbial CRISPR-Cas systems include, without limitation, Cas9, Cas12a (Cpf1), Cas12b1 (C2c1), Cas13a (C2c2), and Cas12c (C2c3).
  • microbial CRISPR-Cas systems are divided into Class 1 and Class 2 systems. Class 1 systems have multi-subunit effector complexes, while Class 2 systems have a single protein effector.
  • Cas9 and Cas12a (Cpf1) are Class 2 effectors.
  • Cas9 and Cas12a Cpf1
  • Cas12b1, Cas13a, and Cas12c three distinct Class 2 CRISPR-Cas systems
  • Shmakov et 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 are hereby incorporated by reference.
  • Effectors of two of the systems, Cas12b1 and Cas12c contain RuvC-like endonuclease domains related to Cas12a.
  • Cas13a contains an effector with two predicted HEPN RNase domains.
  • Cas12b1 depends on both CRISPR RNA and tracrRNA for DNA cleavage.
  • Bacterial Cas13a 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 Cas12a.
  • 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.
  • AacC2c1 The crystal structure of Alicyclobaccillus acidoterrastris Cas12b1 (AacC2c1) has been reported in complex with a chimeric single-molecule guide RNA (sgRNA). See e.g., Liu et al., “C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism”, Mol.
  • the napDNAbp is a naturally-occurring Cas12b1 (C2c1), Cas13a (C2c2), or Cas12c (C2c3) protein.
  • C2c1 Cas12b1
  • C2c2 Cas13a
  • Cas12c Cas12c
  • H. Cas9 circular permutants [0404]
  • the multi-flap prime 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
  • pyogenes Cas9 1368 amino acids of UniProtKB - Q99ZW2 (CAS9_STRP1) (numbering is based on the amino acid position in SEQ ID NO: 18)): N-terminus-[1268-1368]-[optional linker]-[1-1267]-C-terminus; N-terminus-[1168-1368]-[optional linker]-[1-1167]-C-terminus; N-terminus-[1068-1368]-[optional linker]-[1-1067]-C-terminus; N-terminus-[968-1368]-[optional linker]-[1-967]-C-terminus; N-terminus-[868-1368]-[optional linker]-[1-867]-C-terminus; N-terminus-[768-1368]-[optional linker]-[1-767]-C-terminus; N-terminus-[668-1368]-[optional linker]-[
  • 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: 18): N-terminus-[102-1368]-[optional linker]-[1-101]-C-terminus; N-terminus-[1028-1368]-[optional linker]-[1-1027]-C-terminus; N-terminus-[1041-1368]-[optional linker]-[1-1043]-C-terminus; N-terminus-[1249-1368]-[optional linker]-[1-1248]-C-terminus; or N-terminus-[1300-1368]-[optional linker]-[1-1299]-C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs,
  • 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: 18): N-terminus-[103-1368]-[optional linker]-[1-102]-C-terminus; N-terminus-[1029-1368]-[optional linker]-[1-1028]-C-terminus; N-terminus-[1042-1368]-[optional linker]-[1-1041]-C-terminus; N-terminus-[1250-1368]-[optional linker]-[1-1249]-C-terminus; or N-terminus-[1301-1368]-[optional linker]-[1-1300]-C-terminus, or the corresponding circular permutants of other Cas9 proteins (including other Cas9 orthologs)
  • 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: 18).
  • 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 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: 18) 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.
  • 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: 18.
  • 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: 18 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: 18 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 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 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: 18.
  • 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 multi-flap prime 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.
  • the napDNAbp that functions with a non-canonical PAM sequence is an Argonaute protein.
  • 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 base editing fusion proteins 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”), 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. Accordingly, in some embodiments, any of the fusion proteins 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.
  • a canonical e.g., NGG
  • 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. P., et al., “Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition” Nature Biotechnology 33, 1293-1298 (2015); the entire contents of each are hereby incorporated by reference.
  • 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 Cpf1 (D917, E1006, and D1255) (SEQ ID NO: 74), 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: 75), which has the following amino acid sequence: [0435]
  • the nucleic acid programmable DNA binding protein is a nucleic acid programmable DNA binding protein that does not require a canonical (NGG) PAM 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.
  • Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)).
  • 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.
  • telomeres are then transformed into host bacteria and plaques are screened for the desired mutation.
  • 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.
  • PCR-based site-directed mutagenesis is performed.
  • a selection must be employed in order to reduce the number of non-mutated parental molecules persisting in the reaction.
  • an extended-length PCR method is preferred in order to allow the use of a single PCR primer set.
  • the prime editors described herein may be delivered to cells as two or more fragments which become assembled inside the cell (either by passive assembly, or by active assembly, such as using split intein sequences) into a reconstituted prime editor.
  • the self assembly may be passive whereby the two or more prime editor fragments associate inside the cell covalently or non-covalently to reconstitute the prime editor.
  • the self-assembly may be catalzyed by dimerization domains installed on each of the fragments.
  • the napDNAbp is a canonical SpCas9 polypeptide of SEQ ID NO: 18, as follows: [0447] In certain embodiments, the SpCas9 is split into two fragments at a split site located between residues 1 and 2, or 2 and 3, or 3 and 4, or 4 and 5, or 5 and 6, or 6 and 7, or 7 and 8, or 8 and 9, or 9 and 10, or between any two pair of residues located anywhere between residues 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 1000-1100, 1100-1200, 1200-1300, or 1300-1368 of canonical SpCas9 of SEQ ID NO: 18.
  • any of the evolved and non-evolved components of the base editors herein described may be expressed with split-intein tags in order to facilitate the formation of a complete base editor comprising the evolved and non-evolved component within a cell.
  • the mechanism of the protein splicing process has been studied in great detail (Chong, et al., J. Biol. Chem.1996, 271, 22159-22168; Xu, M-Q & Perler, F. B. EMBO Journal, 1996, 15, 5146- 5153) and conserved amino acids have been found at the intein and extein splicing points (Xu, et al., EMBO Journal, 1994, 135517-522).
  • third PEgRNA a third prime editing guide RNA that binds to a first binding site on a first strand of a second double-stranded DNA sequence at a second target site to be edited
  • fourth prime editor complex comprising: i. a fourth prime editor comprising a fourth nucleic acid programmable DNA binding protein (fourth napDNAbp) and a fourth polypeptide comprising an RNA-dependent DNA polymerase activity; and ii.
  • the prime editors used in the systems described herein are provided as fusion proteins.
  • the prime editor fusion proteins comprise a napDNAbp and a polymerase (e.g., DNA-dependent DNA polymerase or RNA- dependent DNA polymerase, such as, reverse transcriptase).
  • the napDNAbp and the polymerase are optionally joined by linker to form the fusion protein.
  • FIG.14 An exemplary fusion protein is depicted in FIG.14, which shows a fusion protein comprising an MLV reverse transcriptase (“MLV-RT”) fused to a nickase Cas9 (“Cas9(H840A)”) via a linker sequence.
  • MLV-RT MLV reverse transcriptase
  • Cas9(H840A) nickase Cas9
  • the multi-flap prime editor fusion proteins contemplated herein may include a Cas9 nickase (e.g., Cas9 (H840A)) fused to a truncated version of M-MLV reverse transcriptase.
  • the reverse transcriptase also contains 4 mutations (D200N, T306K, W313F, T330P; noting that the L603W mutation present in PE2 is no longer present due to the truncation).
  • the DNA sequence encoding this truncated editor is 522 bp smaller than PE2, and therefore makes its potentially useful for applications where delivery of the DNA sequence is challenging due to its size (i.e.
  • linkers may be used to link any of the peptides or peptide domains or moieties of the invention (e.g., a napDNAbp linked or fused to a reverse transcriptase).
  • Linkers and other domains may comprise various other domains besides the napDNAbp (e.g., Cas9 domain) and the polymerase domain (e.g., RT domain).
  • the PE fusion proteins may comprise one or more linkers that join the Cas9 domain with the RT domain.
  • linkers may also join other functional domains, such as nuclear localization sequences (NLS) or a FEN1 (or other flap endonuclease) to the PE fusion proteins or a domain thereof.
  • LLS nuclear localization sequences
  • FEN1 flap endonuclease
  • linkers may be used to link tPERT recruitment protein to a prime editor, e.g., between the tPERt recruitment protein and the napDNAbp. See e.g., FIG.3G for an exemplary schematic of a trans prime editor (tPE) that includes linkers to separately fuse a polymerase domain and a recruiting protein domain to a napDNAbp.
  • tPE trans prime editor
  • linker refers to a chemical group or a molecule linking two molecules or moieties, e.g., a binding domain and a cleavage domain of a nuclease.
  • a linker joins a gRNA binding domain of an RNA-programmable nuclease and the catalytic domain of a polymerase (e.g., a reverse transcriptase).
  • a linker joins a dCas9 and reverse transcriptase.
  • the linker is positioned between, or flanked by, two groups, molecules, or other moieties 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 chemical 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 comprises a monomer, dimer, or polymer of aminohexanoic acid (Ahx). In certain embodiments, the linker is based on a carbocyclic moiety (e.g., cyclopentane, cyclohexane). In other embodiments, the linker comprises a polyethylene glycol moiety (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 moiety. In certain embodiments, the linker is based on a phenyl ring.
  • Ahx aminohexanoic acid
  • the linker comprises the amino acid sequence (GGGGS) n (SEQ ID NO: 165), (G) n (SEQ ID NO: 166), (EAAAK) n (SEQ ID NO: 167), (GGS) n (SEQ ID NO: 168), (SGGS) n (SEQ ID NO: 169), (XP) n (SEQ ID NO: 170), 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: 176), wherein n is 1, 3, or 7.
  • the linker comprises the amino acid sequence SGSETPGTSESATPES (SEQ ID NO: 171). In some embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGS (SEQ ID NO: 172). In some embodiments, the linker comprises the amino acid sequence SGGSGGSGGS (SEQ ID NO: 173). In some embodiments, the linker comprises the amino acid sequence SGGS (SEQ ID NO: 174). In other embodiments, the linker comprises the amino acid sequence SGGSSGGSSGSETPGTSESATPESAGSYPYDVPDYAGSAAPAAKKKKLDGSGSGGSSGGS (SEQ ID NO: 175, 60AA).
  • 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. In certain embodiments, the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or heteroaliphatic linker. In certain embodiments, the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid.
  • the linker comprises a peptide. In certain embodiments, the linker comprises an aryl or heteroaryl moiety. In certain embodiments, the linker is based on a phenyl ring.
  • the linker may included funtionalized moieties to facilitate attachment of a nucleophile (e.g., thiol, amino) from the peptide to the linker. 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: 165), (G)n (SEQ ID NO: 166), (EAAAK) n (SEQ ID NO: 167), (GGS) n (SEQ ID NO: 168), (SGGS)n (SEQ ID NO: 169), (XP)n (SEQ ID NO: 170), 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: 176), wherein n is 1, 3, or 7.
  • the PE fusion proteins may comprise one or more nuclear localization sequences (NLS), which help promote translocation of a protein into the cell nucleus.
  • NLS nuclear localization sequences
  • Nuclear localization signals often comprise proline residues.
  • a variety of 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 by reference.
  • the present disclosure contemplates any suitable means by which to modify a multi-flap prime editor to include one or more NLSs.
  • the multi-flap prime editors may be engineered to express a prime editor 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 prime editor-NLS fusion construct.
  • the prime editor-encoding nucleotide sequence may be genetically modified to incorporate a reading frame that encodes one or more NLSs in an internal region of the encoded prime editor.
  • Flap endonucleases are known in the art and can be found described in Patel et al., “Flap endonucleases pass 5 ⁇ -flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5 ⁇ - ends,” Nucleic Acids Research, 2012, 40(10): 4507-4519 and Tsutakawa et al., “Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily,” Cell, 2011, 145(2): 198-211 (each of which are incorporated herein by reference).
  • EXO1 Human exonuclease 1
  • MMR DNA mismatch repair
  • HR homologous recombination
  • Human EXO1 belongs to a family of eukaryotic nucleases, Rad2/XPG, which also include FEN1 and GEN1.
  • the Rad2/XPG family is conserved in the nuclease domain through species from phage to human.
  • the EXO1 gene product exhibits both 5′ exonuclease and 5′ flap activity. Additionally, EXO1 contains an intrinsic 5′ RNase H activity.
  • Human EXO1 has a high affinity for processing double stranded DNA (dsDNA), nicks, gaps, pseudo Y structures and can resolve Holliday junctions using its inherit flap activity. Human EXO1 is implicated in MMR and contain conserved binding domains interacting directly with MLH1 and MSH2. EXO1 nucleolytic activity is positively stimulated by PCNA, MutS ⁇ (MSH2/MSH6 complex), 14-3-3, MRN and 9-1-1 complex. [0631] exonuclease 1 (EXO1) Accession No.
  • inteins are most frequently found as a contiguous domain, some exist in a naturally split form. In this case, the two fragments are expressed as separate polypeptides and must associate before splicing takes place, so-called protein trans-splicing.
  • An exemplary split intein is the Ssp DnaE intein, which comprises two subunits, namely, DnaE-N and DnaE-C. The two different subunits are encoded by separate genes, namely dnaE-n and dnaE-c, which encode the DnaE-N and DnaE-C subunits, respectively.
  • DnaE is a naturally occurring split intein in Synechocytis sp. PCC6803 and is capable of directing trans-splicing of two separate proteins, each comprising a fusion with either DnaE-N or DnaE-C.
  • Additional naturally occurring or engineered split-intein sequences are known in the or can be made from whole-intein sequences described herein or those available in the art.
  • the MS2 tagging technique is based on the natural interaction of the MS2 bacteriophage coat protein (“MCP” or “MS2cp”) with a stem-loop or hairpin structure present in the genome of the phage, i.e., the “MS2 hairpin.” In the case of the MS2 hairpin, it is recognized and bound by the MS2 bacteriophage coat protein (MCP).
  • MCP MS2 bacteriophage coat protein
  • a deaminase-MS2 fusion can recruit a Cas9-MCP fusion.
  • RNA recognition by the MS2 phage coat protein Sem Virol., 1997, Vol.8(3): 176-185
  • Delebecque et al. “Organization of intracellular reactions with rationally designed RNA assemblies,” Science, 2011, Vol.333: 470-474
  • Mali et al. “Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering,” Nat.
  • the amino acid sequence of the MCP or MS2cp is: F. UGI domain
  • the multi-flap prime editors described herein may comprise one or more uracil glycosylase inhibitor domains.
  • uracil glycosylase inhibitor (UGI)” or “UGI domain,” as used herein, refers to a protein that is capable of inhibiting a uracil-DNA glycosylase base-excision repair enzyme.
  • a UGI domain comprises a wild-type UGI or a UGI as set forth in SEQ ID NO: 3873.
  • the UGI proteins provided herein include fragments of UGI and proteins homologous to a UGI or a UGI fragment.
  • a UGI domain comprises a fragment of the amino acid sequence set forth in SEQ ID NO: 3873.
  • a UGI fragment comprises an amino acid sequence that comprises 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% of the amino acid sequence as set forth in SEQ ID NO: 3873.
  • a UGI comprises an amino acid sequence homologous to the amino acid sequence set forth in SEQ ID NO: 3873, or an amino acid sequence homologous to a fragment of the amino acid sequence set forth in SEQ ID NO: 3873.
  • proteins comprising UGI or fragments of UGI or homologs of UGI or UGI fragments are referred to as “UGI variants.”
  • a UGI variant shares homology to UGI, or a fragment thereof.
  • a UGI variant is at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or at least 99.9% identical to a wild type UGI or a UGI as set forth in SEQ ID NO: 3873.
  • the IBR is an inhibitor of base excision repair (“iBER”).
  • Exemplary inhibitors of base excision repair include inhibitors of APE1, Endo III, Endo IV, Endo V, Endo VIII, Fpg, hOGG1, hNEIL1, T7 EndoI, T4PDG, UDG, hSMUG1, and hAAG.
  • the IBR is an inhibitor of Endo V or hAAG.
  • the IBR is an iBER that may be a catalytically inactive glycosylase or catalytically inactive dioxygenase or a small molecule or peptide inhibitor of an oxidase, or variants threreof.
  • the IBR is an iBER that may be a TDG inhibitor, MBD4 inhibitor or an inhibitor of an AlkBH enzyme. In some embodiments, the IBR is an iBER that comprises a catalytically inactive TDG or catalytically inactive MBD4.
  • An exemplary catalytically inactive TDG is an N140A mutant of SEQ ID NO: 3872 (human TDG).
  • Some exemplary glycosylases are provided below. The catalytically inactivated variants of any of these glycosylase domains are iBERs that may be fused to the napDNAbp or polymerase domain of the multi-flap prime editors provided in this disclosure.
  • 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 that are useful for solubilization, purification, or detection of the fusion proteins.
  • localization sequences such as cytoplasmic localization sequences, export sequences, such as nuclear export sequences, or other localization sequences, as well as sequence tags that are useful for solubilization, purification, or detection of the fusion proteins.
  • Examples of protein domains that may be fused to a multi-flap prime editor or component thereof include, without limitation, epitope tags, and reporter gene sequences.
  • Non-limiting examples of 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-glucuronidase
  • Suitable protein tags include, but are not limited to, biotin carboxylase carrier protein (BCCP) tags, myc-tags, calmodulin-tags, FLAG-tags, hemagglutinin (HA)-tags, polyhistidine tags, 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-transferase
  • GST green fluorescent protein
  • S-tags Softags (e.g., Softag 1, Softag 3
  • the RNA (such as, e.g., the nuclease transcript) transcribed from the coding sequence on the vectors may further comprise at least one element that is capable of modifying the intracellular half-life of the RNA and/or modulating translational control.
  • the half-life of the RNA may be increased.
  • the half-life of the RNA may be decreased.
  • the element may be capable of increasing the stability of the RNA.
  • the element may be capable of decreasing the stability of the RNA.
  • the element may be within the 3' UTR of the RNA.
  • the element may include a polyadenylation signal (PA).
  • PA polyadenylation signal
  • the element may include a cap, e.g., an upstream mRNA or PEgRNA end.
  • the RNA may comprise no PA such that it is subject to quicker degradation in the cell after transcription.
  • the element may include at least one AU-rich element (ARE).
  • the AREs may be bound by ARE binding proteins (ARE-BPs) in a manner that is dependent upon tissue type, cell type, timing, cellular localization, and environment.
  • the destabilizing element may promote RNA decay, affect RNA stability, or activate translation.
  • the ARE may comprise 50 to 150 nucleotides in length.
  • the ARE may comprise at least one copy of the sequence AUUUA.
  • At least one ARE may be added to the 3' UTR of the RNA.
  • the element may be a Woodchuck Hepatitis Virus (WHP).
  • WPRE Posttranscriptional Regulatory Element
  • the element is a modified and/or truncated WPRE sequence that is capable of enhancing expression from the transcript, as described, for example in Zufferey et al., J Virol, 73(4): 2886-92 (1999) and Flajolet et al., J Virol, 72(7): 6175-80 (1998).
  • the WPRE or equivalent may be added to the 3' UTR of the RNA.
  • the element may be selected from other RNA sequence motifs that are enriched in either fast- or slow-decaying transcripts.
  • the vector encoding the PE or the PEgRNA may be self-destroyed via cleavage of a target sequence present on the vector by the PE system. The cleavage may prevent continued transcription of a PE or a PEgRNA from the vector. Although transcription may occur on the linearized vector for some amount of time, the expressed transcripts or proteins subject to intracellular degradation will have less time to produce off-target effects without continued supply from expression of the encoding vectors.
  • FIG.3A shows one embodiment of an extended guide RNA usable in the multi-flap prime editing system disclosed herein whereby a traditional guide RNA (the green portion) includes a ⁇ 20 nt protospacer sequence and a gRNA core region, which binds with the napDNAbp.
  • the guide RNA includes an extended RNA segment at the 5 ⁇ end, i.e., a 5 ⁇ extension.
  • FIG.3C shows another embodiment of an extend guide RNA usable in the prime editing system disclosed herein whereby a traditional guide RNA (the green portion) includes a ⁇ 20 nt protospacer sequence and a gRNA core, which binds with the napDNAbp.
  • the guide RNA includes an extended RNA segment at an intermolecular position within the gRNA core, i.e., an intramolecular extension.
  • the intramolecular extension includes a reverse transcription template sequence, and a reverse transcription primer binding site.
  • the intermolecular RNA extension is inserted into the gRNA, which refers to the portion of the guide RNA corresponding or comprising the tracrRNA, which binds and/or interacts with the Cas9 protein or equivalent thereof (i.e, a different napDNAbp).
  • the insertion of the intermolecular RNA extension does not disrupt or minimally disrupts the interaction betweeen the tracrRNA portion and the napDNAbp.
  • the length of the RNA extension (which includes at least the RT template and primer binding site, e.g., see FIG.92) can be any useful length.
  • the RNA extension is at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 21 nucleotides, at least 22 nucleotides, at least 23 nucleotides, at least 24 nucleotides, at least 25 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least
  • the reverse transcription primer binding site sequence is at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least
  • the optional linker or spacer sequence is at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, at least 90 nucleotides, at least 100 nucleotides, at least 200
  • the RT template sequence encodes a single-stranded DNA molecule which is homologous to the non-target strand (and thus, complementary to the corresponding site of the target strand) but includes one or more nucleotide changes.
  • the least one nucleotide change may include one or more single-base nucleotide changes, one or more deletions, and one or more insertions.
  • the synthesized single-stranded DNA product of the RT template sequence is homologous to the non-target strand and contains one or more nucleotide changes.
  • the single-stranded DNA product of the RT template sequence hybridizes in equilibrium with the complementary target strand sequence, thereby displacing the homologous endogenous target strand sequence.
  • the displaced endogenous strand may be referred to in some embodiments as a 5 ⁇ endogenous DNA flap species (e.g., see FIG.1E).
  • This 5 ⁇ endogenous DNA flap species can be removed by a 5 ⁇ flap endonuclease (e.g., FEN1) and the single-stranded DNA product, now hybridized to the endogenous target strand, may be ligated, thereby creating a mismatch between the endogenous sequence and the newly synthesized strand.
  • the mismatch may be resolved by the cell’s innate DNA repair and/or replication processes.
  • the nucleotide sequence of the RT template sequence corresponds to the nucleotide sequence of the non-target strand which becomes displaced as the 5 ⁇ flap species and which overlaps with the site to be edited.
  • the reverse transcription template sequence may encode a single-strand DNA flap that is complementary to an endogenous DNA sequence adjacent to a nick site, wherein the single-strand DNA flap comprises a desired nucleotide change. The single-stranded DNA flap may displace an endogenous single-strand DNA at the nick site.
  • the extended guide RNAs are modified versions of a guide RNA.
  • Guide RNAs maybe naturally occurring, expressed from an encoding nucleic acid, or synthesized chemically. Methods are well known in the art for obtaining or otherwise synthesizing guide RNAs and for determining the appropriate sequence of the guide RNA, including the protospacer sequence which interacts and hybridizes with the target strand of a genomic target site of interest.
  • 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 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.c
  • 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. [0695] In some embodiments, 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 multi-flap prime editor to a target sequence may be assessed by any suitable assay.
  • 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: 204) where NNNNNNNNNNXGG (SEQ ID NO: 205) (N is A, G, T, or C; and X can be anything).
  • a unique target sequence in a genome may include an S.
  • a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNNNNNNNXGGXG (SEQ ID NO: 212) where NNNNNNNNNNNNXGGXG (SEQ ID NO: 213) (N is A, G, T, or C; and X can be anything).
  • a unique target sequence in a genome may include an S. pyogenes Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNNNXGGXG (SEQ ID NO: 214) where NNNNNNNNNXGGXG (SEQ ID NO: 215) (N is A, G, T, or C; and X can be anything).
  • SEQ ID NO: 214 N is A, G, T, or C; and X can be anything.
  • 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.
  • 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 preferred embodiments, the transcript has two, three, four or five hairpins. In a further embodiment of the invention, 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 transcription termination sequence preferably this is 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: [0700] (2)NNNNNNNNNNNNNNNNNNNNNNGTTTTTGTACTCTCAGAAATGCAGAAGCTACAAAG ATAAGGCTTCATGCCGAAATCAACACCCTGTCATTTTATGGCAGGGTGTTTTCGTTATTTAA TTTTTT
  • 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 RNA comprises a structure 5 ⁇ -[guide sequence]- GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAAGGCUAGUCCGUUAUCAACUUGAAA AAGUGGCACCGAGUCGGUGCUUUUU-3 ⁇ (SEQ ID NO: 222), wherein the guide sequence comprises a sequence that is complementary to the target sequence.
  • the guide sequence is typically 20 nucleotides long.
  • 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 well known in the art and can be used with the multi-flap prime editor described herein.
  • the PEgRNAs include those depicted in FIG.3D.
  • the PEgRNAs may include those depicted in FIG.3E.
  • FIG.3D provides the structure of an embodiment of a PEgRNA contemplated herein and which may be designed in accordance with the methodology defined in Example 2.
  • the PEgRNA comprises three main component elements ordered in the 5 ⁇ to 3 ⁇ direction, namely: a spacer, a gRNA core, and an extension arm at the 3 ⁇ end.
  • the extension arm may further be divided into the following structural elements in the 5 ⁇ to 3 ⁇ direction, namely: a primer binding site (A), an edit template (B), and a homology arm (C).
  • the PEgRNA may comprise an optional 3 ⁇ end modifier region (e1) and an optional 5 ⁇ end modifier region (e2).
  • the PEgRNA may comprise a transcriptional termination signal at the 3 ⁇ end of the PEgRNA (not depicted).
  • These structural elements are further defined herein. The depiction of the structure of the PEgRNA is not meant to be limiting and embraces variations in the arrangement of the elements.
  • the optional sequence modifiers (e1) and (e2) could be positioned within or between any of the other regions shown, and not limited to being located at the 3 ⁇ and 5 ⁇ ends.
  • FIG.3E provides the structure of another embodiment of a PEgRNA contemplated herein may be designed in accordance with the methodology defined in Example 2.
  • the PEgRNA comprises three main component elements ordered in the 5 ⁇ to 3 ⁇ direction, namely: a spacer, a gRNA core, and an extension arm at the 3 ⁇ end.
  • the extension arm may further be divided into the following structural elements in the 5 ⁇ to 3 ⁇ direction, namely: a primer binding site (A), an edit template (B), and a homology arm (C).
  • the PEgRNA may comprise an optional 3 ⁇ end modifier region (e1) and an optional 5 ⁇ end modifier region (e2).
  • the PEgRNA may comprise a transcriptional termination signal on the 3 ⁇ end of the PEgRNA (not depicted).
  • PEgRNA improvements [0712]
  • the PEgRNAs may also include additional design improvements that may modify the properties and/or characteristics of PEgRNAs thereby improving the efficacy of multi-flap prime editing.
  • these improvements may belong to one or more of a number of different categories, including but not limited to: (1) designs to enable efficient expression of functional PEgRNAs from non-polymerase III (pol III) promoters, which would enable the expression of longer PEgRNAs without burdensome sequence requirements; (2) improvements to the core, Cas9- binding PEgRNA scaffold, which could improve efficacy; (3) modifications to the PEgRNA to improve RT processivity, enabling the insertion of longer sequences at targeted genomic loci; and (4) addition of RNA motifs to the 5 ⁇ or 3 ⁇ termini of the PEgRNA that improve PEgRNA stability, enhance RT processivity, prevent misfolding of the PEgRNA, or recruit additional factors important for genome editing.
  • poly III polymerase III
  • PEgRNA could be designed with polIII promoters to improve the expression of longer-length PEgRNA with larger extension arms.
  • sgRNAs are typically expressed from the U6 snRNA promoter. This promoter recruits pol III to express the associated RNA and is useful for expression of short RNAs that are retained within the nucleus.
  • pol III is not highly processive and is unable to express RNAs longer than a few hundred nucleotides in length at the levels required for efficient genome editing. Additionally, pol III can stall or terminate at stretches of U’s, potentially limiting the sequence diversity that could be inserted using a PEgRNA.
  • promoters that recruit polymerase II (such as pCMV) or polymerase I (such as the U1 snRNA promoter) have been examined for their ability to express longer sgRNAs.
  • these promoters are typically partially transcribed, which would result in extra sequence 5 ⁇ of the spacer in the expressed PEgRNA, which has been shown to result in markedly reduced Cas9:sgRNA activity in a site-dependent manner.
  • pol III-transcribed PEgRNAs can simply terminate in a run of 6-7 U’s, PEgRNAs transcribed from pol II or pol I would require a different termination signal. Often such signals also result in polyadenylation, which would result in undesired transport of the PEgRNA from the nucleus.
  • Example improvements to the core can include: [0724] PEgRNA containing a 6 nt extension to P1 ( Q ) [0725] PEgRNA containing a T-A to G-C mutation within P1 [0726] In various other embodiments, the PEgRNA may be improved by introducing modifications to the edit template region.
  • the size of the insertion templated by the PEgRNA increases, it is more likely to be degraded by endonucleases, undergo spontaneous hydrolysis, or fold into secondary structures unable to be reverse-transcribed by the RT or that disrupt folding of the PEgRNA scaffold and subsequent Cas9-RT binding. Accordingly, it is likely that modification to the template of the PEgRNA might be necessary to affect large insertions, such as the insertion of whole genes.
  • Some strategies to do so include the incorporation of modified nucleotides within a synthetic or semi- synthetic PEgRNA that render the RNA more resistant to degradation or hydrolysis or less likely to adopt inhibitory secondary structures 196 .
  • Such modifications could include 8-aza-7-deazaguanosine, which would reduce RNA secondary structure in G-rich sequences; locked-nucleic acids (LNA) that reduce degradation and enhance certain kinds of RNA secondary structure; 2’-O-methyl, 2’-fluoro, or 2’-O-methoxyethoxy modifications that enhance RNA stability. Such modifications could also be included elsewhere in the PEgRNA to enhance stability and activity.
  • the template of the PEgRNA could be designed such that it both encodes for a desired protein product and is also more likely to adopt simple secondary structures that are able to be unfolded by the RT. Such simple structures would act as a thermodynamic sink, making it less likely that more complicated structures that would prevent reverse transcription would occur.
  • a PE would be used to initiate transcription and also recruit a separate template RNA to the targeted site via an RNA-binding protein fused to Cas9 or an RNA recognition element on the PEgRNA itself such as the MS2 aptamer.
  • the RT could either directly bind to this separate template RNA, or initiate reverse transcription on the original PEgRNA before swapping to the second template.
  • Such an approach could enable long insertions by both preventing misfolding of the PEgRNA upon addition of the long template and also by not requiring dissociation of Cas9 from the genome for long insertions to occur, which could possibly be inhibiting PE-based long insertions.
  • the PEgRNA may be improved by introducing additional RNA motifs at the 5 ⁇ and 3 ⁇ termini of the PEgRNAs, or even at positions therein between (e.g., in the gRNA core region, or the the spacer).
  • additional RNA motifs such as the PAN ENE from KSHV and the ENE from MALAT1 were discussed above as possible means to terminate expression of longer PEgRNAs from non-pol III promoters.
  • These elements form RNA triple helices that engulf the polyA tail, resulting in their being retained within the nucleus 184, 187 .
  • RNA motifs could also improve RT processivity or enhance PEgRNA activity by enhancing RT binding to the DNA-RNA duplex. Addition of the native sequence bound by the RT in its cognate retroviral genome could enhance RT activity 199 . This could include the native primer binding site (PBS), polypurine tract (PPT), or kissing loops involved in retroviral genome dimerization and initiation of transcription 199 .
  • dimerization motifs such as kissing loops or a GNRA tetraloop/tetraloop receptor pair 200 - at the 5 ⁇ and 3 ⁇ termini of the PEgRNA could also result in effective circularization of the PEgRNA, improving stability. Additionally, it is envisioned that addition of these motifs could enable the physical separation of the PEgRNA spacer and primer, prevention occlusion of the spacer which would hinder PE activity.
  • the PEgRNA depicted in FIG.3D and FIG.3E list a number secondary RNA structures that may be engineered into any region of the PEgRNA, including in the terminal portions of the extension arm (i.e., e1and e2), as shown.
  • Example improvements include, but are not limited to: [0732] PEgRNA-HDV fusion [0733] PEgRNA-MMLV kissing loop ) [0734] PEgRNA-VS ribozyme kissing loop ( Q ) [0735] PEgRNA-GNRA tetraloop/tetraloop receptor [0736] PEgRNA template switching secondary RNA-HDV fusion [0737] PEgRNA scaffolds could be further improved via directed evolution, in an analogous fashion to how SpCas9 and prime editors (PE) have been improved. Directed evolution could enhance PEgRNA recognition by Cas9 or evolved Cas9 variants.
  • PE prime editors
  • strings of at least consecutive three T’s, at least consecutive four T’s, at least consecutive five T’s, at least consecutive six T’s, at least consecutive seven T’s, at least consecutive eight T’s, at least consecutive nine T’s, at least consecutive ten T’s, at least consecutive elevent T’s, at least consecutive twelve T’s, at least consecutive thirteen T’s , at least consecutive fourteen T’s, or at least consecutive fifteen T’s should be avoided when designing the PEgRNA, or should be at least removed from the final designed sequence.
  • trans prime editing refers to a modified version of prime editing which operates by separating the PEgRNA into two distinct molecules: a guide RNA and a tPERT molecule.
  • the tPERT molecule is programmed to co-localize with the prime editor complex at a target DNA site, bringing the primer binding site and the DNA synthesis template to the prime editor in trans.
  • FIG.3G for an embodiment of a trans prime editor (tPE) which shows a two-component system comprising (1) an recruiting protein (RP)- PE:gRNA complex and (2) a tPERT that includes a primer binding site and a DNA synthesis template joined to an RNA-protein recruitment domain (e.g., stem loop or hairpin), wherein the recruiting protein component of the RP-PE:gRNA complex recruits the tPERT to a target site to be edited, thereby associating the PBS and DNA synthesis template with the prime editor in trans.
  • the tPERT is engineered to contain (all or part of) the extension arm of a PEgRNA, which includes the primer binding site and the DNA synthesis template.
  • a key feature of trans prime editing is the ability of the trans prime editor to recruit the tPERT to the site of DNA editing, thereby effectively co-localizing all of the functions of a PEgRNA at the site of prime editing.
  • RNA-protein recruitment domain such as a MS2 aptamer
  • a corresponding recruiting protein to the prime editor (e.g., via a linker to the napDNAbp or via a linker to the polymerase) that is capable of specifically binding to the RNA-protein recruitment domain, thereby recruiting the tPERT molecule to the prime editor complex.
  • the RP-PE:gRNA complex binds to and nicks the target DNA sequence.
  • the tPERT is shown in FIG.3G and FIG.3H as comprising the PBS and DNA synthesis template on the 5 ⁇ end of the RNA-protein recruitment domain, the tPERT in other configurations may be designed with the PBS and DNA synthesis template located on the 3 ⁇ end of the RNA-protein recruitment domain.
  • the tPERT with the 5’ extension has the advantage that synthesis of the single strand of DNA will naturally terminate at the 5’ end of the tPERT and thus, does not risk using any portion of the RNA-protein recruitment domain as a template during the DNA synthesis stage of prime editing.
  • PEgRNA design method [0743] The present disclosure also relates to methods for designing PEgRNAs.
  • prime editing can be used, without limitation, to (a) install mutation-correcting changes to a nucleotide sequence, (b) install protein and RNA tags, (c) install immunoepitopes on proteins of interest, (d) install inducible dimerization domains in proteins, (e) install or remove sequences to alter that activity of a biomolecule, (f) install recombinase target sites to direct specific genetic changes, and (g) mutagenesis of a target sequence by using an error-prone RT.
  • prime editors can also be used to construct highly programmable libraries, as well as to conduct cell data recording and lineage tracing studies.
  • prime editors there may be as described herein particular design aspects pertaining to the preparation of a PEgRNA that is particularly useful for any given of these applications.
  • a number of considerations may be taken into account, which include, but are not limited to: (a) the target sequence, i.e., the nucleotide sequence in which one or more nucleobase modifications are desired to be installed by the prime editor; (b) the location of the cut site within the target sequence, i.e., the specific nucleobase position at which the prime editor will induce a single-stand nick to create a 3 ⁇ end RT primer sequence on one side of the nick and the 5 ⁇ end endogenous flap on the other side of the nick (which ultimately is removed by FEN1 or equivalent thereto and replaced by the 3 ⁇ ssDNA flap.
  • the target sequence i.e., the nucleotide sequence in which one or more nucleobase modifications are desired to be installed by the prime editor
  • the location of the cut site within the target sequence i.e., the specific nucleobase position at which the prime editor will induce a single-stand nick to create a 3 ⁇ end RT primer sequence on one side of the
  • the available PAM sequences including the canonical SpCas9 PAM sites, as well as non- canonical PAM sites recognized by Cas9 variants and equivalents with expanded or differing PAM specificities); (d) the spacing between the available PAM sequences and the location of the cut site in the target sequence; (e) the particular Cas9, Cas9 variant, or Cas9 equivalent of the prime editor being used; (f) the sequence and length of the primer binding site; (g) the sequence and length of the edit template; (h) the sequence and length of the homology arm; (i) the spacer sequence and length; and (j) the core sequence. [0746] The instant disclosure discusses these aspects above.
  • an approach to designing a suitable PEgRNA, and optionally a nicking- sgRNA design guide for second-site nicking is hereby provided.
  • This embodiment provides a step- by-step set of instructions for designing PEgRNAs and nicking-sgRNAs for prime editing which takes into account one or more of the above considerations.
  • the steps reference the examples shown in FIGs.70A-70I. 1. Define the target sequence and the edit. Retrieve the sequence of the target DNA region ( ⁇ 200bp) centered around the location of the desired edit (point mutation, insertion, deletion, or combination thereof). See FIG.70A. 2. Locate target PAMs. Identify PAMs in the proximity to the desired edit location.
  • PAMs can be identified on either strand of DNA proximal to the desired edit location. While PAMs close to the edit position are preferred (i.e., wherein the nick site is less than 30 nt from the edit position, or less than 29 nt, 28 nt, 27 nt, 26 nt, 25 nt, 24 nt, 23 nt, 22 nt, 21 nt, 20 nt, 19 nt, 18 nt, 17 nt, 16 nt, 15 nt, 14 nt, 13 nt, 12 nt, 11 nt, 10 nt, 9 nt, 8 nt, 7 nt, 6 nt, 5 nt, 4 nt, 3 nt, or 2 nt from the edit position to the nick site), it is possible to install edits using protospacers and PAMs that place the nick ⁇ 30 nt from the edit position.

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DE112021002672.0T DE112021002672T5 (de) 2020-05-08 2021-05-07 Vefahren und zusammensetzungen zum gleichzeitigen editieren beider stränge einer doppelsträngigen nukleotid-zielsequenz
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