WO2006025074A3 - Twodimensional strandness- and length-dependent separation of nucleic acid fragments - Google Patents

Twodimensional strandness- and length-dependent separation of nucleic acid fragments Download PDF

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Publication number
WO2006025074A3
WO2006025074A3 PCT/IS2005/000019 IS2005000019W WO2006025074A3 WO 2006025074 A3 WO2006025074 A3 WO 2006025074A3 IS 2005000019 W IS2005000019 W IS 2005000019W WO 2006025074 A3 WO2006025074 A3 WO 2006025074A3
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WIPO (PCT)
Prior art keywords
electrophoresis
strandness
length
nucleic acid
dimension
Prior art date
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Ceased
Application number
PCT/IS2005/000019
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French (fr)
Other versions
WO2006025074A2 (en
Inventor
Gudmundur H Gunnarsson
Hans Guttormur Thormar
Bjarki Gudmundsson
Jon Johannes Jonsson
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Lifeind ehf
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Lifeind ehf
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Publication date
Application filed by Lifeind ehf filed Critical Lifeind ehf
Priority to AU2005278786A priority Critical patent/AU2005278786A1/en
Priority to AT05781069T priority patent/ATE498682T1/en
Priority to CA002614580A priority patent/CA2614580A1/en
Priority to JP2007529144A priority patent/JP5079509B2/en
Priority to EP05781069A priority patent/EP1791955B1/en
Priority to DE602005026412T priority patent/DE602005026412D1/en
Priority to US11/661,607 priority patent/US8241475B2/en
Publication of WO2006025074A2 publication Critical patent/WO2006025074A2/en
Publication of WO2006025074A3 publication Critical patent/WO2006025074A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • 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
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • C12N15/101—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers by chromatography, e.g. electrophoresis, ion-exchange, reverse phase
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/416—Systems
    • G01N27/447—Systems using electrophoresis
    • G01N27/44704—Details; Accessories
    • G01N27/44717—Arrangements for investigating the separated zones, e.g. localising zones
    • G01N27/44721—Arrangements for investigating the separated zones, e.g. localising zones by optical means
    • G01N27/44726—Arrangements for investigating the separated zones, e.g. localising zones by optical means using specific dyes, markers or binding molecules
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/416—Systems
    • G01N27/447—Systems using electrophoresis
    • G01N27/44704—Details; Accessories
    • G01N27/44747—Composition of gel or of carrier mixture
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/416—Systems
    • G01N27/447—Systems using electrophoresis
    • G01N27/44756—Apparatus specially adapted therefor
    • G01N27/44773—Multi-stage electrophoresis, e.g. two-dimensional electrophoresis

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Pathology (AREA)
  • General Physics & Mathematics (AREA)
  • Electrochemistry (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Biophysics (AREA)
  • Microbiology (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Dispersion Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Saccharide Compounds (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)

Abstract

A method is provided for separating single- and double-stranded nucleic acid molecules based on their strandness and length. The method is based on novel two-dimensional gel electrophoresis techniques comprises loading a sample of nucleic acid molecules in a gel electrophoresis apparatus and electrophoresing in a first dimension said sample through a gel matrix under a first set of pre-determined electrophoresis conditions; electrophoresing said gel matrix in a second dimension under a second set of electrophoresis conditions, such that populations of single- and double-stranded nucleic acids are separated, said first and second electrophoresis conditions being different, such that in one dimension electrophoresis allows separation of the sample molecules based on strandness and length, and in the other dimension electrophoresis allows separation based substantially on length, wherein said difference is established with a chemical agent and/or physical parameter affecting the strandness-dependent electrophoresis migration rate of nucleic acids
PCT/IS2005/000019 2004-09-02 2005-09-02 Twodimensional strandness- and length-dependent separation of nucleic acid fragments Ceased WO2006025074A2 (en)

Priority Applications (7)

Application Number Priority Date Filing Date Title
AU2005278786A AU2005278786A1 (en) 2004-09-02 2005-09-02 Twodimensional strandness- and length-dependent separation of nucleic acid fragments
AT05781069T ATE498682T1 (en) 2004-09-02 2005-09-02 TWO-DIMENSIONAL STRAND SHAPE AND LENGTH-DEPENDENT SEPARATION OF NUCLEIC ACID FRAGMENTS
CA002614580A CA2614580A1 (en) 2004-09-02 2005-09-02 Two-dimensional strandness- and length-dependent separation of nucleic acid fragments
JP2007529144A JP5079509B2 (en) 2004-09-02 2005-09-02 Two-dimensional strand number-dependent and length-dependent separation of nucleic acid fragments
EP05781069A EP1791955B1 (en) 2004-09-02 2005-09-02 Twodimensional strandness- and length-dependent separation of nucleic acid fragments
DE602005026412T DE602005026412D1 (en) 2004-09-02 2005-09-02 TWO-DIMENSIONAL STRUCTURE AND LENGTH-RELATED SEPARATION OF NUCLEIC ACID FRAGMENTS
US11/661,607 US8241475B2 (en) 2004-09-02 2005-09-02 Two-dimensional strandness-and length-dependent separation of nucleic acid fragments

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
IS7436 2004-09-02
IS7436 2004-09-02

Publications (2)

Publication Number Publication Date
WO2006025074A2 WO2006025074A2 (en) 2006-03-09
WO2006025074A3 true WO2006025074A3 (en) 2006-06-15

Family

ID=35601867

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IS2005/000019 Ceased WO2006025074A2 (en) 2004-09-02 2005-09-02 Twodimensional strandness- and length-dependent separation of nucleic acid fragments

Country Status (8)

Country Link
US (1) US8241475B2 (en)
EP (1) EP1791955B1 (en)
JP (1) JP5079509B2 (en)
AT (1) ATE498682T1 (en)
AU (1) AU2005278786A1 (en)
CA (1) CA2614580A1 (en)
DE (1) DE602005026412D1 (en)
WO (1) WO2006025074A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012037394A1 (en) * 2010-09-16 2012-03-22 Ibis Biosciences, Inc. Stabilization of ozone-labile fluorescent dyes by thiourea
GB201102385D0 (en) 2011-02-10 2011-03-30 Biocule Scotland Ltd Two-dimensional gel electrophoresis apparatus and method
JP6404785B2 (en) * 2015-08-12 2018-10-17 日本電信電話株式会社 Biomolecular mobility control method and electrophoresis tank
JP7305812B2 (en) * 2016-07-19 2023-07-10 株式会社バイオダイナミクス研究所 Method for preparing long single-stranded DNA
WO2020086366A1 (en) * 2018-10-22 2020-04-30 Merck Sharp & Dohme Corp. Methods for separating large nucleic acids under denatured conditions
CN111855982B (en) * 2019-04-25 2022-07-22 武汉华大医学检验所有限公司 Method for detecting nucleic acid fragment length
WO2025203643A1 (en) * 2024-03-29 2025-10-02 株式会社日立ハイテク Method for detecting single-stranded nucleic acid

Citations (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5074980A (en) * 1989-11-29 1991-12-24 E. I. Du Pont De Nemours And Company Method of characterizing polynucleotides
WO1997030062A1 (en) * 1996-02-14 1997-08-21 Akzo Nobel N.V. Isolation and amplification of nucleic acid materials
WO1997039149A1 (en) * 1996-04-17 1997-10-23 Ramot-University Authority For Applied Research And Industrial Development, Ltd. Method and kit for detecting genomic instability
US6210931B1 (en) * 1998-11-30 2001-04-03 The United States Of America As Represented By The Secretary Of Agriculture Ribozyme-mediated synthesis of circular RNA
WO2002010182A2 (en) * 2000-08-02 2002-02-07 Applera Corporation Methods for isolating one strand of a double-stranded nucleic acid
US20030124611A1 (en) * 1988-09-15 2003-07-03 Wisconsin Alumni Research Foundation Methods and compositions for the manipulation and characterization of individual nucleic acid molecules
WO2003058230A1 (en) * 2002-01-11 2003-07-17 Ludesi Ab Method and computer program for digital image processing for two-dimensional electrophoresis
WO2003070943A1 (en) * 2002-02-25 2003-08-28 Lifeind Ehf. Methods for two-dimensional conformation-dependent separation of non-circular nucleic acids
US20040129567A1 (en) * 2001-04-17 2004-07-08 Auton Kevin Andrew Electorphoretic separation system

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
NL8801147A (en) * 1988-05-02 1989-12-01 Tno METHOD FOR DETECTING GENETIC VARIATION, AND SUITABLE KIT.
US5162514A (en) * 1990-05-15 1992-11-10 Board Of Regents, University Of Texas High molecular weight dna compositions for use in electrophoresis of large nucleic acids
US5212299A (en) * 1991-05-10 1993-05-18 Fmc Corporation Glyceryl agarose and borate compositions
WO1997030152A1 (en) * 1996-02-14 1997-08-21 Amsterdam Support Diagnostics B.V. Separation of single stranded and double stranded nucleic acid materials
WO1998044156A1 (en) * 1997-03-27 1998-10-08 Life Technologies, Inc. Nucleic acid ladders
EP1001963B1 (en) * 1997-07-15 2011-01-05 Life Technologies, Inc. Nucleic acid ladders
AU2003279697A1 (en) * 2002-05-17 2004-02-16 Nugen Technologies, Inc. Methods for fragmentation, labeling and immobilizaton of nucleic acids

Patent Citations (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030124611A1 (en) * 1988-09-15 2003-07-03 Wisconsin Alumni Research Foundation Methods and compositions for the manipulation and characterization of individual nucleic acid molecules
US5074980A (en) * 1989-11-29 1991-12-24 E. I. Du Pont De Nemours And Company Method of characterizing polynucleotides
WO1997030062A1 (en) * 1996-02-14 1997-08-21 Akzo Nobel N.V. Isolation and amplification of nucleic acid materials
WO1997039149A1 (en) * 1996-04-17 1997-10-23 Ramot-University Authority For Applied Research And Industrial Development, Ltd. Method and kit for detecting genomic instability
US6210931B1 (en) * 1998-11-30 2001-04-03 The United States Of America As Represented By The Secretary Of Agriculture Ribozyme-mediated synthesis of circular RNA
WO2002010182A2 (en) * 2000-08-02 2002-02-07 Applera Corporation Methods for isolating one strand of a double-stranded nucleic acid
US20040129567A1 (en) * 2001-04-17 2004-07-08 Auton Kevin Andrew Electorphoretic separation system
WO2003058230A1 (en) * 2002-01-11 2003-07-17 Ludesi Ab Method and computer program for digital image processing for two-dimensional electrophoresis
WO2003070943A1 (en) * 2002-02-25 2003-08-28 Lifeind Ehf. Methods for two-dimensional conformation-dependent separation of non-circular nucleic acids

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
ANDERSON J N: "Detection, sequence patterns and function of unusual DNA structures.", NUCLEIC ACIDS RESEARCH. 11 NOV 1986, vol. 14, no. 21, 11 November 1986 (1986-11-11), pages 8513 - 8533, XP002364541, ISSN: 0305-1048 *
ANDERSON N L ET AL: "The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns.", CLINICAL CHEMISTRY. NOV 1981, vol. 27, no. 11, November 1981 (1981-11-01), pages 1807 - 1820, XP002364539, ISSN: 0009-9147 *
KOVAR H ET AL: "Two dimensional single-strand conformation polymorphism analysis: a useful tool for the detection of mutations in long DNA fragments", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 19, no. 13, 11 July 1991 (1991-07-11), pages 3507 - 3510, XP002245287, ISSN: 0305-1048 *
MIZUNO T: "Random cloning of bent DNA segments from Escherichia coli chromosome and primary characterization of their structures.", NUCLEIC ACIDS RESEARCH. 11 SEP 1987, vol. 15, no. 17, 11 September 1987 (1987-09-11), pages 6827 - 6841, XP002364540, ISSN: 0305-1048 *

Also Published As

Publication number Publication date
US20090107841A1 (en) 2009-04-30
JP5079509B2 (en) 2012-11-21
EP1791955B1 (en) 2011-02-16
EP1791955A2 (en) 2007-06-06
AU2005278786A1 (en) 2006-03-09
JP2008511308A (en) 2008-04-17
ATE498682T1 (en) 2011-03-15
US8241475B2 (en) 2012-08-14
DE602005026412D1 (en) 2011-03-31
WO2006025074A2 (en) 2006-03-09
CA2614580A1 (en) 2006-03-09

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