AU2014349817B2 - 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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AU2014349817B2
AU2014349817B2 AU2014349817A AU2014349817A AU2014349817B2 AU 2014349817 B2 AU2014349817 B2 AU 2014349817B2 AU 2014349817 A AU2014349817 A AU 2014349817A AU 2014349817 A AU2014349817 A AU 2014349817A AU 2014349817 B2 AU2014349817 B2 AU 2014349817B2
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dna
interaction
restriction enzyme
fragments
sequence
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AU2014349817A1 (en
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Frank Grosveld
Tobias Knoch
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Cergentis BV
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    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/682—Signal amplification
    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/30—Phosphoric diester hydrolysing, i.e. nuclease
    • C12Q2521/301—Endonuclease
    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/501—Ligase
    • 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
    • C12Q2523/00—Reactions characterised by treatment of reaction samples
    • C12Q2523/10—Characterised by chemical treatment
    • C12Q2523/101—Crosslinking agents, e.g. psoralen
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/10—Detection mode being characterised by the assay principle
    • C12Q2565/133—Detection mode being characterised by the assay principle conformational analysis
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/501—Detection 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)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • General Chemical & Material Sciences (AREA)
AU2014349817A 2013-11-18 2014-11-18 Method for analysing the interaction of nucleotide sequences in a three-dimensional DNA structure Active AU2014349817B2 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
GBGB1320351.8A GB201320351D0 (en) 2013-11-18 2013-11-18 Method
GB1320351.8 2013-11-18
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
AU2014349817A1 AU2014349817A1 (en) 2016-05-19
AU2014349817B2 true AU2014349817B2 (en) 2020-11-12

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AU2014349817A Active AU2014349817B2 (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 (https=)
EP (1) EP3071710B1 (https=)
JP (1) JP2016537029A (https=)
KR (1) KR102332522B1 (https=)
CN (1) CN105992825A (https=)
AU (1) AU2014349817B2 (https=)
CA (1) CA2928012C (https=)
GB (1) GB201320351D0 (https=)
WO (1) WO2015071748A1 (https=)

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US11807896B2 (en) * 2015-03-26 2023-11-07 Dovetail Genomics, Llc Physical linkage preservation in DNA storage
US11802305B2 (en) * 2015-06-24 2023-10-31 Oxford BioDynamics PLC Detection processes using sites of chromosome interaction
US10900031B2 (en) * 2015-10-19 2021-01-26 Zhejiang Annoroad Bio-Technology Co. Ltd. Method for constructing high-resolution single cell Hi-C library with a lot of information
SG11201804086VA (en) * 2015-12-04 2018-06-28 10X Genomics Inc Methods and compositions for nucleic acid analysis
GB201608000D0 (en) * 2016-05-06 2016-06-22 Oxford Biodynamics Ltd Chromosome detection
WO2017197300A1 (en) 2016-05-13 2017-11-16 Dovetail Genomics Llc Recovering long-range linkage information from preserved samples
MY190153A (en) * 2016-12-01 2022-03-31 Oxford BioDynamics PLC Application of epigenetic chromosomal 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
WO2019152543A1 (en) * 2018-01-31 2019-08-08 Dovetail Genomics, Llc Sample prep for dna linkage recovery
WO2020049106A1 (en) * 2018-09-05 2020-03-12 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
US12540141B2 (en) 2020-11-23 2026-02-03 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
US11352363B1 (en) 2020-11-23 2022-06-07 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
US11384090B2 (en) 2020-11-23 2022-07-12 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
KR20230124583A (ko) 2020-11-23 2023-08-25 이난타 파마슈티칼스, 인코포레이티드 신규한 스피로피롤리딘 유래 항바이러스제
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

Citations (3)

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WO2007004057A2 (en) * 2005-07-04 2007-01-11 Erasmus University Medical Center Chromosome conformation capture-on-chip (4c) assay
WO2008084405A2 (en) * 2007-01-11 2008-07-17 Erasmus University Medical Center Circular chromosome conformation capture (4c)
WO2014168575A1 (en) * 2013-04-11 2014-10-16 Sahlén Pelin Targeted chromosome conformation capture

Family Cites Families (2)

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US7348178B1 (en) * 1994-03-14 2008-03-25 New York University Medical Center Recombinant adenoviral vector system
WO2012005595A2 (en) * 2010-07-09 2012-01-12 Wouter Leonard De Laat V3-d genomic region of interest sequencing strategies

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007004057A2 (en) * 2005-07-04 2007-01-11 Erasmus University Medical Center Chromosome conformation capture-on-chip (4c) assay
WO2008084405A2 (en) * 2007-01-11 2008-07-17 Erasmus University Medical Center Circular chromosome conformation capture (4c)
WO2014168575A1 (en) * 2013-04-11 2014-10-16 Sahlén Pelin Targeted chromosome conformation capture

Also Published As

Publication number Publication date
JP2016537029A (ja) 2016-12-01
GB201320351D0 (en) 2014-01-01
EP3071710B1 (en) 2019-05-15
US10934575B2 (en) 2021-03-02
KR20160079120A (ko) 2016-07-05
CA2928012C (en) 2023-05-16
AU2014349817A1 (en) 2016-05-19
EP3071710A1 (en) 2016-09-28
KR102332522B1 (ko) 2021-11-29
WO2015071748A1 (en) 2015-05-21
US20160289738A1 (en) 2016-10-06
CN105992825A (zh) 2016-10-05
CA2928012A1 (en) 2015-05-21

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