CA3049989A1 - A modular universal plasmid design strategy for the assembly and editing of multiple dna constructs for multiple hosts - Google Patents

A modular universal plasmid design strategy for the assembly and editing of multiple dna constructs for multiple hosts Download PDF

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Publication number
CA3049989A1
CA3049989A1 CA3049989A CA3049989A CA3049989A1 CA 3049989 A1 CA3049989 A1 CA 3049989A1 CA 3049989 A CA3049989 A CA 3049989A CA 3049989 A CA3049989 A CA 3049989A CA 3049989 A1 CA3049989 A1 CA 3049989A1
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dna
crispr
ctag
insert
ctags
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CA3049989A
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English (en)
French (fr)
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Brian CHAIKIND
Hendrik Marinus VAN ROSSUM
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Zymergen Inc
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Zymergen Inc
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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
    • 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
    • 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
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • 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
    • 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
    • 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
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • 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
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/64—General methods for preparing the vector, for introducing it into the cell or for selecting the vector-containing host
    • 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
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/66—General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
    • 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
    • C12N2310/3517—Marker; Tag

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  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Biomedical Technology (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Cell Biology (AREA)
  • Analytical Chemistry (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA3049989A 2017-02-10 2018-02-09 A modular universal plasmid design strategy for the assembly and editing of multiple dna constructs for multiple hosts Pending CA3049989A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762457493P 2017-02-10 2017-02-10
US62/457,493 2017-02-10
PCT/US2018/017573 WO2018148511A1 (en) 2017-02-10 2018-02-09 A modular universal plasmid design strategy for the assembly and editing of multiple dna constructs for multiple hosts

Publications (1)

Publication Number Publication Date
CA3049989A1 true CA3049989A1 (en) 2018-08-16

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
CA3049989A Pending CA3049989A1 (en) 2017-02-10 2018-02-09 A modular universal plasmid design strategy for the assembly and editing of multiple dna constructs for multiple hosts

Country Status (7)

Country Link
US (2) US11098305B2 (cg-RX-API-DMAC10.html)
EP (1) EP3580337A4 (cg-RX-API-DMAC10.html)
JP (1) JP2020507312A (cg-RX-API-DMAC10.html)
KR (1) KR20190116282A (cg-RX-API-DMAC10.html)
CN (1) CN110312797A (cg-RX-API-DMAC10.html)
CA (1) CA3049989A1 (cg-RX-API-DMAC10.html)
WO (1) WO2018148511A1 (cg-RX-API-DMAC10.html)

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110312797A (zh) 2017-02-10 2019-10-08 齐默尔根公司 组装和编辑用于多个宿主的多个dna构建体的模块化通用质粒设计策略
KR20210044795A (ko) * 2018-08-15 2021-04-23 지머젠 인코포레이티드 고 처리량 대사 공학에서 CRISPRi의 응용
AU2020253531C1 (en) 2019-04-04 2022-06-16 Regeneron Pharmaceuticals, Inc. Methods for scarless introduction of targeted modifications into targeting vectors
KR102421129B1 (ko) * 2019-10-14 2022-07-15 연세대학교 산학협력단 신규 프로토스페이서 인접 모티프 서열 및 이를 이용한 세포의 유전체에서 표적 핵산을 변형시키는 방법
KR102178813B1 (ko) 2019-10-18 2020-11-13 주식회사 다우진유전자연구소 Dna 구조체를 적용한 간이 키트
CN115052980B (zh) * 2019-11-18 2024-09-10 苏州齐禾生科生物科技有限公司 衍生自黄杆菌的基因编辑系统
EP4065701A4 (en) * 2019-11-27 2023-11-29 Danmarks Tekniske Universitet CONSTRUCTS, COMPOSITIONS AND METHODS THEREOF WITH IMPROVED GENOMEDITING EFFICIENCY AND SPECIFICITY
AU2021230464A1 (en) 2020-03-03 2022-09-01 Codex Dna, Inc. Methods for assembling nucleic acids
CN113373130B (zh) * 2021-05-31 2023-12-22 复旦大学 Cas12蛋白、含有Cas12蛋白的基因编辑系统及应用
GB202117455D0 (en) * 2021-12-02 2022-01-19 Academisch Ziekenhuis Leiden Method of editing nucleic acid
TW202405168A (zh) * 2022-04-08 2024-02-01 英商葛蘭素史密斯克藍智慧財產發展有限公司 製造含有寡核苷酸之聚核苷酸的新穎方法
CN116284436B (zh) * 2022-11-25 2026-04-07 广州美格生物科技有限公司 嵌合体TsCas12a蛋白及其制备方法和应用
CN119432813A (zh) * 2023-12-29 2025-02-14 武汉艾迪晶生物科技有限公司 Cas蛋白、组合蛋白、核酸分子、核糖核蛋白复合物、重组载体、转基因细胞及其应用
WO2025165780A1 (en) * 2024-02-01 2025-08-07 The Board Of Trustees Of The Leland Stanford Junior University Combinatorial gene editing and screening

Family Cites Families (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ES2204913T3 (es) 1993-04-12 2004-05-01 Northwestern University Metodo para formacion de oligonucleotidos.
US5773258A (en) 1995-08-25 1998-06-30 Roche Molecular Systems, Inc. Nucleic acid amplification using a reversibly inactivated thermostable enzyme
ATE362986T1 (de) 1998-10-30 2007-06-15 Cornell Res Foundation Inc High fidelity thermostabile ligase und ihre verwendung
KR20100133319A (ko) * 2009-06-11 2010-12-21 주식회사 툴젠 표적 특이적인 게놈의 재배열을 위한 표적 특이적 뉴클레아제 및 이의 용도
GB2481425A (en) * 2010-06-23 2011-12-28 Iti Scotland Ltd Method and device for assembling polynucleic acid sequences
ES2728782T3 (es) 2012-05-25 2019-10-28 Univ California Métodos y composiciones para la modificación de ADN objetivo dirigida por ARN y para la modulación de la transcripción dirigida por ARN
US8697359B1 (en) 2012-12-12 2014-04-15 The Broad Institute, Inc. CRISPR-Cas systems and methods for altering expression of gene products
WO2014093694A1 (en) 2012-12-12 2014-06-19 The Broad Institute, Inc. Crispr-cas nickase systems, methods and compositions for sequence manipulation in eukaryotes
MX380562B (es) 2012-12-12 2025-03-12 Broad Inst Inc Modificaciones de sistemas, métodos y composiciones guía optimizadas para la manipulación de secuencias.
CN105209621B (zh) 2012-12-12 2021-05-25 布罗德研究所有限公司 对用于序列操纵的改进的系统、方法和酶组合物进行的工程化和优化
PT2931898E (pt) 2012-12-12 2016-06-16 Harvard College Manipulação e otimização de sistemas, métodos e composições para manipulação de sequências com domínios funcionais
KR102955556B1 (ko) 2012-12-12 2026-04-22 더 브로드 인스티튜트, 인코퍼레이티드 서열 조작을 위한 crispr-cas 성분 시스템, 방법 및 조성물
CN105408483A (zh) * 2013-03-15 2016-03-16 通用医疗公司 遗传和表观遗传调节蛋白至特定基因组基因座的rna引导的靶向
US9873907B2 (en) 2013-05-29 2018-01-23 Agilent Technologies, Inc. Method for fragmenting genomic DNA using CAS9
WO2014197748A2 (en) 2013-06-05 2014-12-11 Duke University Rna-guided gene editing and gene regulation
ES2777217T3 (es) * 2013-06-17 2020-08-04 Broad Inst Inc Suministro, modificación y optimización de sistemas de guía en tándem, métodos y composiciones para la manipulación de secuencias
JP6738728B2 (ja) * 2013-06-17 2020-08-19 ザ・ブロード・インスティテュート・インコーポレイテッド 肝臓ターゲティングおよび治療のためのＣＲＩＳＰＲ−Ｃａｓ系、ベクターおよび組成物の送達および使用
US10287590B2 (en) 2014-02-12 2019-05-14 Dna2.0, Inc. Methods for generating libraries with co-varying regions of polynuleotides for genome modification
US9738897B2 (en) * 2014-06-23 2017-08-22 Regeneron Pharmaceuticals, Inc. Nuclease-mediated DNA assembly
US20180002706A1 (en) * 2014-12-30 2018-01-04 University Of South Florida Methods and compositions for cloning into large vectors
CA3012631A1 (en) * 2015-06-18 2016-12-22 The Broad Institute Inc. Novel crispr enzymes and systems
WO2016205759A1 (en) * 2015-06-18 2016-12-22 The Broad Institute Inc. Engineering and optimization of systems, methods, enzymes and guide scaffolds of cas9 orthologs and variants for sequence manipulation
US9790490B2 (en) * 2015-06-18 2017-10-17 The Broad Institute Inc. CRISPR enzymes and systems
US20190330659A1 (en) 2016-07-15 2019-10-31 Zymergen Inc. Scarless dna assembly and genome editing using crispr/cpf1 and dna ligase
CN109563505A (zh) * 2016-07-28 2019-04-02 帝斯曼知识产权资产管理有限公司 用于真核细胞的组装系统
CN110312797A (zh) 2017-02-10 2019-10-08 齐默尔根公司 组装和编辑用于多个宿主的多个dna构建体的模块化通用质粒设计策略
KR20210044795A (ko) 2018-08-15 2021-04-23 지머젠 인코포레이티드 고 처리량 대사 공학에서 CRISPRi의 응용

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Publication number Publication date
EP3580337A1 (en) 2019-12-18
US11098305B2 (en) 2021-08-24
WO2018148511A1 (en) 2018-08-16
US20210371856A1 (en) 2021-12-02
KR20190116282A (ko) 2019-10-14
JP2020507312A (ja) 2020-03-12
EP3580337A4 (en) 2020-12-02
US20200123540A1 (en) 2020-04-23
CN110312797A (zh) 2019-10-08

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