WO2008127213A3 - Methods, systems, and software for regulated oligonucleotide-mediated recombination - Google Patents

Methods, systems, and software for regulated oligonucleotide-mediated recombination Download PDF

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Publication number
WO2008127213A3
WO2008127213A3 PCT/US2002/014866 US0214866W WO2008127213A3 WO 2008127213 A3 WO2008127213 A3 WO 2008127213A3 US 0214866 W US0214866 W US 0214866W WO 2008127213 A3 WO2008127213 A3 WO 2008127213A3
Authority
WO
WIPO (PCT)
Prior art keywords
recombination
methods
systems
software
regulated
Prior art date
Application number
PCT/US2002/014866
Other languages
French (fr)
Other versions
WO2008127213A2 (en
Inventor
Jeremy Minshull
Claes Gustafsson
Sridar Govindarajan
Ajoy Roy
Original Assignee
Maxygen Inc
Jeremy Minshull
Claes Gustafsson
Sridar Govindarajan
Ajoy Roy
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 Maxygen Inc, Jeremy Minshull, Claes Gustafsson, Sridar Govindarajan, Ajoy Roy filed Critical Maxygen Inc
Priority to AU2002368549A priority Critical patent/AU2002368549A1/en
Publication of WO2008127213A2 publication Critical patent/WO2008127213A2/en
Publication of WO2008127213A3 publication Critical patent/WO2008127213A3/en

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Classifications

    • 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
    • C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/007—Simulation or vitual synthesis
    • 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

Abstract

The present invention provides novel in silico recombination techniques in which all or part of a nucleic acid recombination procedure is performed or modeled in a digital system. In particular, this invention relates to methods of designing oligonucleotides for regulated recombination that approximates linkage characteristics obtained from fragmentation-based recombination techniques, such as family-based recombination. The methods of this invention include adjusting overlap regions in pairs of overlapping oligonucleotide character strings to bias recombination towards a desired genetic linkage. This invention also provides systems, computer program products, and kits for practicing the methods of the invention.
PCT/US2002/014866 2001-05-09 2002-05-09 Methods, systems, and software for regulated oligonucleotide-mediated recombination WO2008127213A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002368549A AU2002368549A1 (en) 2001-05-09 2002-05-09 Methods, systems, and software for regulated oligonucleotide-mediated recombination

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US28994701P 2001-05-09 2001-05-09
US60/289,947 2001-05-09

Publications (2)

Publication Number Publication Date
WO2008127213A2 WO2008127213A2 (en) 2008-10-23
WO2008127213A3 true WO2008127213A3 (en) 2008-12-11

Family

ID=39864489

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/014866 WO2008127213A2 (en) 2001-05-09 2002-05-09 Methods, systems, and software for regulated oligonucleotide-mediated recombination

Country Status (2)

Country Link
AU (1) AU2002368549A1 (en)
WO (1) WO2008127213A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
EP3235010A4 (en) 2014-12-18 2018-08-29 Agilome, Inc. Chemically-sensitive field effect transistor
US10020300B2 (en) 2014-12-18 2018-07-10 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9618474B2 (en) 2014-12-18 2017-04-11 Edico Genome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US10006910B2 (en) 2014-12-18 2018-06-26 Agilome, Inc. Chemically-sensitive field effect transistors, systems, and methods for manufacturing and using the same
US9859394B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US10811539B2 (en) 2016-05-16 2020-10-20 Nanomedical Diagnostics, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000042560A2 (en) * 1999-01-19 2000-07-20 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000042560A2 (en) * 1999-01-19 2000-07-20 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
ZHA ET AL.: "Assembly of designed oligonucleotides as an efficient method for gene recombination: a new tool in directed evolution", CHEMBIOCHEM.: A EUROPEAN JOURNAL OF CHEMICAL BIOLOGY, vol. 4, no. 1, January 2003 (2003-01-01), pages 34 - 39, XP002491068 *

Also Published As

Publication number Publication date
WO2008127213A2 (en) 2008-10-23
AU2002368549A1 (en) 2008-10-23
AU2002368549A8 (en) 2009-01-08

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