CA3234217A1 - Base editing enzymes - Google Patents

Base editing enzymes Download PDF

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Publication number
CA3234217A1
CA3234217A1 CA3234217A CA3234217A CA3234217A1 CA 3234217 A1 CA3234217 A1 CA 3234217A1 CA 3234217 A CA3234217 A CA 3234217A CA 3234217 A CA3234217 A CA 3234217A CA 3234217 A1 CA3234217 A1 CA 3234217A1
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CA
Canada
Prior art keywords
seq
sequence
polypeptide
endonuclease
nos
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
CA3234217A
Other languages
English (en)
French (fr)
Inventor
Brian C. Thomas
Jyun-Liang LIN
Alan Brooks
Cristina Butterfield
Christopher Brown
Cindy CASTELLE
Morayma TEMOCHE-DIAZ
Benjamin Freeman
Christine ROMANO
Rebecca LAMOTHE
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Metagenomi Therapeutics Inc
Original Assignee
Metagenomi Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Metagenomi Inc filed Critical Metagenomi Inc
Publication of CA3234217A1 publication Critical patent/CA3234217A1/en
Pending legal-status Critical Current

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    • 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
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • 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
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    • 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
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    • 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
    • C12N15/113—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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04001—Cytosine deaminase (3.5.4.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04002—Adenine deaminase (3.5.4.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04004—Adenosine deaminase (3.5.4.4)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04005—Cytidine deaminase (3.5.4.5)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/80—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor
    • 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
    • C12N15/113—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
    • C12N15/1138—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 against receptors or cell surface 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
    • 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
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
    • 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
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/344—Position-specific modifications, e.g. on every purine, at the 3'-end

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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)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Plant Pathology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Mycology (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)
CA3234217A 2021-11-05 2022-11-04 Base editing enzymes Pending CA3234217A1 (en)

Applications Claiming Priority (11)

Application Number Priority Date Filing Date Title
US202163276461P 2021-11-05 2021-11-05
US63/276,461 2021-11-05
US202163289998P 2021-12-15 2021-12-15
US63/289,998 2021-12-15
US202263342824P 2022-05-17 2022-05-17
US63/342,824 2022-05-17
US202263356888P 2022-06-29 2022-06-29
US63/356,888 2022-06-29
US202263378171P 2022-10-03 2022-10-03
US63/378,171 2022-10-03
PCT/US2022/079345 WO2023081855A1 (en) 2021-11-05 2022-11-04 Base editing enzymes

Publications (1)

Publication Number Publication Date
CA3234217A1 true CA3234217A1 (en) 2023-05-11

Family

ID=86242250

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3234217A Pending CA3234217A1 (en) 2021-11-05 2022-11-04 Base editing enzymes

Country Status (8)

Country Link
US (1) US12503710B2 (https=)
EP (1) EP4426826A4 (https=)
JP (1) JP2024541811A (https=)
KR (1) KR20240099283A (https=)
AU (1) AU2022380842A1 (https=)
CA (1) CA3234217A1 (https=)
MX (1) MX2024005505A (https=)
WO (1) WO2023081855A1 (https=)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA3192224A1 (en) 2020-09-11 2022-03-17 Jyun-Liang LIN Base editing enzymes
BR112023014719A2 (pt) * 2021-01-22 2023-12-05 Metagenomi Inc Novas nucleases quiméricas e manipuladas
AU2022380842A1 (en) 2021-11-05 2024-05-23 Metagenomi Therapeutics, Inc. Base editing enzymes
WO2023178115A2 (en) * 2022-03-14 2023-09-21 Metagenomi, Inc. Engineered and chimeric nucleases
CN119351373A (zh) * 2023-07-24 2025-01-24 北京志道生物科技有限公司 一种核酸内切酶及其应用
WO2025081064A2 (en) * 2023-10-11 2025-04-17 Illumina, Inc. Thermophilic deaminase and methods for identifying modified cytosine
WO2025119295A1 (zh) * 2023-12-05 2025-06-12 广州瑞风生物科技有限公司 脱氨酶、融合蛋白、核酸、药物组合物及其应用
WO2025207709A1 (en) * 2024-03-26 2025-10-02 Arbor Biotechnologies, Inc. Reverse transcription-mediated gene editing systems and uses thereof

Family Cites Families (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11192929B2 (en) 2016-12-08 2021-12-07 Regents Of The University Of Minnesota Site-specific DNA base editing using modified APOBEC enzymes
EP3572525A4 (en) 2017-01-17 2020-09-30 Institute for Basic Science PROCEDURE FOR IDENTIFYING AN OFF-TARGET BASIC EDITING SITE BY BREAKING A SINGLE DNA STRAND
CA3057192A1 (en) * 2017-03-23 2018-09-27 President And Fellows Of Harvard College Nucleobase editors comprising nucleic acid programmable dna binding proteins
KR102758434B1 (ko) 2017-03-30 2025-01-21 고쿠리츠 다이가쿠 호진 교토 다이가쿠 게놈 편집에 의한 엑손 스키핑 유도 방법
US9982279B1 (en) 2017-06-23 2018-05-29 Inscripta, Inc. Nucleic acid-guided nucleases
AU2018290843B2 (en) 2017-06-26 2025-04-24 Massachusetts Institute Of Technology CRISPR/Cas-adenine deaminase based compositions, systems, and methods for targeted nucleic acid editing
JP2021506251A (ja) 2017-12-14 2021-02-22 クリスパー セラピューティクス アーゲー 新規ｒｎａプログラム可能エンドヌクレアーゼ系、ならびにゲノム編集および他の適用におけるその使用
US11946040B2 (en) 2019-02-04 2024-04-02 The General Hospital Corporation Adenine DNA base editor variants with reduced off-target RNA editing
US20220298494A1 (en) 2019-02-14 2022-09-22 Metagenomi Ip Technologies, Llc Enzymes with ruvc domains
AU2020223370B2 (en) 2019-02-14 2023-04-20 Metagenomi Therapeutics, Inc. Enzymes with RuvC domains
WO2021097118A1 (en) 2019-11-12 2021-05-20 The Broad Institute, Inc. Small type ii cas proteins and methods of use thereof
GB2608292B (en) 2020-03-31 2024-02-14 Metagenomi Inc Class II, type II CRISPR systems
GB2700205B (en) 2020-09-11 2026-04-15 Metagenomi Therapeutics Inc Base editing enzymes
CA3192224A1 (en) 2020-09-11 2022-03-17 Jyun-Liang LIN Base editing enzymes
AU2022380842A1 (en) 2021-11-05 2024-05-23 Metagenomi Therapeutics, Inc. Base editing enzymes

Also Published As

Publication number Publication date
KR20240099283A (ko) 2024-06-28
US20240309404A1 (en) 2024-09-19
WO2023081855A1 (en) 2023-05-11
JP2024541811A (ja) 2024-11-13
EP4426826A4 (en) 2025-08-20
US12503710B2 (en) 2025-12-23
AU2022380842A1 (en) 2024-05-23
MX2024005505A (es) 2024-05-23
EP4426826A1 (en) 2024-09-11

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