CA3127493A1 - Nucleobase editors having reduced non-target deamination and assays for characterizing nucleobase editors - Google Patents

Nucleobase editors having reduced non-target deamination and assays for characterizing nucleobase editors Download PDF

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Publication number
CA3127493A1
CA3127493A1 CA3127493A CA3127493A CA3127493A1 CA 3127493 A1 CA3127493 A1 CA 3127493A1 CA 3127493 A CA3127493 A CA 3127493A CA 3127493 A CA3127493 A CA 3127493A CA 3127493 A1 CA3127493 A1 CA 3127493A1
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Prior art keywords
deaminase
fusion protein
amino acid
cas9
terminal fragment
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Pending
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CA3127493A
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English (en)
French (fr)
Inventor
Ian SLAYMAKER
Jason Michael GEHRKE
Nicole GAUDELLI
Yi Yu
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Beam Therapeutics Inc
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Beam Therapeutics Inc
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Publication of CA3127493A1 publication Critical patent/CA3127493A1/en
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102Mutagenizing nucleic acids
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111General methods applicable to biologically active non-coding nucleic acids
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/62DNA sequences coding for fusion proteins
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14Hydrolases (3)
    • C12N9/16Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14Hydrolases (3)
    • C12N9/78Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14Hydrolases (3)
    • C12N9/78Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C12N9/80Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5) acting on amide bonds in linear amides (3.5.1)
    • CCHEMISTRY; METALLURGY
    • C40COMBINATORIAL TECHNOLOGY
    • C40BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00Libraries per se, e.g. arrays, mixtures
    • C40B40/04Libraries containing only organic compounds
    • C40B40/10Libraries containing peptides or polypeptides, or derivatives thereof
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K2319/00Fusion polypeptide
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/10Type of nucleic acid
    • C12N2310/20Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00Applications; Uses
    • C12N2320/10Applications; Uses in screening processes
    • C12N2320/11Applications; Uses in screening processes for the determination of target sites, i.e. of active nucleic acids
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12YENZYMES
    • C12Y305/00Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04005Cytidine deaminase (3.5.4.5)

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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)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Medicinal Chemistry (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Physics & Mathematics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Peptides Or Proteins (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
CA3127493A 2019-01-31 2020-01-31 Nucleobase editors having reduced non-target deamination and assays for characterizing nucleobase editors Pending CA3127493A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201962799702P 2019-01-31 2019-01-31
US62/799,702 2019-01-31
PCT/US2020/016285 WO2020160514A1 (en) 2019-01-31 2020-01-31 Nucleobase editors having reduced non-target deamination and assays for characterizing nucleobase editors

Publications (1)

Publication Number Publication Date
CA3127493A1 true CA3127493A1 (en) 2020-08-06

Family

ID=71842366

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3127493A Pending CA3127493A1 (en) 2019-01-31 2020-01-31 Nucleobase editors having reduced non-target deamination and assays for characterizing nucleobase editors

Country Status (8)

Country Link
US (1) US20220098572A1 (enExample)
EP (1) EP3918078A4 (enExample)
JP (2) JP7646552B2 (enExample)
KR (1) KR20210121113A (enExample)
CN (1) CN114040977B (enExample)
AU (1) AU2020215730A1 (enExample)
CA (1) CA3127493A1 (enExample)
WO (1) WO2020160514A1 (enExample)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3204496A1 (en) 2014-10-10 2017-08-16 Editas Medicine, Inc. Compositions and methods for promoting homology directed repair
KR102852347B1 (ko) 2018-05-11 2025-09-01 빔 테라퓨틱스, 인크. 프로그래밍가능한 염기 편집기 시스템을 이용하여 병원성 아미노산을 치환하는 방법
WO2020051562A2 (en) 2018-09-07 2020-03-12 Beam Therapeutics Inc. Compositions and methods for improving base editing
IL296024A (en) 2020-03-04 2022-10-01 Flagship Pioneering Innovations Vi Llc Methods and compositions for modulating a genome
US20230159913A1 (en) 2020-04-28 2023-05-25 The Broad Institute, Inc. Targeted base editing of the ush2a gene
US20230323335A1 (en) * 2020-09-04 2023-10-12 National University Corporation Kobe University Miniaturized cytidine deaminase-containing complex for modifying double-stranded dna
CN116601293A (zh) * 2020-12-07 2023-08-15 中国科学院动物研究所 工程化的Cas效应蛋白及其使用方法
CN113308451B (zh) * 2020-12-07 2023-07-25 中国科学院动物研究所 工程化的Cas效应蛋白及其使用方法
JP2024511163A (ja) * 2021-03-26 2024-03-12 ビーム セラピューティクス インク. アデノシンデアミナーゼバリアント及びその使用
CA3224970A1 (en) * 2021-07-06 2023-01-12 Holly A. REES Compositions and methods for efficient genome editing
AU2022343268A1 (en) 2021-09-08 2024-03-28 Flagship Pioneering Innovations Vi, Llc Methods and compositions for modulating a genome
US20250361530A1 (en) * 2022-05-14 2025-11-27 The Regents Of The University Of California Genome editing systems for multiplexing point mutation introduction in living cells
WO2025119307A1 (zh) * 2023-12-06 2025-06-12 北京齐禾生科生物科技有限公司 优化的qbe碱基编辑系统及其应用

Family Cites Families (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11053481B2 (en) * 2013-12-12 2021-07-06 President And Fellows Of Harvard College Fusions of Cas9 domains and nucleic acid-editing domains
WO2015089486A2 (en) * 2013-12-12 2015-06-18 The Broad Institute Inc. Systems, methods and compositions for sequence manipulation with optimized functional crispr-cas systems
CN107406875B (zh) * 2014-12-20 2021-12-07 阿克生物公司 使用CRISPR/Cas系统蛋白靶向消减、富集、和分割核酸的组合物及方法
WO2016123243A1 (en) * 2015-01-28 2016-08-04 The Regents Of The University Of California Methods and compositions for labeling a single-stranded target nucleic acid
EP3303634B1 (en) * 2015-06-03 2023-08-30 The Regents of The University of California Cas9 variants and methods of use thereof
MX392008B (es) * 2015-06-18 2025-03-21 Broad Inst Inc Mutaciones de la enzima crispr que reducen los efectos fuera del blanco
EP3350203A4 (en) * 2015-09-17 2019-06-26 The Regents of The University of California POLYPEPTIDES OF CAS9 VARIANT WITH INTERNAL INSERTIONS
IL294014B2 (en) * 2015-10-23 2024-07-01 Harvard College Nucleobase editors and uses thereof
WO2018027078A1 (en) * 2016-08-03 2018-02-08 President And Fellows Of Harard College Adenosine nucleobase editors and uses thereof
SG10201913505WA (en) * 2016-10-17 2020-02-27 Univ Nanyang Tech Truncated crispr-cas proteins for dna targeting
US10745677B2 (en) * 2016-12-23 2020-08-18 President And Fellows Of Harvard College Editing of CCR5 receptor gene to protect against HIV infection
GB2575930A (en) * 2017-03-23 2020-01-29 Harvard College Nucleobase editors comprising nucleic acid programmable DNA binding proteins
US12297436B2 (en) * 2017-05-18 2025-05-13 The Broad Institute, Inc. Systems, methods, and compositions for targeted nucleic acid editing
KR102761791B1 (ko) * 2017-06-26 2025-02-05 더 브로드 인스티튜트, 인코퍼레이티드 표적화된 핵산 편집을 위한 crispr/cas-아데닌 데아미나아제 기반 조성물, 시스템 및 방법

Also Published As

Publication number Publication date
JP2022519507A (ja) 2022-03-24
EP3918078A1 (en) 2021-12-08
WO2020160514A1 (en) 2020-08-06
JP2025102784A (ja) 2025-07-08
AU2020215730A1 (en) 2021-07-29
JP7646552B2 (ja) 2025-03-17
US20220098572A1 (en) 2022-03-31
CN114040977A (zh) 2022-02-11
EP3918078A4 (en) 2022-12-14
CN114040977B (zh) 2024-09-03
KR20210121113A (ko) 2021-10-07

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