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
Pending legal-status Critical Current

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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)
  • Cell Biology (AREA)
  • Mycology (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)
  • Apparatus Associated With Microorganisms And Enzymes (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 (https=)
EP (1) EP4381057A2 (https=)
JP (1) JP2024530487A (https=)
AU (1) AU2022325166A1 (https=)
CA (1) CA3227004A1 (https=)
WO (1) WO2023015309A2 (https=)

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9388430B2 (en) 2013-09-06 2016-07-12 President And Fellows Of Harvard College Cas9-recombinase fusion proteins and uses thereof
US9340799B2 (en) 2013-09-06 2016-05-17 President And Fellows Of Harvard College MRNA-sensing switchable gRNAs
WO2016022363A2 (en) 2014-07-30 2016-02-11 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
JP2020510038A (ja) 2017-03-09 2020-04-02 プレジデント アンド フェローズ オブ ハーバード カレッジ がんワクチン
WO2019023680A1 (en) 2017-07-28 2019-01-31 President And Fellows Of Harvard College METHODS AND COMPOSITIONS FOR EVOLUTION OF BASIC EDITORS USING PHAGE-ASSISTED CONTINUOUS EVOLUTION (PACE)
WO2019118949A1 (en) 2017-12-15 2019-06-20 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
JP7657726B2 (ja) 2019-03-19 2025-04-07 ザ ブロード インスティテュート，インコーポレーテッド 編集ヌクレオチド配列を編集するための方法および組成物
US12473543B2 (en) 2019-04-17 2025-11-18 The Broad Institute, Inc. Adenine base editors with reduced off-target effects
JP2024533311A (ja) 2021-09-08 2024-09-12 フラッグシップ パイオニアリング イノベーションズ シックス，エルエルシー ゲノムを調節するための方法及び組成物
KR20240099164A (ko) 2021-09-08 2024-06-28 플래그쉽 파이어니어링 이노베이션스 브이아이, 엘엘씨 Pah-조절 조성물 및 방법
WO2024077267A1 (en) 2022-10-07 2024-04-11 The Broad Institute, Inc. Prime editing methods and compositions for treating triplet repeat disorders
CN118995664B (zh) * 2023-05-22 2026-03-20 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
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
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
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
CA2392490A1 (en) 1999-11-24 2001-05-31 Mcs Micro Carrier Systems Gmbh 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
EP2137300B1 (en) 2007-04-26 2011-10-26 Ramot at Tel-Aviv University Ltd. Pluripotent autologous stem cells from oral or gastrointestinal mucosa
EP2342336B1 (en) 2008-09-05 2016-12-14 President and Fellows of Harvard College Continuous directed evolution of proteins and nucleic acids
BRPI1009221A2 (pt) 2009-03-04 2016-03-15 Univ Texas proteínas de fusão transcriptase reversa estabilizadas.
US8889394B2 (en) 2009-09-07 2014-11-18 Empire Technology Development Llc Multiple domain proteins
US9458484B2 (en) 2010-10-22 2016-10-04 Bio-Rad Laboratories, Inc. Reverse transcriptase mixtures with improved storage stability
EP3202903B1 (en) 2010-12-22 2020-02-12 President and Fellows of Harvard College Continuous directed evolution
EP2761006B1 (en) 2011-09-28 2016-12-14 Zera Intein Protein Solutions, S.L. Split inteins and uses thereof
DK3431497T3 (da) 2012-06-27 2022-10-10 Univ Princeton Spaltede inteiner, konjugater og anvendelser deraf
WO2014055778A2 (en) 2012-10-03 2014-04-10 Agrivida, Inc. Multiprotein expression cassettes
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
US10179911B2 (en) 2014-01-20 2019-01-15 President And Fellows Of Harvard College Negative selection and stringency modulation in continuous evolution systems
WO2016069774A1 (en) 2014-10-28 2016-05-06 Agrivida, Inc. Methods and compositions for stabilizing trans-splicing intein modified proteases
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
WO2018226855A1 (en) * 2017-06-06 2018-12-13 The General Hospital Corporation Engineered crispr-cas9 nucleases
EP3707252A1 (en) * 2017-11-10 2020-09-16 Novozymes A/S Temperature-sensitive cas9 protein
JP7657726B2 (ja) * 2019-03-19 2025-04-07 ザ ブロード インスティテュート，インコーポレーテッド 編集ヌクレオチド配列を編集するための方法および組成物
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
IL296024A (en) * 2020-03-04 2022-10-01 Flagship Pioneering Innovations Vi Llc Methods and compositions for modulating a genome

Also Published As

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

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