WO2004076683A3 - Random array dna analysis by hybridization - Google Patents

Random array dna analysis by hybridization Download PDF

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Publication number
WO2004076683A3
WO2004076683A3 PCT/US2004/006022 US2004006022W WO2004076683A3 WO 2004076683 A3 WO2004076683 A3 WO 2004076683A3 US 2004006022 W US2004006022 W US 2004006022W WO 2004076683 A3 WO2004076683 A3 WO 2004076683A3
Authority
WO
WIPO (PCT)
Prior art keywords
hybridization
dna analysis
random array
array dna
methods
Prior art date
Application number
PCT/US2004/006022
Other languages
French (fr)
Other versions
WO2004076683A2 (en
Inventor
Radoje T Drmanac
Original Assignee
Callida Genomics Inc
Radoje T Drmanac
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
Priority to US10/547,214 priority Critical patent/US8105771B2/en
Priority to AU2004214891A priority patent/AU2004214891B2/en
Priority to JP2006503913A priority patent/JP4691014B2/en
Priority to EP04715167.5A priority patent/EP1601791B1/en
Priority to CA2555962A priority patent/CA2555962C/en
Priority to CN2004800108063A priority patent/CN1791682B/en
Application filed by Callida Genomics Inc, Radoje T Drmanac filed Critical Callida Genomics Inc
Publication of WO2004076683A2 publication Critical patent/WO2004076683A2/en
Publication of WO2004076683A3 publication Critical patent/WO2004076683A3/en
Priority to HK06113554.5A priority patent/HK1091871A1/en
Priority to US11/981,685 priority patent/US7906285B2/en
Priority to US11/981,730 priority patent/US7910304B2/en
Priority to US11/981,797 priority patent/US8278039B2/en
Priority to AU2010201296A priority patent/AU2010201296B2/en
Priority to US13/633,034 priority patent/US8785127B2/en
Priority to US14/335,827 priority patent/US20150038345A1/en
Priority to US14/877,814 priority patent/US20160023180A1/en

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Classifications

    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J19/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J19/0046—Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y10/00—Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y20/00—Nanooptics, e.g. quantum optics or photonic crystals
    • 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
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y5/00—Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
    • 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
    • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
    • 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
    • C12Q1/6825—Nucleic acid detection involving sensors
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00479—Means for mixing reactants or products in the reaction vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00585—Parallel processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G01N2021/6439—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" with indicators, stains, dyes, tags, labels, marks
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2201/00—Features of devices classified in G01N21/00
    • G01N2201/06—Illumination; Optics
    • G01N2201/061—Sources
    • G01N2201/06113—Coherent sources; lasers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2223/00—Investigating materials by wave or particle radiation
    • G01N2223/40—Imaging
    • G01N2223/413—Imaging sensor array [CCD]

Abstract

The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.
PCT/US2004/006022 2002-12-20 2004-02-26 Random array dna analysis by hybridization WO2004076683A2 (en)

Priority Applications (14)

Application Number Priority Date Filing Date Title
US10/547,214 US8105771B2 (en) 2003-02-26 2004-02-26 Random array DNA analysis by hybridization
AU2004214891A AU2004214891B2 (en) 2003-02-26 2004-02-26 Random array DNA analysis by hybridization
JP2006503913A JP4691014B2 (en) 2003-02-26 2004-02-26 Random array DNA analysis by hybridization
EP04715167.5A EP1601791B1 (en) 2003-02-26 2004-02-26 Random array dna analysis by hybridization
CA2555962A CA2555962C (en) 2003-02-26 2004-02-26 Random array dna analysis by hybridization
CN2004800108063A CN1791682B (en) 2003-02-26 2004-02-26 Random array DNA analysis by hybridization
HK06113554.5A HK1091871A1 (en) 2003-02-26 2006-12-08 Random array dna analysis by hybridization
US11/981,685 US7906285B2 (en) 2003-02-26 2007-10-31 Random array DNA analysis by hybridization
US11/981,797 US8278039B2 (en) 2003-02-26 2007-10-31 Random array DNA analysis by hybridization
US11/981,730 US7910304B2 (en) 2003-02-26 2007-10-31 Random array DNA analysis by hybridization
AU2010201296A AU2010201296B2 (en) 2003-02-26 2010-03-31 Random array DNA analysis by hybridization
US13/633,034 US8785127B2 (en) 2003-02-26 2012-10-01 Random array DNA analysis by hybridization
US14/335,827 US20150038345A1 (en) 2002-12-20 2014-07-18 Random Array DNA Analysis by Hybridization
US14/877,814 US20160023180A1 (en) 2002-12-20 2015-10-07 Random array dna analysis by hybridization

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US45056603P 2003-02-26 2003-02-26
US60/450,566 2003-02-26

Related Child Applications (4)

Application Number Title Priority Date Filing Date
US10/547,214 A-371-Of-International US8105771B2 (en) 2003-02-26 2004-02-26 Random array DNA analysis by hybridization
US11/981,685 Continuation US7906285B2 (en) 2003-02-26 2007-10-31 Random array DNA analysis by hybridization
US11/981,797 Continuation US8278039B2 (en) 2002-12-20 2007-10-31 Random array DNA analysis by hybridization
US11/981,730 Continuation US7910304B2 (en) 2003-02-26 2007-10-31 Random array DNA analysis by hybridization

Publications (2)

Publication Number Publication Date
WO2004076683A2 WO2004076683A2 (en) 2004-09-10
WO2004076683A3 true WO2004076683A3 (en) 2004-12-09

Family

ID=32927668

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/006022 WO2004076683A2 (en) 2002-12-20 2004-02-26 Random array dna analysis by hybridization

Country Status (8)

Country Link
US (7) US8105771B2 (en)
EP (2) EP1601791B1 (en)
JP (1) JP4691014B2 (en)
CN (4) CN103396933B (en)
AU (2) AU2004214891B2 (en)
CA (3) CA2930400A1 (en)
HK (3) HK1091871A1 (en)
WO (1) WO2004076683A2 (en)

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US9499863B2 (en) 2007-12-05 2016-11-22 Complete Genomics, Inc. Reducing GC bias in DNA sequencing using nucleotide analogs

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