CA3227004A1 - Improved prime editors and methods of use - Google Patents

Improved prime editors and methods of use Download PDF

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Publication number
CA3227004A1
CA3227004A1 CA3227004A CA3227004A CA3227004A1 CA 3227004 A1 CA3227004 A1 CA 3227004A1 CA 3227004 A CA3227004 A CA 3227004A CA 3227004 A CA3227004 A CA 3227004A CA 3227004 A1 CA3227004 A1 CA 3227004A1
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CA
Canada
Prior art keywords
reverse transcriptase
seq
variant
amino acid
acid sequence
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Pending
Application number
CA3227004A
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English (en)
French (fr)
Inventor
David R. Liu
Peter J. Chen
Jordan Leigh Doman
Smriti PANDEY
Monica NEUGEBAUER
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Broad Institute Inc
Harvard University
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Broad Institute Inc
Harvard University
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Publication of CA3227004A1 publication Critical patent/CA3227004A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/62—DNA sequences coding for fusion proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/07—Nucleotidyltransferases (2.7.7)
    • C12Y207/07049—RNA-directed DNA polymerase (2.7.7.49), i.e. telomerase or reverse-transcriptase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y301/00—Hydrolases acting on ester bonds (3.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3519—Fusion with another nucleic acid

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Zoology (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Medicinal Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
  • Cell Biology (AREA)
  • Mycology (AREA)
CA3227004A 2021-08-06 2022-08-05 Improved prime editors and methods of use Pending CA3227004A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202163230688P 2021-08-06 2021-08-06
US63/230,688 2021-08-06
US202263388888P 2022-07-13 2022-07-13
US63/388,888 2022-07-13
PCT/US2022/074628 WO2023015309A2 (en) 2021-08-06 2022-08-05 Improved prime editors and methods of use

Publications (1)

Publication Number Publication Date
CA3227004A1 true CA3227004A1 (en) 2023-02-09

Family

ID=83188605

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3227004A Pending CA3227004A1 (en) 2021-08-06 2022-08-05 Improved prime editors and methods of use

Country Status (6)

Country Link
US (1) US20250270593A1 (enExample)
EP (1) EP4381057A2 (enExample)
JP (1) JP2024530487A (enExample)
AU (1) AU2022325166A1 (enExample)
CA (1) CA3227004A1 (enExample)
WO (1) WO2023015309A2 (enExample)

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9322037B2 (en) 2013-09-06 2016-04-26 President And Fellows Of Harvard College Cas9-FokI fusion proteins and uses thereof
US9228207B2 (en) 2013-09-06 2016-01-05 President And Fellows Of Harvard College Switchable gRNAs comprising aptamers
US10077453B2 (en) 2014-07-30 2018-09-18 President And Fellows Of Harvard College CAS9 proteins including ligand-dependent inteins
EP3592853A1 (en) 2017-03-09 2020-01-15 President and Fellows of Harvard College Suppression of pain by gene editing
US12390514B2 (en) 2017-03-09 2025-08-19 President And Fellows Of Harvard College Cancer vaccine
CN111801345A (zh) 2017-07-28 2020-10-20 哈佛大学的校长及成员们 使用噬菌体辅助连续进化(pace)的进化碱基编辑器的方法和组合物
US12406749B2 (en) 2017-12-15 2025-09-02 The Broad Institute, Inc. Systems and methods for predicting repair outcomes in genetic engineering
US12522807B2 (en) 2018-07-09 2026-01-13 The Broad Institute, Inc. RNA programmable epigenetic RNA modifiers and uses thereof
US12351837B2 (en) 2019-01-23 2025-07-08 The Broad Institute, Inc. Supernegatively charged proteins and uses thereof
WO2020191233A1 (en) 2019-03-19 2020-09-24 The Broad Institute, Inc. Methods and compositions for editing nucleotide sequences
US12473543B2 (en) 2019-04-17 2025-11-18 The Broad Institute, Inc. Adenine base editors with reduced off-target effects
AU2022343268A1 (en) 2021-09-08 2024-03-28 Flagship Pioneering Innovations Vi, Llc Methods and compositions for modulating a genome
CA3231712A1 (en) 2021-09-08 2023-03-16 Flagship Pioneering Innovations Vi, Llc Pah-modulating compositions and methods
WO2024077267A1 (en) 2022-10-07 2024-04-11 The Broad Institute, Inc. Prime editing methods and compositions for treating triplet repeat disorders
WO2024240138A1 (zh) * 2023-05-22 2024-11-28 江西农业大学 基于perv逆转录酶的先导编辑系统
WO2024243415A1 (en) 2023-05-23 2024-11-28 The Broad Institute, Inc. Evolved and engineered prime editors with improved editing efficiency
AU2024301706A1 (en) 2023-07-21 2026-02-05 Crispr Therapeutics Ag Modulating expression of alas1 (5'-aminolevulinate synthase 1) gene
WO2025048436A1 (ko) * 2023-08-29 2025-03-06 성균관대학교산학협력단 Eys 유전자 교정 프라임 에디터 및 그 용도
WO2025096936A2 (en) 2023-11-03 2025-05-08 The Broad Institute, Inc. Use of prime editing in correcting mutations in cdkl5
WO2025151814A1 (en) 2024-01-10 2025-07-17 The Broad Institute, Inc. Use of prime editing in correcting mutations in cftr
WO2025217616A1 (en) 2024-04-12 2025-10-16 The Broad Institute, Inc. Prime editing and base editing of the atp1a3 gene for the treatment of alternating hemiplegia of childhood
WO2026015829A2 (en) * 2024-07-12 2026-01-15 Arbor Biotechnologies, Inc. Small reverse transcriptases and gene editing systems comprising such
WO2026015832A2 (en) * 2024-07-12 2026-01-15 Arbor Biotechnologies, Inc. Reverse transcriptases and gene editing systems comprising such
WO2026069163A1 (en) 2024-09-25 2026-04-02 Crispr Therapeutics Ag Differentiation method for producing immature beta cells
CN120536504B (zh) * 2025-07-29 2026-01-06 江西农业大学 基于内源性多基因编辑的阿尔茨海默病模型猪的构建方法

Family Cites Families (38)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4217344A (en) 1976-06-23 1980-08-12 L'oreal Compositions containing aqueous dispersions of lipid spheres
US4235871A (en) 1978-02-24 1980-11-25 Papahadjopoulos Demetrios P Method of encapsulating biologically active materials in lipid vesicles
US4186183A (en) 1978-03-29 1980-01-29 The United States Of America As Represented By The Secretary Of The Army Liposome carriers in chemotherapy of leishmaniasis
US4261975A (en) 1979-09-19 1981-04-14 Merck & Co., Inc. Viral liposome particle
US4485054A (en) 1982-10-04 1984-11-27 Lipoderm Pharmaceuticals Limited Method of encapsulating biologically active materials in multilamellar lipid vesicles (MLV)
US4501728A (en) 1983-01-06 1985-02-26 Technology Unlimited, Inc. Masking of liposomes from RES recognition
US4897355A (en) 1985-01-07 1990-01-30 Syntex (U.S.A.) Inc. N[ω,(ω-1)-dialkyloxy]- and N-[ω,(ω-1)-dialkenyloxy]-alk-1-yl-N,N,N-tetrasubstituted ammonium lipids and uses therefor
US5049386A (en) 1985-01-07 1991-09-17 Syntex (U.S.A.) Inc. N-ω,(ω-1)-dialkyloxy)- and N-(ω,(ω-1)-dialkenyloxy)Alk-1-YL-N,N,N-tetrasubstituted ammonium lipids and uses therefor
US4946787A (en) 1985-01-07 1990-08-07 Syntex (U.S.A.) Inc. N-(ω,(ω-1)-dialkyloxy)- and N-(ω,(ω-1)-dialkenyloxy)-alk-1-yl-N,N,N-tetrasubstituted ammonium lipids and uses therefor
US4774085A (en) 1985-07-09 1988-09-27 501 Board of Regents, Univ. of Texas Pharmaceutical administration systems containing a mixture of immunomodulators
US4837028A (en) 1986-12-24 1989-06-06 Liposome Technology, Inc. Liposomes with enhanced circulation time
US5244797B1 (en) 1988-01-13 1998-08-25 Life Technologies Inc Cloned genes encoding reverse transcriptase lacking rnase h activity
US5264618A (en) 1990-04-19 1993-11-23 Vical, Inc. Cationic lipids for intracellular delivery of biologically active molecules
WO1991017424A1 (en) 1990-05-03 1991-11-14 Vical, Inc. Intracellular delivery of biologically active substances by means of self-assembling lipid complexes
US6534261B1 (en) 1999-01-12 2003-03-18 Sangamo Biosciences, Inc. Regulation of endogenous gene expression in cells using zinc finger proteins
EP1235914A2 (en) 1999-11-24 2002-09-04 Joseph Rosenecker Polypeptides comprising multimers of nuclear localization signals or of protein transduction domains and their use for transferring molecules into cells
US8178291B2 (en) 2005-02-18 2012-05-15 Monogram Biosciences, Inc. Methods and compositions for determining hypersusceptibility of HIV-1 to non-nucleoside reverse transcriptase inhibitors
US9783791B2 (en) 2005-08-10 2017-10-10 Agilent Technologies, Inc. Mutant reverse transcriptase and methods of use
CN101668848B (zh) 2007-04-26 2014-10-22 雷蒙特亚特特拉维夫大学有限公司 来自口腔粘膜的多能自体干细胞和使用方法
WO2010028347A2 (en) 2008-09-05 2010-03-11 President & Fellows Of Harvard College Continuous directed evolution of proteins and nucleic acids
US10113156B2 (en) 2009-03-04 2018-10-30 Board Of Regents, The University Of Texas System Stabilized reverse transcriptase fusion proteins
US8889394B2 (en) 2009-09-07 2014-11-18 Empire Technology Development Llc Multiple domain proteins
WO2012054727A1 (en) 2010-10-22 2012-04-26 Bio-Rad Laboratories, Inc. Reverse transcriptase mixtures with improved storage stability
CA2825370A1 (en) 2010-12-22 2012-06-28 President And Fellows Of Harvard College Continuous directed evolution
KR102096534B1 (ko) 2011-09-28 2020-04-03 에라 바이오테크, 에스.에이. 분할된 인테인 및 그의 이용
EP3431497B1 (en) 2012-06-27 2022-07-27 The Trustees of Princeton University Split inteins, conjugates and uses thereof
DK2904101T3 (da) 2012-10-03 2019-08-12 Agrivida Inc Intein-modificerede proteaser, fremstilling deraf og industrielle anvendelser
JO3470B1 (ar) 2012-10-08 2020-07-05 Merck Sharp & Dohme مشتقات 5- فينوكسي-3h-بيريميدين-4-أون واستخدامها كمثبطات ناسخ عكسي ل hiv
US9526784B2 (en) 2013-09-06 2016-12-27 President And Fellows Of Harvard College Delivery system for functional nucleases
WO2015134121A2 (en) 2014-01-20 2015-09-11 President And Fellows Of Harvard College Negative selection and stringency modulation in continuous evolution systems
CN107075491B (zh) 2014-10-28 2021-07-06 谷万达公司 用于稳定反式剪接的内含肽修饰的蛋白酶的方法和组合物
WO2016168631A1 (en) 2015-04-17 2016-10-20 President And Fellows Of Harvard College Vector-based mutagenesis system
US9580698B1 (en) 2016-09-23 2017-02-28 New England Biolabs, Inc. Mutant reverse transcriptase
US20200140835A1 (en) * 2017-06-06 2020-05-07 The General Hospital Corporation Engineered CRISPR-Cas9 Nucleases
EP3707252A1 (en) * 2017-11-10 2020-09-16 Novozymes A/S Temperature-sensitive cas9 protein
WO2020191233A1 (en) * 2019-03-19 2020-09-24 The Broad Institute, Inc. Methods and compositions for editing nucleotide sequences
US20220411768A1 (en) * 2019-10-21 2022-12-29 The Trustees Of Columbia University In The City Of New York Methods of performing rna templated genome editing
CN116209756A (zh) * 2020-03-04 2023-06-02 旗舰先锋创新Vi有限责任公司 调控基因组的方法和组合物

Also Published As

Publication number Publication date
WO2023015309A2 (en) 2023-02-09
EP4381057A2 (en) 2024-06-12
AU2022325166A1 (en) 2024-02-08
JP2024530487A (ja) 2024-08-21
WO2023015309A3 (en) 2023-03-16
US20250270593A1 (en) 2025-08-28

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