CN116194593A - 被称为“CTL-seq”(CRISPR Tag Linear-seq)的核酸酶中靶/脱靶编辑位点的提名方法 - Google Patents

被称为“CTL-seq”(CRISPR Tag Linear-seq)的核酸酶中靶/脱靶编辑位点的提名方法 Download PDF

Info

Publication number
CN116194593A
CN116194593A CN202180059744.9A CN202180059744A CN116194593A CN 116194593 A CN116194593 A CN 116194593A CN 202180059744 A CN202180059744 A CN 202180059744A CN 116194593 A CN116194593 A CN 116194593A
Authority
CN
China
Prior art keywords
misc
phosphorothioate linkage
sequence
tag
dna
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
CN202180059744.9A
Other languages
English (en)
Chinese (zh)
Inventor
马修·麦克尼尔
罗尔夫·土耳克
加勒特·雷提伽
艾伦·布拉克
孙永明
克里斯·塞勒
王彧
基思·甘德森
凯尔•金尼
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.)
Integrated DNA Technologies Inc
Original Assignee
Integrated DNA Technologies 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 Integrated DNA Technologies Inc filed Critical Integrated DNA Technologies Inc
Publication of CN116194593A publication Critical patent/CN116194593A/zh
Pending legal-status Critical Current

Links

Images

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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • 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
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • 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]

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Plant Pathology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Enzymes And Modification Thereof (AREA)
CN202180059744.9A 2020-07-23 2021-07-22 被称为“CTL-seq”(CRISPR Tag Linear-seq)的核酸酶中靶/脱靶编辑位点的提名方法 Pending CN116194593A (zh)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063055460P 2020-07-23 2020-07-23
US63/055,460 2020-07-23
PCT/US2021/042733 WO2022020567A2 (en) 2020-07-23 2021-07-22 Methods for nomination of nuclease on-/off-target editing locations, designated "ctl-seq" (crispr tag linear-seq)

Publications (1)

Publication Number Publication Date
CN116194593A true CN116194593A (zh) 2023-05-30

Family

ID=77338877

Family Applications (1)

Application Number Title Priority Date Filing Date
CN202180059744.9A Pending CN116194593A (zh) 2020-07-23 2021-07-22 被称为“CTL-seq”(CRISPR Tag Linear-seq)的核酸酶中靶/脱靶编辑位点的提名方法

Country Status (8)

Country Link
US (2) US20220025365A1 (https=)
EP (1) EP4185708A2 (https=)
JP (2) JP2023535407A (https=)
KR (1) KR20230040370A (https=)
CN (1) CN116194593A (https=)
AU (1) AU2021311713A1 (https=)
CA (1) CA3185571A1 (https=)
WO (1) WO2022020567A2 (https=)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB202013141D0 (en) 2020-08-21 2020-10-07 Univ College Cardiff Consultants Ltd A screening method for the detection of DNA damage
WO2025151661A1 (en) * 2024-01-10 2025-07-17 Sequre Dx, Inc. Methods for single-ended oligonucleotide enrichment and sequencing
WO2026039499A1 (en) 2024-08-14 2026-02-19 Integrated Dna Technologies, Inc. Adaptered-tag blocking oligonucleotides

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20120283110A1 (en) * 2011-04-21 2012-11-08 Jay Shendure Methods for retrieval of sequence-verified dna constructs
WO2014093330A1 (en) * 2012-12-10 2014-06-19 Clearfork Bioscience, Inc. Methods for targeted genomic analysis
WO2014143228A1 (en) * 2013-03-15 2014-09-18 Integrated Dna Technologies, Inc. Rnase h-based assays utilizing modified rna monomers
WO2015200378A1 (en) * 2014-06-23 2015-12-30 The General Hospital Corporation Genomewide unbiased identification of dsbs evaluated by sequencing (guide-seq)
WO2016030899A1 (en) * 2014-08-28 2016-03-03 Yeda Research And Development Co. Ltd. Methods of treating amyotrophic lateral scleroses
WO2016081798A1 (en) * 2014-11-20 2016-05-26 Children's Medical Center Corporation Methods relating to the detection of recurrent and non-specific double strand breaks in the genome

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
IL269431B2 (en) * 2017-03-23 2025-05-01 Univ Washington Methods for targeted nucleic acid sequence enrichment with applications to error corrected nucleic acid sequencing
CN111868260B (zh) * 2017-08-07 2025-02-21 约翰斯霍普金斯大学 用于评估和治疗癌症的方法和材料
WO2019110067A1 (en) * 2017-12-07 2019-06-13 Aarhus Universitet Hybrid nanoparticle

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20120283110A1 (en) * 2011-04-21 2012-11-08 Jay Shendure Methods for retrieval of sequence-verified dna constructs
WO2014093330A1 (en) * 2012-12-10 2014-06-19 Clearfork Bioscience, Inc. Methods for targeted genomic analysis
WO2014143228A1 (en) * 2013-03-15 2014-09-18 Integrated Dna Technologies, Inc. Rnase h-based assays utilizing modified rna monomers
WO2015200378A1 (en) * 2014-06-23 2015-12-30 The General Hospital Corporation Genomewide unbiased identification of dsbs evaluated by sequencing (guide-seq)
WO2016030899A1 (en) * 2014-08-28 2016-03-03 Yeda Research And Development Co. Ltd. Methods of treating amyotrophic lateral scleroses
WO2016081798A1 (en) * 2014-11-20 2016-05-26 Children's Medical Center Corporation Methods relating to the detection of recurrent and non-specific double strand breaks in the genome

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
FAIRCLOTH BC 等: "Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels", PLOS ONE., vol. 7, no. 8, 31 August 2012 (2012-08-31) *
REGIER JC 等: "Increased Yield of PCR Product from Degenerate Primers with Nondegenerate, Nonhomologous 5′ Tails", BIOTECHNIQUES, vol. 38, no. 1, 30 May 2018 (2018-05-30), pages 34 *

Also Published As

Publication number Publication date
WO2022020567A3 (en) 2022-03-10
JP2026048971A (ja) 2026-03-17
JP2023535407A (ja) 2023-08-17
CA3185571A1 (en) 2022-01-27
US20220025365A1 (en) 2022-01-27
KR20230040370A (ko) 2023-03-22
EP4185708A2 (en) 2023-05-31
US20250257352A1 (en) 2025-08-14
AU2021311713A1 (en) 2023-03-09
WO2022020567A2 (en) 2022-01-27

Similar Documents

Publication Publication Date Title
EP3555305B1 (en) Method for increasing throughput of single molecule sequencing by concatenating short dna fragments
CN112313241B (zh) 核酸结合、修饰、和切割试剂的底物偏好和位点的灵敏体外试验
EP4090766B1 (en) Methods of targeted sequencing
EP4582805A2 (en) Methods of generating libraries of nucleic acid sequences for detection via fluorescent in situ sequencing
AU2019282812B2 (en) Compositions and methods for making guide nucleic acids
US20130123117A1 (en) Capture probe and assay for analysis of fragmented nucleic acids
JP2026048971A (ja) 「ＣＴＬ－ｓｅｑ」（ＣＲＩＳＰＲ Ｔａｇ Ｌｉｎｅａｒ－ｓｅｑ）と称するヌクレアーゼオン／オフターゲット編集位置を指定するための方法
JP2023553983A (ja) 二重鎖シーケンシングのための方法
CN117098855A (zh) 用于从扩增文库中选择性地耗尽不期望的片段的阻断寡核苷酸
CN116829706A (zh) 基于引导编辑的精确的基因组删除和替换方法
US20230122979A1 (en) Methods of sample normalization
WO2025024703A1 (en) Dual-tagmentation single-cell dnaseq
WO2021058145A1 (en) Phage t7 promoters for boosting in vitro transcription
US20260085308A1 (en) Methods for generating cdna library from rna
WO2022243437A1 (en) Sample preparation with oppositely oriented guide polynucleotides
WO2024157194A1 (en) Methods and assays for off-target analysis
WO2024174032A1 (en) Sequence analysis of manufactured genetic constructs
WO2010065576A2 (en) The antisense transcriptomes of cells

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination