WO2001088196A3 - Sequence based screening - Google Patents

Sequence based screening Download PDF

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Publication number
WO2001088196A3
WO2001088196A3 PCT/US2001/015692 US0115692W WO0188196A3 WO 2001088196 A3 WO2001088196 A3 WO 2001088196A3 US 0115692 W US0115692 W US 0115692W WO 0188196 A3 WO0188196 A3 WO 0188196A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
sequence based
based screening
clone
organisms
Prior art date
Application number
PCT/US2001/015692
Other languages
French (fr)
Other versions
WO2001088196A2 (en
Inventor
Jay M Short
Original Assignee
Diversa Corp
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 Diversa Corp filed Critical Diversa Corp
Priority to AU63148/01A priority Critical patent/AU782529C/en
Priority to EP01937406A priority patent/EP1356090A2/en
Priority to CA002375082A priority patent/CA2375082A1/en
Priority to IL14763701A priority patent/IL147637A0/en
Priority to JP2001584578A priority patent/JP2004504014A/en
Publication of WO2001088196A2 publication Critical patent/WO2001088196A2/en
Publication of WO2001088196A3 publication Critical patent/WO2001088196A3/en

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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
    • C12N15/1034—Isolating an individual clone by screening libraries
    • 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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • 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
    • 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
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • 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
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Provided is a method of obtaining a nucleic acid profile of a sample. The method includes creating a DNA library from a plurality of nucleic acid sequences of a mixed population of organisms and sequencing at least one clone in the DNA library. The sequence is compared to a database and identifying sequences in the database which have homology to a clone in the library thereby obtaining a nucleic acid profile of the mixed population of organisms.
PCT/US2001/015692 2000-05-15 2001-05-15 Sequence based screening WO2001088196A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
AU63148/01A AU782529C (en) 2000-05-15 2001-05-15 Sequence based screening
EP01937406A EP1356090A2 (en) 2000-05-15 2001-05-15 Sequence based screening
CA002375082A CA2375082A1 (en) 2000-05-15 2001-05-15 Sequence based screening
IL14763701A IL147637A0 (en) 2000-05-15 2001-05-15 Sequence based screening
JP2001584578A JP2004504014A (en) 2000-05-15 2001-05-15 Sequence-based screening

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US09/571,499 US6455254B1 (en) 1995-07-18 2000-05-15 Sequence based screening
US09/571,499 2000-05-15

Publications (2)

Publication Number Publication Date
WO2001088196A2 WO2001088196A2 (en) 2001-11-22
WO2001088196A3 true WO2001088196A3 (en) 2003-08-14

Family

ID=24283949

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/015692 WO2001088196A2 (en) 2000-05-15 2001-05-15 Sequence based screening

Country Status (7)

Country Link
US (2) US6455254B1 (en)
EP (1) EP1356090A2 (en)
JP (1) JP2004504014A (en)
AU (1) AU782529C (en)
CA (1) CA2375082A1 (en)
IL (1) IL147637A0 (en)
WO (1) WO2001088196A2 (en)

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ATE341621T1 (en) * 1997-10-24 2006-10-15 Invitrogen Corp RECOMBINATORY CLONING USING NUCLIC ACIDS HAVING RECOMBINATION SITE
US6917882B2 (en) * 1999-01-19 2005-07-12 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
US6961664B2 (en) 1999-01-19 2005-11-01 Maxygen Methods of populating data structures for use in evolutionary simulations
US7024312B1 (en) * 1999-01-19 2006-04-04 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
US7430477B2 (en) * 1999-10-12 2008-09-30 Maxygen, Inc. Methods of populating data structures for use in evolutionary simulations
US7198924B2 (en) 2000-12-11 2007-04-03 Invitrogen Corporation Methods and compositions for synthesis of nucleic acid molecules using multiple recognition sites
EP1488365A4 (en) * 2002-03-11 2007-05-09 Athenix Corp Integrated system for high throughput capture of genetic diversity
EP1697534B1 (en) 2003-12-01 2010-06-02 Life Technologies Corporation Nucleic acid molecules containing recombination sites and methods of using the same
US20050282155A1 (en) * 2004-06-17 2005-12-22 Lucigen Corporation Viral libraries from uncultivated viruses and polypeptides produced therefrom
AU2005299413A1 (en) 2004-10-22 2006-05-04 Revivicor, Inc. Ungulates with genetically modified immune systems
KR101502920B1 (en) 2005-06-21 2015-03-17 조마 (유에스) 엘엘씨 IL-1β Binding antibodies and fragments thereof
ES2548377T3 (en) 2008-10-27 2015-10-16 Revivicor, Inc. Immunosuppressed ungulates
CA2779750C (en) 2009-11-06 2019-03-19 The Board Of Trustees Of The Leland Stanford Junior University Non-invasive diagnosis of graft rejection in organ transplant patients
JP6055152B1 (en) * 2015-08-27 2016-12-27 花王株式会社 Binder resin composition for toner

Family Cites Families (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0528881A4 (en) 1990-04-24 1993-05-26 Stratagene Methods for phenotype creation from multiple gene populations
US5500363A (en) 1990-04-26 1996-03-19 New England Biolabs, Inc. Recombinant thermostable DNA polymerase from archaebacteria
US5352778A (en) 1990-04-26 1994-10-04 New England Biolabs, Inc. Recombinant thermostable DNA polymerase from archaebacteria
US5837458A (en) 1994-02-17 1998-11-17 Maxygen, Inc. Methods and compositions for cellular and metabolic engineering
US5605793A (en) 1994-02-17 1997-02-25 Affymax Technologies N.V. Methods for in vitro recombination
EP0822990A4 (en) 1995-04-24 2002-07-03 Chromaxome Corp Methods for generating and screening novel metabolic pathways
US5783431A (en) * 1996-04-24 1998-07-21 Chromaxome Corporation Methods for generating and screening novel metabolic pathways
US5763239A (en) * 1996-06-18 1998-06-09 Diversa Corporation Production and use of normalized DNA libraries

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DIATCHENKO L ET AL: "SUPPRESSION SUBTRACTIVE HYBRIDIZATION: A METHOD FOR GENERATING DIFFERENTIALLY REGULATED OR TISSUE-SPECIFIC CDNA PROBES AND LIBRARIES", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 93, 1 June 1996 (1996-06-01), pages 6025 - 6030, XP002911922, ISSN: 0027-8424 *
RÖLLEKE S ET AL: "Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA.", APPLIED AND ENVIRONMENTAL MICROBIOLOGY. UNITED STATES JUN 1996, vol. 62, no. 6, June 1996 (1996-06-01), pages 2059 - 2065, XP000874454, ISSN: 0099-2240 *
VELCULESCU V E ET AL: "SERIAL ANALYSIS OF GENE EXPRESSION", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,, US, vol. 270, 20 October 1995 (1995-10-20), pages 484 - 487, XP002053721, ISSN: 0036-8075 *

Also Published As

Publication number Publication date
JP2004504014A (en) 2004-02-12
US20020037505A1 (en) 2002-03-28
AU6314801A (en) 2001-11-26
AU782529B2 (en) 2005-08-04
AU782529C (en) 2006-02-23
WO2001088196A2 (en) 2001-11-22
EP1356090A2 (en) 2003-10-29
US20030008319A1 (en) 2003-01-09
CA2375082A1 (en) 2001-11-22
US6455254B1 (en) 2002-09-24
IL147637A0 (en) 2002-08-14

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