WO2006042022A3 - Array-based methods for producing ribonucleic acids - Google Patents

Array-based methods for producing ribonucleic acids Download PDF

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Publication number
WO2006042022A3
WO2006042022A3 PCT/US2005/035998 US2005035998W WO2006042022A3 WO 2006042022 A3 WO2006042022 A3 WO 2006042022A3 US 2005035998 W US2005035998 W US 2005035998W WO 2006042022 A3 WO2006042022 A3 WO 2006042022A3
Authority
WO
WIPO (PCT)
Prior art keywords
array
subject methods
ribonucleic acids
based methods
methods
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2005/035998
Other languages
French (fr)
Other versions
WO2006042022A2 (en
Inventor
Arindam Bhattacharjee
Stephanie B Fulmer-Smentek
Diane D Ilsley
Eric M Leproust
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Agilent Technologies Inc
Original Assignee
Agilent Technologies Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Agilent Technologies Inc filed Critical Agilent Technologies Inc
Priority to EP05808459A priority Critical patent/EP1807535A2/en
Priority to JP2007535815A priority patent/JP2008515432A/en
Publication of WO2006042022A2 publication Critical patent/WO2006042022A2/en
Anticipated expiration legal-status Critical
Publication of WO2006042022A3 publication Critical patent/WO2006042022A3/en
Ceased legal-status Critical Current

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Classifications

    • 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
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6865—Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]

Landscapes

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

Abstract

Methods and compositions for generating pluralities of ribonucleic acids are provided. In the subject methods, an array is employed as a template in an in vitro transcription reaction. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods. The ribonucleic acid pluralities produced by the subject methods find use in a variety of different applications, including differential gene expression analysis and gene-silencing applications.
PCT/US2005/035998 2004-10-08 2005-10-06 Array-based methods for producing ribonucleic acids Ceased WO2006042022A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP05808459A EP1807535A2 (en) 2004-10-08 2005-10-06 Array-based methods for producing ribonucleic acids
JP2007535815A JP2008515432A (en) 2004-10-08 2005-10-06 Array-based method for producing ribonucleic acid

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US10/961,991 2004-10-08
US10/961,991 US20060078889A1 (en) 2004-10-08 2004-10-08 Array-based methods for producing ribonucleic acids

Publications (2)

Publication Number Publication Date
WO2006042022A2 WO2006042022A2 (en) 2006-04-20
WO2006042022A3 true WO2006042022A3 (en) 2007-04-19

Family

ID=36145795

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/035998 Ceased WO2006042022A2 (en) 2004-10-08 2005-10-06 Array-based methods for producing ribonucleic acids

Country Status (4)

Country Link
US (1) US20060078889A1 (en)
EP (1) EP1807535A2 (en)
JP (1) JP2008515432A (en)
WO (1) WO2006042022A2 (en)

Families Citing this family (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9528939B2 (en) 2006-03-10 2016-12-27 Indx Lifecare, Inc. Waveguide-based optical scanning systems
US9976192B2 (en) 2006-03-10 2018-05-22 Ldip, Llc Waveguide-based detection system with scanning light source
US8675199B2 (en) * 2006-03-10 2014-03-18 Plc Diagnostics, Inc. Waveguide-based detection system with scanning light source
US8288157B2 (en) * 2007-09-12 2012-10-16 Plc Diagnostics, Inc. Waveguide-based optical scanning systems
US9423397B2 (en) 2006-03-10 2016-08-23 Indx Lifecare, Inc. Waveguide-based detection system with scanning light source
US7951583B2 (en) 2006-03-10 2011-05-31 Plc Diagnostics, Inc. Optical scanning system
KR101625363B1 (en) 2007-05-10 2016-05-30 애질런트 테크놀로지스, 인크. Thiocarbon-protecting groups for rna synthesis
GB2461026B (en) * 2008-06-16 2011-03-09 Plc Diagnostics Inc System and method for nucleic acids sequencing by phased synthesis
WO2012064850A1 (en) * 2010-11-09 2012-05-18 Michael Andregg Liquid-gas interface mediated molecule manipulation
EP2694709B1 (en) 2011-04-08 2016-09-14 Prognosys Biosciences, Inc. Peptide constructs and assay systems
GB201108041D0 (en) 2011-05-13 2011-06-29 Univ Portsmouth Method
WO2013119948A1 (en) * 2012-02-10 2013-08-15 Wisconsin Alumni Research Foundation Rna-mediated gene assembly from dna oligonucleotides
US10018566B2 (en) 2014-02-28 2018-07-10 Ldip, Llc Partially encapsulated waveguide based sensing chips, systems and methods of use
WO2016138427A1 (en) 2015-02-27 2016-09-01 Indx Lifecare, Inc. Waveguide-based detection system with scanning light source
CN111511928A (en) * 2017-12-21 2020-08-07 库瑞瓦格股份公司 Linear double-stranded DNA coupled to a single support or tag and method for preparing the linear double-stranded DNA

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1993017126A1 (en) * 1992-02-19 1993-09-02 The Public Health Research Institute Of The City Of New York, Inc. Novel oligonucleotide arrays and their use for sorting, isolating, sequencing, and manipulating nucleic acids
US5795714A (en) * 1992-11-06 1998-08-18 Trustees Of Boston University Method for replicating an array of nucleic acid probes
WO1999007888A1 (en) * 1997-08-05 1999-02-18 President & Fellows Of Harvard College Surface-bound, bimolecular, double-stranded dna arrays
US20010036632A1 (en) * 1999-12-29 2001-11-01 Zailin Yu Methods for amplifying and detecting multiple polynucleotides on a solid phase support
EP1180548A2 (en) * 2000-07-31 2002-02-20 Agilent Technologies, Inc. Array based methods for synthesizing nucleic acid mixtures
WO2002052038A2 (en) * 2000-12-27 2002-07-04 Geneka Biotechnology Inc. Method for normalizing the relative intensities of detection signals in hybridization arrays
WO2002072889A2 (en) * 2001-01-12 2002-09-19 Applera Corporation Methods and compositions for microarray control
US20050064432A1 (en) * 2003-09-19 2005-03-24 Linden Technologies, Inc. Nucleic acid amplification and detection

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4734363A (en) * 1984-11-27 1988-03-29 Molecular Diagnostics, Inc. Large scale production of DNA probes
SE8801070D0 (en) * 1988-03-23 1988-03-23 Pharmacia Ab METHOD FOR IMMOBILIZING A DNA SEQUENCE ON A SOLID SUPPORT
US5925525A (en) * 1989-06-07 1999-07-20 Affymetrix, Inc. Method of identifying nucleotide differences
US5215899A (en) * 1989-11-09 1993-06-01 Miles Inc. Nucleic acid amplification employing ligatable hairpin probe and transcription
DE4322277A1 (en) * 1993-07-05 1995-01-12 Basf Ag Improved process for the production of astaxanthin, new intermediates therefor and a process for their production
US6013440A (en) * 1996-03-11 2000-01-11 Affymetrix, Inc. Nucleic acid affinity columns
ATE319856T1 (en) * 1997-06-13 2006-03-15 Affymetrix Inc A Delaware Corp METHOD FOR DETECTING GENE POLYMORPHISMS AND ALLELE EXPRESSION USING PROBE CHIPS
US6235483B1 (en) * 2000-01-31 2001-05-22 Agilent Technologies, Inc. Methods and kits for indirect labeling of nucleic acids
US20020001810A1 (en) * 2000-06-05 2002-01-03 Farrell Michael Patrick Q-beta replicase based assays; the use of chimeric DNA-RNA molecules as probes from which efficient Q-beta replicase templates can be generated in a reverse transcriptase dependent manner
US20030148284A1 (en) * 2001-12-17 2003-08-07 Vision Todd J. Solid phase detection of nucleic acid molecules

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1993017126A1 (en) * 1992-02-19 1993-09-02 The Public Health Research Institute Of The City Of New York, Inc. Novel oligonucleotide arrays and their use for sorting, isolating, sequencing, and manipulating nucleic acids
US5795714A (en) * 1992-11-06 1998-08-18 Trustees Of Boston University Method for replicating an array of nucleic acid probes
WO1999007888A1 (en) * 1997-08-05 1999-02-18 President & Fellows Of Harvard College Surface-bound, bimolecular, double-stranded dna arrays
US20010036632A1 (en) * 1999-12-29 2001-11-01 Zailin Yu Methods for amplifying and detecting multiple polynucleotides on a solid phase support
EP1180548A2 (en) * 2000-07-31 2002-02-20 Agilent Technologies, Inc. Array based methods for synthesizing nucleic acid mixtures
WO2002052038A2 (en) * 2000-12-27 2002-07-04 Geneka Biotechnology Inc. Method for normalizing the relative intensities of detection signals in hybridization arrays
WO2002072889A2 (en) * 2001-01-12 2002-09-19 Applera Corporation Methods and compositions for microarray control
US20050064432A1 (en) * 2003-09-19 2005-03-24 Linden Technologies, Inc. Nucleic acid amplification and detection

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
KIM H ET AL: "Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses", BIOTECHNIQUES, vol. 33, no. 4, October 2002 (2002-10-01), pages 924 - 930, XP001248975, ISSN: 0736-6205 *
NOVORADOVSKAYA NATALIA ET AL: "Universal Reference RNA as a standard for microarray experiments", BMC GENOMICS, BIOMED CENTRAL, LONDON, GB, vol. 5, no. 1, 9 March 2004 (2004-03-09), pages 20, XP021002100, ISSN: 1471-2164 *

Also Published As

Publication number Publication date
EP1807535A2 (en) 2007-07-18
WO2006042022A2 (en) 2006-04-20
JP2008515432A (en) 2008-05-15
US20060078889A1 (en) 2006-04-13

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