WO2006079009A3 - Methods for separating short single-stranded nucleic acid from long single- and double-stranded nucleic acid, and associated biomolecular assays - Google Patents

Methods for separating short single-stranded nucleic acid from long single- and double-stranded nucleic acid, and associated biomolecular assays Download PDF

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Publication number
WO2006079009A3
WO2006079009A3 PCT/US2006/002233 US2006002233W WO2006079009A3 WO 2006079009 A3 WO2006079009 A3 WO 2006079009A3 US 2006002233 W US2006002233 W US 2006002233W WO 2006079009 A3 WO2006079009 A3 WO 2006079009A3
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
stranded nucleic
methods
nucleic acids
double
Prior art date
Application number
PCT/US2006/002233
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French (fr)
Other versions
WO2006079009A2 (en
Inventor
Lewis J Rothberg
Huixiang Li
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Univ Rochester
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Publication date
Application filed by Univ Rochester filed Critical Univ Rochester
Priority to JP2007552328A priority Critical patent/JP2008527999A/en
Priority to EP06719184A priority patent/EP1848823A4/en
Publication of WO2006079009A2 publication Critical patent/WO2006079009A2/en
Publication of WO2006079009A3 publication Critical patent/WO2006079009A3/en

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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • 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
    • 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
    • C12Q1/6832—Enhancement of hybridisation reaction
    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Investigating Or Analysing Materials By The Use Of Chemical Reactions (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

Methods and kits are provided for detecting the presence or absence of target nucleic acid sequences in a sample. The methods and kits involve the use of negatively charged nanoparticles and the electrostatic interactions between the metal nanoparticles and nucleic acid molecules. The methods rely upon the differential interaction of ss-nucleic acids and ds-nucleic acids with the negatively charged nanoparticles that differentiate between tagged oligonucleotide probes that hybridize with a target and those that do not. Improvements in sensitivity for a fluorescent variation of the method have been obtained by including a step of separating the ds-nucleic acids in solution from the negatively charged nanoparticles to which ss-nucleic acids have been bound, and then detecting for the presence of the ds-target nucleic acids in the solution. The same separation protocols can be used to make the detection approach viable with electrochemical or radioactive tags.
PCT/US2006/002233 2005-01-21 2006-01-23 Methods for separating short single-stranded nucleic acid from long single- and double-stranded nucleic acid, and associated biomolecular assays WO2006079009A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
JP2007552328A JP2008527999A (en) 2005-01-21 2006-01-23 Methods for separating short single stranded nucleic acids from long single stranded nucleic acids and double stranded nucleic acids, and related biomolecular assays
EP06719184A EP1848823A4 (en) 2005-01-21 2006-01-23 Methods for separating short single-stranded nucleic acid from long single- and double-stranded nucleic acid, and associated biomolecular assays

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US64582105P 2005-01-21 2005-01-21
US60/645,821 2005-01-21

Publications (2)

Publication Number Publication Date
WO2006079009A2 WO2006079009A2 (en) 2006-07-27
WO2006079009A3 true WO2006079009A3 (en) 2007-11-08

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2006/002233 WO2006079009A2 (en) 2005-01-21 2006-01-23 Methods for separating short single-stranded nucleic acid from long single- and double-stranded nucleic acid, and associated biomolecular assays

Country Status (3)

Country Link
EP (1) EP1848823A4 (en)
JP (1) JP2008527999A (en)
WO (1) WO2006079009A2 (en)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JPWO2008018305A1 (en) * 2006-08-08 2009-12-24 アークレイ株式会社 Mutation detection method and kit used therefor
JPWO2009081967A1 (en) * 2007-12-26 2011-05-06 アークレイ株式会社 Amplification method of target nucleic acid sequence and probe used therefor
KR101974577B1 (en) * 2012-05-21 2019-05-02 삼성전자주식회사 Template for manufacturing nanoparticle and method for preparing nanoparticle using the same
WO2013176740A1 (en) * 2012-05-25 2013-11-28 Health Diagnostic Laboratory, Inc. Rapid and high-throughput analysis of sterols/stanols or derivatives thereof
JP6070246B2 (en) * 2013-02-15 2017-02-01 ニプロ株式会社 Kit containing test piece
CN108298502B (en) * 2018-01-15 2021-06-01 东南大学 Method for preparing dispersed nano metal oxide and nano metal powder
CN110878344A (en) * 2019-12-17 2020-03-13 臻准生物科技（上海）有限公司 Method for shortening PCR amplification time
CN115555576B (en) * 2022-09-26 2024-03-12 青牧科技南京有限公司 Plasma resonance surface multilayer self-assembled small molecular structure and assembling method

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6488855B2 (en) * 1997-12-05 2002-12-03 Transgenomic, Inc. Non-polar media for polynucleotide separations
US20030018179A1 (en) * 2001-06-22 2003-01-23 Technische Universitat Dresden Method for generating nucleation centers for selective heterogeneous growth of metal clusters on DNA molecules
US6555376B2 (en) * 2001-08-01 2003-04-29 University Of Delhi, Department Of Chemistry Process of entrapping genetic materials in ultra-low size nanoparticles of inorganic compounds to form non-viral carriers
US20030186216A1 (en) * 2002-03-27 2003-10-02 Hitachi Software Engineering Co., Ltd. Reaction measurement method for reactions using semiconductor nanoparticles, and quality evaluation method for semiconductor nanoparticles using the same
US20040038264A1 (en) * 2002-05-14 2004-02-26 Souza Glauco R. Fractal dimension analysis of nanoparticle aggregates using angle dependent light scattering for the detection and characterization of nucleic acids and proteins
WO2004111602A2 (en) * 2003-05-16 2004-12-23 University Of Rochester Colorimetric and fluorescent methods for sensing of oligonucleotides

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JPH07227299A (en) * 1994-02-14 1995-08-29 Kyoto Daiichi Kagaku:Kk Method for detecting specific base sequence of dna and device therefor
WO1998004740A1 (en) * 1996-07-29 1998-02-05 Nanosphere Llc Nanoparticles having oligonucleotides attached thereto and uses therefor
EP1238114A2 (en) 1999-12-09 2002-09-11 Motorola, Inc. Methods and compositions relating to electrical detection of nucleic acid reactions
WO2003027678A1 (en) * 2001-09-26 2003-04-03 Psychiatric Genomics, Inc. Fluorescence proximity assay

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6488855B2 (en) * 1997-12-05 2002-12-03 Transgenomic, Inc. Non-polar media for polynucleotide separations
US20030018179A1 (en) * 2001-06-22 2003-01-23 Technische Universitat Dresden Method for generating nucleation centers for selective heterogeneous growth of metal clusters on DNA molecules
US6555376B2 (en) * 2001-08-01 2003-04-29 University Of Delhi, Department Of Chemistry Process of entrapping genetic materials in ultra-low size nanoparticles of inorganic compounds to form non-viral carriers
US20030186216A1 (en) * 2002-03-27 2003-10-02 Hitachi Software Engineering Co., Ltd. Reaction measurement method for reactions using semiconductor nanoparticles, and quality evaluation method for semiconductor nanoparticles using the same
US20040038264A1 (en) * 2002-05-14 2004-02-26 Souza Glauco R. Fractal dimension analysis of nanoparticle aggregates using angle dependent light scattering for the detection and characterization of nucleic acids and proteins
WO2004111602A2 (en) * 2003-05-16 2004-12-23 University Of Rochester Colorimetric and fluorescent methods for sensing of oligonucleotides

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of EP1848823A4 *

Also Published As

Publication number Publication date
EP1848823A2 (en) 2007-10-31
EP1848823A4 (en) 2008-06-25
JP2008527999A (en) 2008-07-31
WO2006079009A2 (en) 2006-07-27

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