WO2001038580A3 - Nucleic acid probe arrays - Google Patents

Nucleic acid probe arrays Download PDF

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Publication number
WO2001038580A3
WO2001038580A3 PCT/US2000/032131 US0032131W WO0138580A3 WO 2001038580 A3 WO2001038580 A3 WO 2001038580A3 US 0032131 W US0032131 W US 0032131W WO 0138580 A3 WO0138580 A3 WO 0138580A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
anchor primer
array
target nucleic
acid
Prior art date
Application number
PCT/US2000/032131
Other languages
French (fr)
Other versions
WO2001038580A9 (en
WO2001038580A2 (en
Inventor
Jonathan M Rothberg
Joel S Bader
Original Assignee
Curagen Corp
Jonathan M Rothberg
Joel S Bader
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 Curagen Corp, Jonathan M Rothberg, Joel S Bader filed Critical Curagen Corp
Priority to CA002392474A priority Critical patent/CA2392474A1/en
Priority to AU17927/01A priority patent/AU783841B2/en
Priority to JP2001539921A priority patent/JP2003515149A/en
Priority to EP00980700A priority patent/EP1234058A2/en
Publication of WO2001038580A2 publication Critical patent/WO2001038580A2/en
Publication of WO2001038580A3 publication Critical patent/WO2001038580A3/en
Publication of WO2001038580A9 publication Critical patent/WO2001038580A9/en

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Classifications

    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y30/00—Nanotechnology for materials or surface science, e.g. nanocomposites
    • 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
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Abstract

Disclosed are nucleic acid probe arrays and methods of identifying and sequencing nucleic acids in a population of nucleic acids using the arrays. The method is preferably performed by annealing a nucleic acid template to an anchor primer attached to a durface of the array. At least one anchor in the array has a sequence complementary to sequences at the 5' and 3' termini of a target nucleic acid.The annealed linear target nucleic acid is circularized using one or two ligation reactions. In one embodiment, one liggation is issued. Annealing of of the linear nucleic acid results in juxtaposition of the 5' and 3' termini of the target nucleic acid on the anchor primer. Addition of a ligase results in circulization of the target nucleic acid. This circularized nucleic acid is a template for extension of the anchor primer in a rolling circle amplification reaction. An extended anchor primer containing multiple copies of a sequence complementary to the circular mucleic acid is also referred to herein as a anchor primer nucleid acid-nucleic acid concatamer. The presence of multiple copies of the complementary sequence facilitates detection of the nucleic acid. Thus, the method provides for a highly sensitive method of detecting a desired nucleic acid attached at a discrete location on the array.
PCT/US2000/032131 1999-11-26 2000-11-27 Nucleic acid probe arrays WO2001038580A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
CA002392474A CA2392474A1 (en) 1999-11-26 2000-11-27 Nucleic acid probe arrays
AU17927/01A AU783841B2 (en) 1999-11-26 2000-11-27 Nucleic acid probe arrays
JP2001539921A JP2003515149A (en) 1999-11-26 2000-11-27 Nucleic acid probe array
EP00980700A EP1234058A2 (en) 1999-11-26 2000-11-27 Nucleic acid probe arrays

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US44940299A 1999-11-26 1999-11-26
US09/449,402 1999-11-26

Publications (3)

Publication Number Publication Date
WO2001038580A2 WO2001038580A2 (en) 2001-05-31
WO2001038580A3 true WO2001038580A3 (en) 2002-04-25
WO2001038580A9 WO2001038580A9 (en) 2002-12-05

Family

ID=23784034

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/032131 WO2001038580A2 (en) 1999-11-26 2000-11-27 Nucleic acid probe arrays

Country Status (5)

Country Link
EP (1) EP1234058A2 (en)
JP (1) JP2003515149A (en)
AU (1) AU783841B2 (en)
CA (1) CA2392474A1 (en)
WO (1) WO2001038580A2 (en)

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US9487823B2 (en) 2002-12-20 2016-11-08 Qiagen Gmbh Nucleic acid amplification
US6977153B2 (en) * 2002-12-31 2005-12-20 Qiagen Gmbh Rolling circle amplification of RNA
EP1598427A1 (en) * 2004-05-17 2005-11-23 Charité - Universitätsmedizin Berlin Method for the amplification of a target nucleic acid
EP2471922A1 (en) 2004-05-28 2012-07-04 Asuragen, Inc. Methods and compositions involving microRNA
EP2322616A1 (en) 2004-11-12 2011-05-18 Asuragen, Inc. Methods and compositions involving miRNA and miRNA inhibitor molecules
CA2611671C (en) * 2005-06-15 2013-10-08 Callida Genomics, Inc. Single molecule arrays for genetic and chemical analysis
EP1762627A1 (en) 2005-09-09 2007-03-14 Qiagen GmbH Method for the activation of a nucleic acid for performing a polymerase reaction
US11306351B2 (en) 2005-12-21 2022-04-19 Affymetrix, Inc. Methods for genotyping
WO2008036776A2 (en) 2006-09-19 2008-03-27 Asuragen, Inc. Mir-15, mir-26, mir -31,mir -145, mir-147, mir-188, mir-215, mir-216 mir-331, mmu-mir-292-3p regulated genes and pathways as targets for therapeutic intervention
US20090131348A1 (en) 2006-09-19 2009-05-21 Emmanuel Labourier Micrornas differentially expressed in pancreatic diseases and uses thereof
AU2008261869B2 (en) 2007-06-08 2014-12-18 Biogen Ma Inc. Biomarkers for predicting anti-TNF responsiveness or non-responsiveness
JP5020734B2 (en) * 2007-07-31 2012-09-05 株式会社日立ハイテクノロジーズ Nucleic acid analysis method and apparatus
US8258111B2 (en) 2008-05-08 2012-09-04 The Johns Hopkins University Compositions and methods related to miRNA modulation of neovascularization or angiogenesis
US8486630B2 (en) 2008-11-07 2013-07-16 Industrial Technology Research Institute Methods for accurate sequence data and modified base position determination
GB0921264D0 (en) 2009-12-03 2010-01-20 Olink Genomics Ab Method for amplification of target nucleic acid
US10273544B2 (en) 2010-02-11 2019-04-30 Dana-Farber Cancer Institute, Inc. Methods for predicting likelihood of responding to treatment
WO2011108930A1 (en) 2010-03-04 2011-09-09 Interna Technologies Bv A MiRNA MOLECULE DEFINED BY ITS SOURCE AND ITS DIAGNOSTIC AND THERAPEUTIC USES IN DISEASES OR CONDITIONS ASSOCIATED WITH EMT
CA2804599C (en) 2010-07-06 2023-01-31 Interna Technologies Bv Mirna and its diagnostic and therapeutic uses in diseases or conditions associated with melanoma, or in diseases or conditions associated with activated braf pathway
WO2012068400A2 (en) 2010-11-17 2012-05-24 Asuragen, Inc. Mirnas as biomarkers for distinguishing benign from malignant thyroid neoplasms
EP2474617A1 (en) 2011-01-11 2012-07-11 InteRNA Technologies BV Mir for treating neo-angiogenesis
US20140057295A1 (en) 2011-02-28 2014-02-27 Barbara J. Stegmann Anti-mullerian hormone changes in pregnancy and prediction of adverse pregnancy outcomes and gender
CN102732598B (en) * 2011-04-11 2017-03-01 陈先锋 A kind of complete genome DNA sequence assembly sequence measurement
EP2718866B1 (en) * 2011-06-07 2020-09-09 Koninklijke Philips N.V. Providing nucleotide sequence data
US9644241B2 (en) 2011-09-13 2017-05-09 Interpace Diagnostics, Llc Methods and compositions involving miR-135B for distinguishing pancreatic cancer from benign pancreatic disease
WO2013063519A1 (en) 2011-10-26 2013-05-02 Asuragen, Inc. Methods and compositions involving mirna expression levels for distinguishing pancreatic cysts
WO2013063544A1 (en) 2011-10-27 2013-05-02 Asuragen, Inc. Mirnas as diagnostic biomarkers to distinguish benign from malignant thyroid tumors
EP2870263A1 (en) 2012-07-03 2015-05-13 InteRNA Technologies B.V. Diagnostic portfolio and its uses
US20140100124A1 (en) 2012-10-04 2014-04-10 Asuragen, Inc. Diagnostic mirnas for differential diagnosis of incidental pancreatic cystic lesions
KR101984700B1 (en) * 2012-11-19 2019-05-31 삼성전자주식회사 Polynucleotide and use thereof
US9868992B2 (en) 2013-03-15 2018-01-16 Baylor Research Institute Tissue and blood-based miRNA biomarkers for the diagnosis, prognosis and metastasis-predictive potential in colorectal cancer
EP4163387A1 (en) 2013-03-15 2023-04-12 The University of Chicago Methods and compositions related to t-cell activity
EP2971149B1 (en) 2013-03-15 2018-05-09 Baylor Research Institute Ulcerative colitis (uc)-associated colorectal neoplasia markers
US11859246B2 (en) * 2013-12-11 2024-01-02 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
US11286519B2 (en) 2013-12-11 2022-03-29 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
EP3080298B1 (en) * 2013-12-11 2018-10-31 AccuraGen Holdings Limited Methods for detecting rare sequence variants
CA2980811A1 (en) 2015-04-02 2016-10-06 Hmnc Value Gmbh Method of treatment using genetic predictors of a response to treatment with crhr1 antagonists
EP3359693A4 (en) 2015-10-09 2019-03-06 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
JPWO2017135383A1 (en) * 2016-02-03 2018-12-06 国立大学法人豊橋技術科学大学 Pseudocyclic double-stranded polynucleotide and gene expression inhibitor using the same
CA3024630A1 (en) 2016-05-16 2017-11-23 Accuragen Holdings Limited Method of improved sequencing by strand identification
WO2018035170A1 (en) 2016-08-15 2018-02-22 Accuragen Holdings Limited Compositions and methods for detecting rare sequence variants
US20190309352A1 (en) * 2016-11-16 2019-10-10 Progenity, Inc Multimodal assay for detecting nucleic acid aberrations
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US11203782B2 (en) 2018-03-29 2021-12-21 Accuragen Holdings Limited Compositions and methods comprising asymmetric barcoding
JP2022526844A (en) 2019-04-12 2022-05-26 ザ リージェンツ オブ ザ ユニバーシティ オブ カリフォルニア Compositions and Methods for Increasing Muscle Mass and Oxidative Metabolism
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Non-Patent Citations (3)

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Also Published As

Publication number Publication date
EP1234058A2 (en) 2002-08-28
WO2001038580A9 (en) 2002-12-05
CA2392474A1 (en) 2001-05-31
AU1792701A (en) 2001-06-04
WO2001038580A2 (en) 2001-05-31
AU783841B2 (en) 2005-12-15
JP2003515149A (en) 2003-04-22

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