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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Publication number
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)
  • 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)
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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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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WO2016154540A1 (en) * 2015-03-26 2016-09-29 Dovetail Genomics Llc Physical linkage preservation in dna storage
JP2018527016A (ja) * 2015-06-24 2018-09-20 オックスフォード バイオダイナミックス リミテッド 染色体相互作用の検出
EP3366818B1 (en) * 2015-10-19 2021-04-14 Zhejiang Annoroad Bio-Technology Co., Ltd. Method for constructing high-resolution single cell hi-c library with a lot of information
KR102723865B1 (ko) * 2015-12-04 2024-10-29 10엑스 제노믹스, 인크. 핵산 분석을 위한 방법 및 조성물
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
ES2971286T3 (es) * 2016-12-01 2024-06-04 Oxford BioDynamics PLC Aplicación de interacciones cromosómicas epigenéticas en diagnóstico de cáncer
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
US20210343368A1 (en) * 2018-09-05 2021-11-04 Max-Delbrück-Centrum Für Molekulare Medizin In Der Helmholtz-Gemeinschaft Method for Engineering Synthetic Cis-Regulatory DNA
GB2581152A (en) 2019-02-05 2020-08-12 Univ Oxford Innovation Ltd Production of 3C library
CN113853440A (zh) * 2019-05-22 2021-12-28 牛津纳米孔科技公开有限公司 用于检测细胞内一个或多个dna分子内相互作用的方案
EP4635972A3 (en) 2020-07-20 2025-12-24 Enanta Pharmaceuticals, Inc. Functionalized peptides as antiviral agents
US11352363B1 (en) 2020-11-23 2022-06-07 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
WO2022109360A1 (en) 2020-11-23 2022-05-27 Enanta Pharmaceuticals, Inc. Novel spiropyrrolidine derived antiviral agents
US11384090B2 (en) 2020-11-23 2022-07-12 Enanta Pharmaceuticals, Inc. Spiropyrrolidine derived antiviral agents
US12540141B2 (en) 2020-11-23 2026-02-03 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

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

Family Cites Families (2)

* 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
AU2011274642B2 (en) 2010-07-09 2015-05-21 Cergentis B.V. 3-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
CA2928012C (en) 2023-05-16
CN105992825A (zh) 2016-10-05
CA2928012A1 (en) 2015-05-21
KR20160079120A (ko) 2016-07-05
US20160289738A1 (en) 2016-10-06
GB201320351D0 (en) 2014-01-01
EP3071710A1 (en) 2016-09-28
US10934575B2 (en) 2021-03-02
JP2016537029A (ja) 2016-12-01
KR102332522B1 (ko) 2021-11-29
EP3071710B1 (en) 2019-05-15
WO2015071748A1 (en) 2015-05-21
AU2014349817A1 (en) 2016-05-19

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