CA2928012C - Method for analysing the interaction of nucleotide sequences in a three-dimensional dna structure - Google Patents

Method for analysing the interaction of nucleotide sequences in a three-dimensional dna structure Download PDF

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Publication number
CA2928012C
CA2928012C CA2928012A CA2928012A CA2928012C CA 2928012 C CA2928012 C CA 2928012C CA 2928012 A CA2928012 A CA 2928012A CA 2928012 A CA2928012 A CA 2928012A CA 2928012 C CA2928012 C CA 2928012C
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dna
interaction
nucleotide sequence
restriction enzyme
interest
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French (fr)
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CA2928012A1 (en
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Frank Grosveld
Tobias Knoch
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Erasmus University Medical Center
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Erasmus University Medical Center
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6816Hybridisation assays characterised by the detection means
    • C12Q1/682Signal amplification
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2521/00Reaction characterised by the enzymatic activity
    • C12Q2521/30Phosphoric diester hydrolysing, i.e. nuclease
    • C12Q2521/301Endonuclease
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2521/00Reaction characterised by the enzymatic activity
    • C12Q2521/50Other enzymatic activities
    • C12Q2521/501Ligase
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2523/00Reactions characterised by treatment of reaction samples
    • C12Q2523/10Characterised by chemical treatment
    • C12Q2523/101Crosslinking agents, e.g. psoralen
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2565/00Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/10Detection mode being characterised by the assay principle
    • C12Q2565/133Detection mode being characterised by the assay principle conformational analysis
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2565/00Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50Detection characterised by immobilisation to a surface
    • C12Q2565/501Detection characterised by immobilisation to a surface being an array of oligonucleotides

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Immunology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA2928012A 2013-11-18 2014-11-18 Method for analysing the interaction of nucleotide sequences in a three-dimensional dna structure Active CA2928012C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
GB1320351.8 2013-11-18
GBGB1320351.8A GB201320351D0 (en) 2013-11-18 2013-11-18 Method
PCT/IB2014/002485 WO2015071748A1 (en) 2013-11-18 2014-11-18 Method for analysing the interaction of nucleotide sequences in a three-dimensional dna structure

Publications (2)

Publication Number Publication Date
CA2928012A1 CA2928012A1 (en) 2015-05-21
CA2928012C true CA2928012C (en) 2023-05-16

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CA2928012A Active CA2928012C (en) 2013-11-18 2014-11-18 Method for analysing the interaction of nucleotide sequences in a three-dimensional dna structure

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US (1) US10934575B2 (enExample)
EP (1) EP3071710B1 (enExample)
JP (1) JP2016537029A (enExample)
KR (1) KR102332522B1 (enExample)
CN (1) CN105992825A (enExample)
AU (1) AU2014349817B2 (enExample)
CA (1) CA2928012C (enExample)
GB (1) GB201320351D0 (enExample)
WO (1) WO2015071748A1 (enExample)

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GB2554572B (en) * 2015-03-26 2021-06-23 Dovetail Genomics Llc Physical linkage preservation in DNA storage
JP2018518203A (ja) * 2015-06-24 2018-07-12 オックスフォード バイオダイナミックス リミテッド エピジェネティックな染色体相互作用
WO2017066908A1 (zh) * 2015-10-19 2017-04-27 安诺优达基因科技(北京)有限公司 构建高分辨率、大信息量单细胞Hi-C文库的方法
CN115369161A (zh) * 2015-12-04 2022-11-22 10X 基因组学有限公司 用于核酸分析的方法和组合物
GB201608000D0 (en) * 2016-05-06 2016-06-22 Oxford Biodynamics Ltd Chromosome detection
EP3455356B1 (en) 2016-05-13 2021-08-04 Dovetail Genomics LLC Recovering long-range linkage information from preserved samples
CA3045070A1 (en) * 2016-12-01 2018-06-07 Oxford Biodynamics Limited Application of epigenetic chromsomal interactions in cancer diagnostics
WO2019005763A1 (en) * 2017-06-26 2019-01-03 Phase Genomics Inc. METHOD FOR REGROUPING DNA SEQUENCES
CN108300767B (zh) * 2017-10-27 2021-08-20 清华大学 一种核酸复合体中核酸区段相互作用的分析方法
CN108197431B (zh) * 2018-01-24 2022-04-05 清华大学 染色质相互作用差异的分析方法和系统
US12378592B2 (en) * 2018-01-31 2025-08-05 Dovetail Genomics, Llc. Sample prep for DNA linkage recovery
EP3847261A1 (en) * 2018-09-05 2021-07-14 Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft A method for engineering synthetic cis-regulatory dna
WO2020234608A1 (en) * 2019-05-22 2020-11-26 Oxford Nanopore Technologies Limited Protocol for detecting interactions within one or more dna molecules within a cell
GB2607514B (en) 2020-07-20 2023-06-21 Enanta Pharm Inc Functionalized peptides as antiviral agents
US11384090B2 (en) 2020-11-23 2022-07-12 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
CN116829571A (zh) 2020-11-23 2023-09-29 英安塔制药有限公司 新型螺旋吡咯烷衍生的抗病毒药物
US11352363B1 (en) 2020-11-23 2022-06-07 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
CN113215141A (zh) * 2021-02-23 2021-08-06 华南农业大学 细菌hi-c基因组及质粒构象捕获方法
US11319325B1 (en) 2021-05-11 2022-05-03 Enanta Pharmaceuticals, Inc. Macrocyclic spiropyrrolidine derived antiviral agents
US11325916B1 (en) 2021-07-29 2022-05-10 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
US11339170B1 (en) 2021-07-23 2022-05-24 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
GB202111195D0 (en) * 2021-08-03 2021-09-15 Cergentis B V Method for targeted sequencing
CN113946730B (zh) * 2021-10-19 2023-03-17 四川大学 一种基于基因数据的染色质层次结构分析的可视化方法
US20240095226A1 (en) * 2022-09-15 2024-03-21 Rodney Kuhn Haffnerson King Methods and related devices for storing and accessing data using multi-level fractal grids

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7348178B1 (en) * 1994-03-14 2008-03-25 New York University Medical Center Recombinant adenoviral vector system
NZ564262A (en) * 2005-07-04 2010-02-26 Univ Erasmus Medical Ct Chromosome conformation capture-on-chip (4C) assay
AU2008204338B2 (en) * 2007-01-11 2014-03-06 Erasmus University Medical Center Circular chromosome conformation capture (4C)
CA2804450C (en) 2010-07-09 2022-10-11 Max Jan van Min 3-d genomic region of interest sequencing strategies
US10287621B2 (en) * 2013-04-11 2019-05-14 Pelin Sahlén Targeted chromosome conformation capture

Also Published As

Publication number Publication date
EP3071710A1 (en) 2016-09-28
AU2014349817B2 (en) 2020-11-12
WO2015071748A1 (en) 2015-05-21
CA2928012A1 (en) 2015-05-21
KR102332522B1 (ko) 2021-11-29
GB201320351D0 (en) 2014-01-01
CN105992825A (zh) 2016-10-05
US10934575B2 (en) 2021-03-02
AU2014349817A1 (en) 2016-05-19
US20160289738A1 (en) 2016-10-06
KR20160079120A (ko) 2016-07-05
EP3071710B1 (en) 2019-05-15
JP2016537029A (ja) 2016-12-01

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