WO2001090346A3 - Gene recombination and hybrid protein development - Google Patents

Gene recombination and hybrid protein development Download PDF

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Publication number
WO2001090346A3
WO2001090346A3 PCT/US2001/016831 US0116831W WO0190346A3 WO 2001090346 A3 WO2001090346 A3 WO 2001090346A3 US 0116831 W US0116831 W US 0116831W WO 0190346 A3 WO0190346 A3 WO 0190346A3
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WO
WIPO (PCT)
Prior art keywords
locations
crossover
methods
directed evolution
crossover locations
Prior art date
Application number
PCT/US2001/016831
Other languages
French (fr)
Other versions
WO2001090346A2 (en
Inventor
Zhen-Gang Wang
Christopher A Voigt
Stephen L Mayo
Frances H Arnold
Original Assignee
California Inst Of Techn
Zhen-Gang Wang
Christopher A Voigt
Stephen L Mayo
Frances H Arnold
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 California Inst Of Techn, Zhen-Gang Wang, Christopher A Voigt, Stephen L Mayo, Frances H Arnold filed Critical California Inst Of Techn
Priority to AU2001263411A priority Critical patent/AU2001263411A1/en
Priority to CA002405520A priority patent/CA2405520A1/en
Priority to EP01937702A priority patent/EP1283877A2/en
Publication of WO2001090346A2 publication Critical patent/WO2001090346A2/en
Publication of WO2001090346A3 publication Critical patent/WO2001090346A3/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
    • C12N15/102—Mutagenizing nucleic acids
    • C12N15/1027—Mutagenizing nucleic acids by DNA shuffling, e.g. RSR, STEP, RPR
    • 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
    • G16B10/00—ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
    • 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
    • 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

Abstract

The invention relates to improved methods for directed evolution of polymers, including directed evolution of nucleic acids and proteins. Specifically, the methods of the invention include analytical methods for identifying 'crossover locations' in a polymer. Crossovers at these locations are less likely to disrupt desirable properties of the protein, such as stability or functionality. The invention further provides improved methods for directed evolution wherein the polymer is selectively recombined at the identified 'crossover locations'. Crossover disruption profiles can be used to identify preferred crossover locations. Structural domains of a biopolymer can also be identified and analyzed, and domains can be organized into schema. Schema disruption profiles can be calculated, for example based on conformational energy or interatomic distances, and these can be used to identify preferred or candidate crossover locations. Computer systems for implementing analytical methods of the invention are also provided.
PCT/US2001/016831 2000-05-23 2001-05-23 Gene recombination and hybrid protein development WO2001090346A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU2001263411A AU2001263411A1 (en) 2000-05-23 2001-05-23 Gene recombination and hybrid protein development
CA002405520A CA2405520A1 (en) 2000-05-23 2001-05-23 Gene recombination and hybrid protein development
EP01937702A EP1283877A2 (en) 2000-05-23 2001-05-23 Gene recombination and hybrid protein development

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US20704800P 2000-05-23 2000-05-23
US60/207,048 2000-05-23
US23596000P 2000-09-27 2000-09-27
US60/235,960 2000-09-27
US28356701P 2001-04-13 2001-04-13
US60/283,567 2001-04-13

Publications (2)

Publication Number Publication Date
WO2001090346A2 WO2001090346A2 (en) 2001-11-29
WO2001090346A3 true WO2001090346A3 (en) 2002-10-10

Family

ID=27395018

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/016831 WO2001090346A2 (en) 2000-05-23 2001-05-23 Gene recombination and hybrid protein development

Country Status (5)

Country Link
US (1) US20020045175A1 (en)
EP (1) EP1283877A2 (en)
AU (1) AU2001263411A1 (en)
CA (1) CA2405520A1 (en)
WO (1) WO2001090346A2 (en)

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US7024312B1 (en) * 1999-01-19 2006-04-04 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
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AU2002251710A1 (en) * 2000-11-10 2002-07-30 The Penn State Research Foundation A modeling framework for predicting the number, type, and distribution of crossovers in directed evolution experiments
US7711490B2 (en) 2001-01-10 2010-05-04 The Penn State Research Foundation Method and system for modeling cellular metabolism
US20040142433A1 (en) * 2001-02-02 2004-07-22 Padgett Hal S. Polynucleotide sequence variants
DE60234159D1 (en) * 2001-02-02 2009-12-10 Large Scale Biology Corp METHOD OF INCREASING COMPLEMENTARITY IN A HETERODUPLEX POLYNUCLEOTIDE
US7582423B2 (en) * 2001-02-02 2009-09-01 Novici Biotech Llc Population of polynucleotide sequence variants
US7838219B2 (en) * 2001-02-02 2010-11-23 Novici Biotech Llc Method of increasing complementarity in a heteroduplex
US7465567B2 (en) * 2001-04-16 2008-12-16 California Institute Of Technology Peroxide-driven cytochrome P450 oxygenase variants
WO2002090496A2 (en) * 2001-05-03 2002-11-14 Rensselaer Polytechnic Institute Novel methods of directed evolution
US20030157495A1 (en) * 2002-02-01 2003-08-21 Padgett Hal S. Nucleic acid molecules encoding CEL I endonuclease and methods of use thereof
US7078211B2 (en) 2002-02-01 2006-07-18 Large Scale Biology Corporation Nucleic acid molecules encoding endonucleases and methods of use thereof
DK2315145T3 (en) * 2002-03-01 2016-01-25 Codexis Mayflower Holdings Llc Methods, systems, and software for identifying the functional biomolecules
US20050084907A1 (en) * 2002-03-01 2005-04-21 Maxygen, Inc. Methods, systems, and software for identifying functional biomolecules
US7747391B2 (en) * 2002-03-01 2010-06-29 Maxygen, Inc. Methods, systems, and software for identifying functional biomolecules
WO2003078583A2 (en) 2002-03-09 2003-09-25 Maxygen, Inc. Optimization of crossover points for directed evolution
US20030211484A1 (en) * 2002-05-13 2003-11-13 Keith Ball Sequence lineage evaluation interface
EP1532516A4 (en) 2002-07-10 2007-05-23 Penn State Res Found Method for determining gene knockout strategies
US7826975B2 (en) 2002-07-10 2010-11-02 The Penn State Research Foundation Method for redesign of microbial production systems
WO2005007806A2 (en) * 2003-05-07 2005-01-27 Duke University Protein design for receptor-ligand recognition and binding
EP1639091B1 (en) 2003-06-17 2012-12-05 California University Of Technology Regio- and enantioselective alkane hydroxylation with modified cytochrome p450
DK1700119T3 (en) * 2003-12-18 2010-06-07 Genencor Int Beta-lactamase CD4 + T cell epitopes
US8715988B2 (en) * 2005-03-28 2014-05-06 California Institute Of Technology Alkane oxidation by modified hydroxylases
US8026085B2 (en) * 2006-08-04 2011-09-27 California Institute Of Technology Methods and systems for selective fluorination of organic molecules
US8252559B2 (en) * 2006-08-04 2012-08-28 The California Institute Of Technology Methods and systems for selective fluorination of organic molecules
JP2010515683A (en) * 2007-01-05 2010-05-13 ザ カリフォルニア インスティチュート オブ テクノロジー Method for producing new stabilized proteins
WO2008121435A2 (en) * 2007-02-02 2008-10-09 The California Institute Of Technology Methods for generating novel stabilized proteins
US20080268517A1 (en) * 2007-02-08 2008-10-30 The California Institute Of Technology Stable, functional chimeric cytochrome p450 holoenzymes
US8802401B2 (en) * 2007-06-18 2014-08-12 The California Institute Of Technology Methods and compositions for preparation of selectively protected carbohydrates
WO2009149218A2 (en) * 2008-06-03 2009-12-10 Codon Devices, Inc. Novel proteins and methods of designing and using same
US9322007B2 (en) 2011-07-22 2016-04-26 The California Institute Of Technology Stable fungal Cel6 enzyme variants
US9684771B2 (en) 2013-01-31 2017-06-20 Codexis, Inc. Methods, systems, and software for identifying bio-molecules using models of multiplicative form
USD815145S1 (en) * 2016-03-25 2018-04-10 Illumina, Inc. Display screen with application icon
USD815146S1 (en) * 2016-03-25 2018-04-10 Illimina, Inc. Display screen with application icon

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Also Published As

Publication number Publication date
AU2001263411A1 (en) 2001-12-03
CA2405520A1 (en) 2001-11-29
WO2001090346A2 (en) 2001-11-29
EP1283877A2 (en) 2003-02-19
US20020045175A1 (en) 2002-04-18

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