WO2000053744A3 - End selection in directed evolution - Google Patents

End selection in directed evolution Download PDF

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Publication number
WO2000053744A3
WO2000053744A3 PCT/US2000/006497 US0006497W WO0053744A3 WO 2000053744 A3 WO2000053744 A3 WO 2000053744A3 US 0006497 W US0006497 W US 0006497W WO 0053744 A3 WO0053744 A3 WO 0053744A3
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WO
WIPO (PCT)
Prior art keywords
methods
molecules
obtaining
stochastic
provides methods
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/US2000/006497
Other languages
French (fr)
Other versions
WO2000053744A9 (en
WO2000053744A2 (en
Inventor
Jay M Short
Gerhard Johann Frey
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
BASF Enzymes LLC
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
Priority claimed from US09/267,118 external-priority patent/US6238884B1/en
Priority claimed from US09/276,860 external-priority patent/US6352842B1/en
Priority claimed from US09/332,835 external-priority patent/US6537776B1/en
Priority to CA002361927A priority Critical patent/CA2361927A1/en
Application filed by Diversa Corp filed Critical Diversa Corp
Priority to JP2000603365A priority patent/JP2002537836A/en
Priority to EP00917887A priority patent/EP1161529A2/en
Priority to AU38793/00A priority patent/AU3879300A/en
Priority to IL14516500A priority patent/IL145165A0/en
Publication of WO2000053744A2 publication Critical patent/WO2000053744A2/en
Publication of WO2000053744A3 publication Critical patent/WO2000053744A3/en
Publication of WO2000053744A9 publication Critical patent/WO2000053744A9/en
Anticipated expiration legal-status Critical
Priority to US10/151,469 priority patent/US20030219752A1/en
Priority to AU2005203719A priority patent/AU2005203719A1/en
Ceased legal-status Critical Current

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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
    • C12N15/1058—Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
    • 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
    • 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
    • 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
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Plant Pathology (AREA)
  • Medicinal Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Ecology (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)
  • Enzymes And Modification Thereof (AREA)

Abstract

This invention provides methods of obtaining novel polynucleotides and encoded polypeptides by the use of non-stochastic methods of directed evolution (DirectEvolution™). A particular advantage of end-selection-based methods is the ability to recover full-length polynucleotides from a library of progeny molecules generated by mutagenesis methods. These methods include non-stochastic polynucleotide site-saturation mutagenesis (Gene Site Saturation Mutagenesis™) and non-stochastic polynucleotide reassembly (GeneReassembly™). This invention provides methods of obtaining novel enzymes that have optmized physical and/or biological properties. Through use of the claimed methods, genetic vaccines, enzymes, small molecules, and other desirable molecules can be evolved towards desirable properties. For example, vaccine vectors can be obtained that exhibit increased efficacy for use as genetic vaccines. Vectors obtained by using the methods can have, for example, enhanced antigen expression, increased uptake into a cell, increased stability in a cell, ability to tailor an immune response, and the like. Furthermore, this invention provides methods of obtaining a variety of novel biologically active molecules, in the fields of antibiotics, pharmacotherapeutics, and transgenic traits.
PCT/US2000/006497 1995-12-07 2000-03-09 End selection in directed evolution Ceased WO2000053744A2 (en)

Priority Applications (7)

Application Number Priority Date Filing Date Title
IL14516500A IL145165A0 (en) 1999-03-09 2000-03-09 End selection in directed evolution
AU38793/00A AU3879300A (en) 1999-03-09 2000-03-09 End selection in directed evolution
EP00917887A EP1161529A2 (en) 1999-03-09 2000-03-09 End selection in directed evolution
CA002361927A CA2361927A1 (en) 1999-03-09 2000-03-09 End selection in directed evolution
JP2000603365A JP2002537836A (en) 1999-03-09 2000-03-09 End selection in directed evolution
US10/151,469 US20030219752A1 (en) 1995-12-07 2002-05-17 Novel antigen binding molecules for therapeutic, diagnostic, prophylactic, enzymatic, industrial, and agricultural applications, and methods for generating and screening thereof
AU2005203719A AU2005203719A1 (en) 1999-03-09 2005-08-18 End selection in directed evolution

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US09/267,118 1999-03-09
US09/267,118 US6238884B1 (en) 1995-12-07 1999-03-09 End selection in directed evolution
US09/276,860 1999-03-26
US09/276,860 US6352842B1 (en) 1995-12-07 1999-03-26 Exonucease-mediated gene assembly in directed evolution
US09/332,835 1999-06-14
US09/332,835 US6537776B1 (en) 1999-06-14 1999-06-14 Synthetic ligation reassembly in directed evolution

Related Child Applications (2)

Application Number Title Priority Date Filing Date
PCT/US1997/012239 Continuation-In-Part WO1998001581A1 (en) 1996-07-09 1997-07-09 Method of dna shuffling with polynucleotides produced by blockingor interrupting a synthesis or amplification process
US10/151,469 Continuation-In-Part US20030219752A1 (en) 1995-12-07 2002-05-17 Novel antigen binding molecules for therapeutic, diagnostic, prophylactic, enzymatic, industrial, and agricultural applications, and methods for generating and screening thereof

Publications (3)

Publication Number Publication Date
WO2000053744A2 WO2000053744A2 (en) 2000-09-14
WO2000053744A3 true WO2000053744A3 (en) 2001-01-18
WO2000053744A9 WO2000053744A9 (en) 2001-06-28

Family

ID=27401940

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/006497 Ceased WO2000053744A2 (en) 1995-12-07 2000-03-09 End selection in directed evolution

Country Status (6)

Country Link
EP (1) EP1161529A2 (en)
JP (1) JP2002537836A (en)
AU (1) AU3879300A (en)
CA (1) CA2361927A1 (en)
IL (1) IL145165A0 (en)
WO (1) WO2000053744A2 (en)

Families Citing this family (33)

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Publication number Priority date Publication date Assignee Title
US6537776B1 (en) * 1999-06-14 2003-03-25 Diversa Corporation Synthetic ligation reassembly in directed evolution
US6326204B1 (en) 1997-01-17 2001-12-04 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
US7148054B2 (en) 1997-01-17 2006-12-12 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
US7390619B1 (en) 1998-02-11 2008-06-24 Maxygen, Inc. Optimization of immunomodulatory properties of genetic vaccines
US7153655B2 (en) 1998-06-16 2006-12-26 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function involving the use of exonuclease enzyme and two populations of parent polynucleotide sequence
US6500639B2 (en) 1998-10-07 2002-12-31 Maxygen, Inc. DNA shuffling to produce nucleic acids for mycotoxin detoxification
US6917882B2 (en) 1999-01-19 2005-07-12 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
US6368861B1 (en) 1999-01-19 2002-04-09 Maxygen, Inc. Oligonucleotide mediated nucleic acid recombination
US6961664B2 (en) 1999-01-19 2005-11-01 Maxygen Methods of populating data structures for use in evolutionary simulations
ATE465459T1 (en) 1999-01-19 2010-05-15 Maxygen Inc THROUGH OLIGONUCLEOTIDE-MEDIATED NUCLEIC ACID RECOMBINATION
US7024312B1 (en) 1999-01-19 2006-04-04 Maxygen, Inc. Methods for making character strings, polynucleotides and polypeptides having desired characteristics
EP1073710A4 (en) * 1999-02-04 2007-12-19 Verenium Corp Non-stochastic generation of genetic vaccines and enzymes
US6531316B1 (en) 1999-03-05 2003-03-11 Maxyag, Inc. Encryption of traits using split gene sequences and engineered genetic elements
US7430477B2 (en) 1999-10-12 2008-09-30 Maxygen, Inc. Methods of populating data structures for use in evolutionary simulations
US6686515B1 (en) 1999-11-23 2004-02-03 Maxygen, Inc. Homologous recombination in plants
US7115712B1 (en) 1999-12-02 2006-10-03 Maxygen, Inc. Cytokine polypeptides
JP2003519495A (en) 2000-01-11 2003-06-24 マキシジェン， インコーポレイテッド Integrated systems and methods for diversity generation and screening
CA2411828A1 (en) 2000-06-23 2002-01-03 Maxygen, Inc. Novel co-stimulatory molecules
US7074590B2 (en) 2000-06-23 2006-07-11 Maxygen, Inc. Chimeric promoters
US6858422B2 (en) 2000-07-13 2005-02-22 Codexis, Inc. Lipase genes
JP2002199890A (en) * 2000-10-23 2002-07-16 Inst Of Physical & Chemical Res Method for modifying biodegradable polyester synthase
US6958213B2 (en) 2000-12-12 2005-10-25 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function
US6958217B2 (en) 2001-01-24 2005-10-25 Genomic Expression Aps Single-stranded polynucleotide tags
WO2002059357A2 (en) * 2001-01-24 2002-08-01 Genomic Expression Aps Assay and kit for analyzing gene expression
ATE501251T1 (en) 2001-01-25 2011-03-15 Evolva Ltd CELL LIBRARY
US8008459B2 (en) 2001-01-25 2011-08-30 Evolva Sa Concatemers of differentially expressed multiple genes
JP2004532038A (en) * 2001-05-17 2004-10-21 ディヴァーサ コーポレイション Application of novel antigen-binding molecules to therapeutic, diagnostic, prophylactic, enzymatic, industrial and agricultural fields, and methods for producing and screening novel antigen-binding molecules therefor
DE60312507T3 (en) 2002-05-17 2011-08-18 Alligator Bioscience Ab A METHOD FOR THE IN VITRO MOLECULAR EVOLUTION OF THE PROTEIN FUNCTION
US20040219579A1 (en) * 2003-02-19 2004-11-04 Natasha Aziz Methods of diagnosis of cancer, compositions and methods of screening for modulators of cancer
EP2374875B1 (en) 2006-10-30 2015-09-02 Promega Corporation Mutant hydrolase proteins with enhanced kinetics and funcitional expression
WO2008121992A2 (en) 2007-03-30 2008-10-09 Research Foundation Of State University Of New York Attenuated viruses useful for vaccines
EP2980217A1 (en) * 2007-12-31 2016-02-03 XOMA Technology Ltd. Methods and materials for targeted mutagenesis
CN110498822A (en) * 2019-09-04 2019-11-26 上海药明康德新药开发有限公司 The synthetic method of on-DNA aryl azide chemical combination object in the building of DNA encoding compound library

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Also Published As

Publication number Publication date
WO2000053744A9 (en) 2001-06-28
IL145165A0 (en) 2002-06-30
JP2002537836A (en) 2002-11-12
AU3879300A (en) 2000-09-28
CA2361927A1 (en) 2000-09-14
WO2000053744A2 (en) 2000-09-14
EP1161529A2 (en) 2001-12-12

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