Methods and compositions for prime editing nucleotide sequences

Abstract

Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named a PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incoporated into the target DNA molecule.

What is claimed is: 
     
         1 . A method for installing a desired nucleotide change in a double-stranded DNA sequence, the method comprising: contacting the double-stranded DNA sequence with a complex comprising a fusion protein and a PEgRNA, wherein the fusion protein comprises a napDNAbp and a polymerase, and wherein the PEgRNA comprises a DNA synthesis template comprising the desired nucleotide change and a primer binding site;
 thereby nicking the double-stranded DNA sequence, thereby generating a free single-strand DNA having a 3′ end;   thereby hybridizing the 3′ end of the free single-strand DNA to the primer binding site, thereby priming the polymerase;   thereby polymerizing a strand of DNA from the 3′ end hybridized to the primer binding site, thereby generating a single-strand DNA flap comprising the desired nucleotide change and which is complementary to the DNA synthesis template;   thereby 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.   
     
     
         2 . The method of  claim 1 , wherein replacing an endogenous DNA strand comprises: (i) hybridizing the single-strand DNA flap to the endogenous DNA strand adjacent the cut site to create a sequence mismatch; (ii) excising the endogenous DNA strand; and (iii) repairing the mismatch to form the desired product comprising the desired nucleotide change in both strands of DNA. 
     
     
         3 . The method of  claim 1 , wherein the desired nucleotide change is a single nucleotide substitution, a deletion, or an insertion. 
     
     
         4 . The method of  claim 3 , wherein the single nucleotide substitution is a transition or a transversion. 
     
     
         5 . The method of  claim 1 , wherein the desired nucleotide change is (1) a G to T substitution, (2) a G to A substitution, (3) a G to C substitution, (4) a T to G substitution, (5) a T to A substitution, (6) a T to C substitution, (7) a C to G substitution, (8) a C to T substitution, (9) a C to A substitution, (10) an A to T substitution, (11) an A to G substitution, or (12) an A to C substitution. 
     
     
         6 . The method of  claim 1 , wherein the desired nucleotide change converts (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, 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. 
     
     
         7 . The method of  claim 1 , wherein the desired nucleotide change is an insertion or deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides. 
     
     
         8 . The method of  claim 1 , wherein the desired nucleotide change corrects a disease-associated gene. 
     
     
         9 . The method of  claim 8 , wherein the disease-associated gene is associated with a monogentic disorder selected from the group consisting of: Adenosine Deaminase (ADA) Deficiency; Alpha-1 Antitrypsin Deficiency; Cystic Fibrosis; Duchenne Muscular Dystrophy; Galactosemia; Hemochromatosis; Huntington's Disease; Maple Syrup Urine Disease; Marfan Syndrome; Neurofibromatosis Type 1; Pachyonychia Congenita; Phenylkeotnuria; Severe Combined Immunodeficiency; Sickle Cell Disease; Smith-Lemli-Opitz Syndrome; a trinucleotide repeat disorder; a prion disease; and Tay-Sachs Disease. 
     
     
         10 . The method of  claim 8 , wherein the disease-associated gene is associated with a polygenic disorder selected from the group consisting of: heart disease; high blood pressure; Alzheimer's disease; arthritis; diabetes; cancer; and obesity. 
     
     
         11 . The method of  claim 1 , wherein the napDNAbp is a nuclease dead Cas9 (dCas9), a Cas9 nickase (nCas9), or a nuclease active Cas9. 
     
     
         12 . The method of  claim 1 , wherein the napDNAbp comprises an amino acid sequence of SEQ ID NO: 18. 
     
     
         13 . The method of  claim 1 , wherein the napDNAbp comprises an amino acid sequence having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity with the amino acid sequence of any one of SEQ ID NOs: 18-88, 126, 130, 137, 141, 147, 153, 157, 445, 460, 467, and 482-487. 
     
     
         14 . The method of  claim 1 , wherein the polymerase is a reverse transcriptase comprising any one of the amino acid sequences of SEQ ID NO: 89-100, 105-122, 128-129, 132, 139, 143, 149, 154, 159, 235, 454, 471, 516, 662, 700, 701-716, 739-741, and 766. 
     
     
         15 . The method of  claim 1 , wherein the polymerase is a reverse transcriptase comprising an amino acid sequence having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity with the amino acid sequence of any one of SEQ ID NOs: 89-100, 105-122, 128-129, 132, 139, 143, 149, 154, 159, 235, 454, 471, 516, 662, 700, 701-716, 739-741, and 766. 
     
     
         16 . The method of  claim 1 , wherein the PEgRNA comprises a nucleic acid extension arm at the 3′ or 5′ ends or at an intramolecular location in the guide RNA, wherein the extension arm comprises the DNA synthesis template sequence and the primer binding site. 
     
     
         17 . The method of  claim 16 , wherein the extension arm 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, or at least 25 nucleotides in length. 
     
     
         18 . The method of  claim 1 , wherein the PEgRNA has a nucleotide sequence selected from the group consisting of SEQ ID NOs: 101-104, 181-183, 223-244, 277, 325-334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 499-505, 735-761, 776-777. 
     
     
         19 . A method for introducing one or more changes in the nucleotide sequence of a DNA molecule at a target locus, comprising: contacting the DNA molecule with a nucleic acid programmable DNA binding protein (napDNAbp) and a PEgRNA which targets the napDNAbp to the target locus, wherein the PEgRNA comprises a reverse transcriptase (RT) template sequence comprising at least one desired nucleotide change and a primer binding site;
 thereby forming an exposed 3′ end in a DNA strand at the target locus;   thereby hybridizing the exposed 3′ end to the primer binding site to prime reverse transcription;   thereby synthesizing a single strand DNA flap comprising the at least one desired nucleotide change based on the RT template sequence by reverse transcriptase;   thereby incorporating the at least one desired nucleotide change into the corresponding endogenous DNA, thereby introducing one or more changes in the nucleotide sequence of the DNA molecule at the target locus.   
     
     
         20 . The method of  claim 19 , wherein the one or more changes in the nucleotide sequence comprises a transition. 
     
     
         21 . The method of  claim 19 , wherein the transition is selected from the group consisting of: (a) T to C; (b) A to G; (c) C to T; and (d) G to A. 
     
     
         22 . The method of  claim 19 , wherein the one or more changes in the nucleotide sequence comprises a transversion. 
     
     
         23 . The method of  claim 22 , wherein the transversion is selected from the group consisting of: (a) T to A; (b) T to G; (c) C to G; (d) C to A; (e) A to T; (f) A to C; (g) G to C; and (h) G to T. 
     
     
         24 . The method of  claim 19 , wherein the one or more changes in the nucleotide sequence comprises changing (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, (9) 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. 
     
     
         25 . The method of  claim 19 , wherein the one or more changes in the nucleotide sequence comprises an insertion or deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides. 
     
     
         26 . The method of  claim 19 , wherein the one or more changes in the nucleotide sequence comprises a correction to a disease-associated gene. 
     
     
         27 . The method of  claim 26 , wherein the disease-associated gene is associated with a monogentic disorder selected from the group consisting of: Adenosine Deaminase (ADA) Deficiency; Alpha-1 Antitrypsin Deficiency; Cystic Fibrosis; Duchenne Muscular Dystrophy; Galactosemia; Hemochromatosis; Huntington's Disease; Maple Syrup Urine Disease; Marfan Syndrome; Neurofibromatosis Type 1; Pachyonychia Congenita; Phenylkeotnuria; Severe Combined Immunodeficiency; Sickle Cell Disease; Smith-Lemli-Opitz Syndrome; a trinucleotide repeat disorder; a prion disease; and Tay-Sachs Disease. 
     
     
         28 . The method of  claim 26 , wherein the disease-associated gene is associated with a polygenic disorder selected from the group consisting of: heart disease; high blood pressure; Alzheimer's disease; arthritis; diabetes; cancer; and obesity. 
     
     
         29 . The method of  claim 19 , wherein the napDNAbp is a nuclease active Cas9 or variant thereof. 
     
     
         30 . The method of  claim 19 , wherein the napDNAbp is a nuclease inactive Cas9 (dCas9) or Cas9 nickase (nCas9), or a variant thereof. 
     
     
         31 . The method of  claim 19 , wherein the napDNAbp comprises an amino acid sequence of SEQ ID NO: 18. 
     
     
         32 . The method of  claim 19 , wherein the napDNAbp comprises an amino acid sequence having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity with the amino acid sequence of any one of SEQ ID NOs: 18-88, 126, 130, 137, 141, 147, 153, 157, 445, 460, 467, and 482-487. 
     
     
         33 . The method of  claim 19 , wherein the reverse transcriptase is introduced in trans. 
     
     
         34 . The method of  claim 19 , wherein the napDNAbp comprises a fusion to a reverse transcriptase. 
     
     
         35 . The method of  claim 19 , wherein the reverse transcriptase comprises any one of the amino acid sequences of SEQ ID NO: 89-100, 105-122, 128-129, 132, 139, 143, 149, 154, 159, 235, 454, 471, 516, 662, 700, 701-716, 739-741, and 766. 
     
     
         36 . The method of  claim 19 , wherein the reverse transcriptase comprises an amino acid sequence having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity with the amino acid sequence of any one of SEQ ID NOs: 89-100, 105-122, 128-129, 132, 139, 143, 149, 154, 159, 235, 454, 471, 516, 662, 700, 701-716, 739-741, and 766. 
     
     
         37 . The method of  claim 19 , wherein the step of forming an exposed 3′ end in the DNA strand at the target locus comprises nicking the DNA strand with a nuclease. 
     
     
         38 . The method of  claim 37 , wherein the nuclease is the napDNAbp, is provided as a fusion domain of napDNAbp, or is provided in trans. 
     
     
         39 . The method of  claim 19 , wherein the step of forming an exposed 3′ end in the DNA strand at the target locus comprises contacting the DNA strand with a chemical agent. 
     
     
         40 . The method of  claim 19 , wherein the step of forming an exposed 3′ end in the DNA strand at the target locus comprises introducing a replication error. 
     
     
         41 . The method of  claim 19 , wherein the step of contacting the DNA molecule with the napDNAbp and the guide RNA forms an R-loop. 
     
     
         42 . The method of  claim 41 , wherein the DNA strand in which the exposed 3′ end is formed is in the R-loop. 
     
     
         43 . The method of  claim 19 , wherein the PEgRNA comprises an extension arm that comprises the reverse transcriptase (RT) template sequence and the primer binding site. 
     
     
         44 . The method of  claim 43 , wherein the extension arm is at the 3′ end of the guide RNA, the 5′ end of the guide RNA, or at an intramolecular position in the guide RNA. 
     
     
         45 . The method of  claim 19 , wherein the PEgRNA further comprises at least one additional structure selected from the group consisting of a linker, a stem loop, a hairpin, a toeloop, an aptamer, or an RNA-protein recruitment domain. 
     
     
         46 . The method of  claim 19 , wherein the PEgRNA further comprises a homology arm. 
     
     
         47 . The method of  claim 19 , wherein the RT template sequence is homologous to the corresponding endogenous DNA. 
     
     
         48 . A method for introducing one or more changes in the nucleotide sequence of a DNA molecule at a target locus by target-primed reverse transcription, the method comprising: (a) contacting the DNA molecule at the target locus with a (i) fusion protein comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a reverse transcriptase and (ii) a guide RNA comprising an RT template comprising a desired nucleotide change;
 thereby conducting target-primed reverse transcription of the RT template to generate a single strand DNA comprising the desired nucleotide change;   thereby incorporating the desired nucleotide change into the DNA molecule at the target locus through a DNA repair and/or replication process.   
     
     
         49 . The method of  claim 48 , wherein the RT template is located at the 3′ end of the guide RNA, the 5′ end of the guide RNA, or at an intramolecular location in the guide RNA. 
     
     
         50 . The method of  claim 48 , wherein the desired nucleotide change comprises a transition, a transversion, an insertion, or a deletion, or any combination thereof. 
     
     
         51 . The method of  claim 48 , wherein the desired nucleotide change comprises a transition selected from the group consisting of: (a) T to C; (b) A to G; (c) C to T; and (d) G to A. 
     
     
         52 . The method of  claim 48 , wherein the desired nucleotide change comprises a transversion selected from the group consisting of: (a) T to A; (b) T to G; (c) C to G; (d) C to A; (e) A to T; (f) A to C; (g) G to C; and (h) G to T. 
     
     
         53 . The method of  claim 48 , wherein the desired nucleotide change comprises changing (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. 
     
     
         54 . A method for replacing a trinucleotide repeat expansion mutation in a target DNA molecule with a healthy sequence comprising a healthy number of repeat trinucleotides, the method comprising: (a) contacting the DNA molecule at the target locus with a (i) fusion protein comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a polymerase and (ii) a PEgRNA comprising DNA synthesis template comprising the replacement sequence and a primer binding site; (b) conducting prime editingto generate a single strand DNA comprising the replacement sequence; and (c) incorporating the single strand DNA into the DNA molecule at the target locus through a DNA repair and/or replication process. 
     
     
         55 . The method of  claim 54 , wherein the fusion protein comprises the amino acid sequence of PE1, PE2, or PE3. 
     
     
         56 . The method of  claim 54 , wherein the napDNAbp is a Cas9 nickase (nCas9). 
     
     
         57 . The method of  claim 54 , wherein the napDNAbp comprises the amino acid sequence of SEQ ID NOs: 18-88, 126, 130, 137, 141, 147, 153, 157, 445, 460, 467, and 482-487. 
     
     
         58 . The method of  claim 54 , wherein the guide RNA comprises SEQ ID NOs: 222. 
     
     
         59 . The method of  claim 54 , wherein the step of (b) conducting prime editing comprises generating a 3′ end primer binding sequence at the target locus that is capable of priming polymerase by annealing to the primer binding site on the guide RNA. 
     
     
         60 . The method of  claim 54 , wherein the trinucleotide repeat expansion mutation is associated with Huntington's Disease, Fragile X syndrome, or Friedreich's ataxia. 
     
     
         61 . The method of  claim 54 , wherein the trinucleotide repeat expansion mutation comprises a repeating unit of CAG triplets. 
     
     
         62 . The method of  claim 54 , wherein the trinucleotide repeat expansion mutation comprises a repeating unit of GAA triplets. 
     
     
         63 . A method for introducing one or more changes in the nucleotide sequence of a DNA molecule at a target locus by target-primed reverse transcription, the method comprising: (a) contacting the DNA molecule at the target locus with a (i) fusion protein comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a reverse transcriptase and (ii) a guide RNA comprising an RT template comprising a desired nucleotide change;
 thereby conducting target-primed reverse transcription of the RT template to generate a single strand DNA comprising the desired nucleotide change;   thereby incorporating the desired nucleotide change into the DNA molecule at the target locus through a DNA repair and/or replication process.   
     
     
         64 . The method of  claim 63 , wherein the RT template is located at the 3′ end of the guide RNA, the 5′ end of the guide RNA, or at an intramolecular location in the guide RNA. 
     
     
         65 . The method of  claim 63 , wherein the desired nucleotide change comprises a transition, a transversion, an insertion, or a deletion, or any combination thereof. 
     
     
         66 . The method of  claim 63 , wherein the desired nucleotide change comprises a transition selected from the group consisting of: (a) T to C; (b) A to G; (c) C to T; and (d) G to A. 
     
     
         67 . The method of  claim 63 , wherein the desired nucleotide change comprises a transversion selected from the group consisting of: (a) T to A; (b) T to G; (c) C to G; (d) C to A; (e) A to T; (f) A to C; (g) G to C; and (h) G to T. 
     
     
         68 . The method of  claim 63 , wherein the desired nucleotide change comprises changing (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. 
     
     
         69 . A method of preventing or halting the progression of a prion disease by installing on or more protective mutations into PRNP encoded by a target nucleotide sequence by prime editing, the method comprising: (a) contacting the target nucleotide sequence with a (i) prime editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a polymerase and (ii) a PEgRNA comprising an edit template encoding the functional moiety;
 thereby polymerizing a single strand DNA sequence encoding the protective mutation;   thereby incorporating the single strand DNA sequence in place of a corresponding endogenous strand at the target nucleotide sequence through a DNA repair and/or replication process;   wherein the method produces a recombinant target nucleotide sequence that encodes a PRNP comprising a protective mutation and which is resistant to misfolding.   
     
     
         70 . The method of  claim 69 , wherein the prion disease is a human prion disease. 
     
     
         71 . The method of  claim 69 , wherein the prion disease is an animal prion disease. 
     
     
         72 . The method of  claim 69 , wherein the prion disease is Creutzfeldt-Jakob Disease (CJD), Variant Creutzfeldt-Jakob Disease (νCJD), Gerstmann-Straussler-Scheinker Syndrome, Fatal Familial Insomnia, or Kuru. 
     
     
         73 . The method of  claim 69 , wherein the prion disease is Bovine Spongiform Encephalopathy (BSE or “mad cow disease”), Chronic Wasting Disease (CWD), Scrapie, Transmissible Mink Encephalopathy, Feline Spongiform Encephalopathy, and Ungulate Spongiform Encephalopathy. 
     
     
         74 . The method of  claim 69 , wherein the wildtype PRNP amino acid sequence is SEQ ID NOs: 291-292. 
     
     
         75 . The method of  claim 69 , wherein the method results in a modified PRNP amino acid sequence selected from the group consisting of SEQ ID NOs: 293-309, 311-323, wherein said modified PRNP protein is resistant to misfolding. 
     
     
         76 . The method of  claim 69 , wherein the fusion protein comprises the amino acid sequence of PE1, PE2, or PE3. 
     
     
         77 . The method of  claim 69 , wherein the napDNAbp is a Cas9 nickase (nCas9). 
     
     
         78 . The method of  claim 69 , wherein the napDNAbp comprises the amino acid sequence of SEQ ID NOs: 18-88, 126, 130, 137, 141, 147, 153, 157, 445, 460, 467, and 482-487. 
     
     
         79 . The method of  claim 69 , wherein the PEgRNA comprises SEQ ID NOs: 101-104, 181-183, 223-244, 277, 325-334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 499-505, 735-761, 776-777. 
     
     
         80 . A method of treating CDKL5 Deficiency Disorder by correcting a mutation in the cyclin-dependent kinase-like 5 gene (CDKL5) in a target nucleotide sequence by prime editing, the method comprising: (a) contacting the target nucleotide sequence with a (i) prime editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) and a polymerase and (ii) a PEgRNA comprising an edit template that corrects the mutation in CDKL5;
 thereby polymerizing a single strand DNA sequence encoding the edit;   thereby incorporating the single strand DNA sequence in place of a corresponding endogenous strand at the target nucleotide sequence through a DNA repair and/or replication process;   wherein the method produces a recombinant target nucleotide sequence that encodes a repaired CDKL5 gene.   
     
     
         81 . The method of claim D 80 , wherein the mutation in CDKL5 is 1412delA.