CA3065384A1 - Creation and use of guide nucleic acids - Google Patents

Creation and use of guide nucleic acids Download PDF

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Publication number
CA3065384A1
CA3065384A1 CA3065384A CA3065384A CA3065384A1 CA 3065384 A1 CA3065384 A1 CA 3065384A1 CA 3065384 A CA3065384 A CA 3065384A CA 3065384 A CA3065384 A CA 3065384A CA 3065384 A1 CA3065384 A1 CA 3065384A1
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CA
Canada
Prior art keywords
dna
sequence
site
adapter
nucleic acids
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
CA3065384A
Other languages
English (en)
French (fr)
Inventor
Stephane B. Gourguechon
Meredith L. CARPENTER
Morten Rasmussen
Srihari RADHAKRISHNAN
Anna Katharina ELMER
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.)
ARC Bio LLC
Original Assignee
Gourguechon Stephane B
Radhakrishnan Srihari
ARC Bio LLC
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 Gourguechon Stephane B, Radhakrishnan Srihari, ARC Bio LLC filed Critical Gourguechon Stephane B
Publication of CA3065384A1 publication Critical patent/CA3065384A1/en
Pending legal-status Critical Current

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Classifications

    • 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
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
    • 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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • 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
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
    • 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
    • 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
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/12—Applications; Uses in screening processes in functional genomics, i.e. for the determination of gene function
    • 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
    • C12N2330/00—Production
    • C12N2330/30—Production chemically synthesised
    • C12N2330/31—Libraries, arrays
    • 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
    • C12N2800/00—Nucleic acids vectors
    • C12N2800/80—Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction sites

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Biomedical Technology (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Plant Pathology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
CA3065384A 2017-06-07 2018-06-07 Creation and use of guide nucleic acids Pending CA3065384A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201762516619P 2017-06-07 2017-06-07
US62/516,619 2017-06-07
US201762548036P 2017-08-21 2017-08-21
US62/548,036 2017-08-21
PCT/US2018/036563 WO2018227025A1 (en) 2017-06-07 2018-06-07 Creation and use of guide nucleic acids

Publications (1)

Publication Number Publication Date
CA3065384A1 true CA3065384A1 (en) 2018-12-13

Family

ID=64566018

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3065384A Pending CA3065384A1 (en) 2017-06-07 2018-06-07 Creation and use of guide nucleic acids

Country Status (7)

Country Link
US (2) US20200190508A1 (enExample)
EP (1) EP3635114B1 (enExample)
JP (1) JP7282692B2 (enExample)
CN (1) CN111094565B (enExample)
AU (1) AU2018279112B2 (enExample)
CA (1) CA3065384A1 (enExample)
WO (1) WO2018227025A1 (enExample)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN119120659A (zh) * 2023-07-13 2024-12-13 上海市第十人民医院 一种基于切刻内切酶的一锅式多靶标正交检测系统及其应用

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2016365720B2 (en) 2015-12-07 2020-11-26 Arc Bio, Llc Methods and compositions for the making and using of guide nucleic acids
EP3861135B1 (en) 2018-10-04 2023-08-02 Arc Bio, LLC Normalization controls for managing low sample inputs in next generation sequencing
WO2020106630A1 (en) * 2018-11-19 2020-05-28 The Regents Of The University Of California Methods for detecting and sequencing a target nucleic acid
AU2020272770B2 (en) * 2019-04-09 2026-01-22 Arc Bio, Llc Compositions and methods for nucleotide modification-based depletion
WO2021142197A1 (en) * 2020-01-09 2021-07-15 Duke University Composistions and methods for crispr enabled dna synthesis
WO2021203047A1 (en) * 2020-04-02 2021-10-07 Altius Institute For Biomedical Sciences Methods, compositions, and kits for identifying regions of genomic dna bound to a protein
WO2021257453A2 (en) * 2020-06-15 2021-12-23 The Broad Institute, Inc. Chimeric amplicon array sequencing
CN119286993A (zh) * 2021-01-08 2025-01-10 武汉大学 用于即时核酸检测的组合物和方法
CN113462755B (zh) * 2021-05-06 2023-03-21 中国人民解放军陆军军医大学第一附属医院 一种用于短链非编码rna检测的模块化酶电路检测系统
AU2022272723A1 (en) * 2021-05-14 2023-11-30 Becton, Dickinson And Company Methods for making libraries for nucleic acid sequencing
CN114293264B (zh) * 2021-12-21 2024-12-27 翌圣生物科技(上海)股份有限公司 酶法靶序列随机sgRNA文库的制备方法
US20250019693A1 (en) * 2022-02-17 2025-01-16 Claret Bioscience, Llc Methods and compositions for analyzing nucleic acid

Family Cites Families (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20050233340A1 (en) 2004-04-20 2005-10-20 Barrett Michael T Methods and compositions for assessing CpG methylation
US8183359B2 (en) * 2007-03-01 2012-05-22 Gen-Probe Incorporated Kits for amplifying DNA
US8323930B2 (en) * 2007-07-28 2012-12-04 Dna Twopointo, Inc. Methods, compositions and kits for one-step DNA cloning using DNA topoisomerase
WO2009133466A2 (en) 2008-04-30 2009-11-05 Population Genetics Technologies Ltd. Asymmetric adapter library construction
KR102146721B1 (ko) * 2012-07-13 2020-08-21 엑스-켐, 인크. 폴리머라제에 의해 판독가능하지 않은 코딩 올리고뉴클레오티드 연결을 갖는 dna-코딩된 라이브러리
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
WO2014165549A1 (en) * 2013-04-01 2014-10-09 University Of Florida Research Foundation, Incorporated Determination of methylation state and chromatin structure of target genetic loci
CA2913236A1 (en) * 2013-06-07 2014-12-11 Keygene N.V. Method for targeted sequencing
KR102160389B1 (ko) * 2013-08-05 2020-09-28 트위스트 바이오사이언스 코포레이션 드 노보 합성된 유전자 라이브러리
EP3052651B1 (en) * 2013-10-01 2019-11-27 Life Technologies Corporation Systems and methods for detecting structural variants
CN107002098A (zh) 2014-09-29 2017-08-01 杰克逊实验室 通过电穿孔高效率、高通量产生遗传修饰哺乳动物
SG11201703779VA (en) * 2014-11-11 2017-06-29 Illumina Inc Polynucleotide amplification using crispr-cas systems
AU2015364286B2 (en) 2014-12-20 2021-11-04 Arc Bio, Llc Compositions and methods for targeted depletion, enrichment, and partitioning of nucleic acids using CRISPR/Cas system proteins
AU2016211517B2 (en) * 2015-01-28 2021-05-13 Caribou Biosciences, Inc. CRISPR hybrid DNA/RNA polynucleotides and methods of use
WO2016130697A1 (en) * 2015-02-11 2016-08-18 Memorial Sloan Kettering Cancer Center Methods and kits for generating vectors that co-express multiple target molecules
WO2016133764A1 (en) * 2015-02-17 2016-08-25 Complete Genomics, Inc. Dna sequencing using controlled strand displacement
US20160362680A1 (en) * 2015-05-15 2016-12-15 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
CA3001683C (en) * 2015-06-05 2024-06-04 The Regents Of The University Of California Methods and compositions for generating crispr/cas guide rnas
EP3985111A1 (en) * 2015-08-19 2022-04-20 Arc Bio, LLC Capture of nucleic acids using a nucleic acid-guided nuclease-based system
AU2016335698B2 (en) * 2015-10-08 2022-12-01 President And Fellows Of Harvard College Multiplexed genome editing
EP3374507A1 (en) * 2015-11-09 2018-09-19 IFOM Fondazione Istituto Firc di Oncologia Molecolare Crispr-cas sgrna library
AU2016365720B2 (en) * 2015-12-07 2020-11-26 Arc Bio, Llc Methods and compositions for the making and using of guide nucleic acids
US20200255823A1 (en) * 2016-10-06 2020-08-13 Pioneer Biolabs, Llc Guide strand library construction and methods of use thereof

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN119120659A (zh) * 2023-07-13 2024-12-13 上海市第十人民医院 一种基于切刻内切酶的一锅式多靶标正交检测系统及其应用

Also Published As

Publication number Publication date
EP3635114B1 (en) 2024-11-06
US20200190508A1 (en) 2020-06-18
US20250179477A1 (en) 2025-06-05
WO2018227025A1 (en) 2018-12-13
JP2020524491A (ja) 2020-08-20
EP3635114C0 (en) 2024-11-06
CN111094565A (zh) 2020-05-01
JP7282692B2 (ja) 2023-05-29
EP3635114A4 (en) 2021-03-17
AU2018279112B2 (en) 2024-11-07
CN111094565B (zh) 2024-02-06
EP3635114A1 (en) 2020-04-15
AU2018279112A1 (en) 2019-12-19

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