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
Authority
WO
WIPO (PCT)
Prior art keywords
methods
molecules
obtaining
stochastic
provides methods
Prior art date
Application number
PCT/US2000/006497
Other languages
French (fr)
Other versions
WO2000053744A9 (en
WO2000053744A2 (en
Inventor
Jay M Short
Gerhard Johann Frey
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 IL14516500A priority Critical patent/IL145165A0/en
Priority to AU38793/00A priority patent/AU3879300A/en
Priority to JP2000603365A priority patent/JP2002537836A/en
Priority to CA002361927A priority patent/CA2361927A1/en
Priority to EP00917887A priority patent/EP1161529A2/en
Application filed by Diversa Corp filed Critical Diversa Corp
Publication of WO2000053744A2 publication Critical patent/WO2000053744A2/en
Publication of WO2000053744A3 publication Critical patent/WO2000053744A3/en
Publication of WO2000053744A9 publication Critical patent/WO2000053744A9/en
Priority to US10/151,469 priority patent/US20030219752A1/en
Priority to AU2005203719A priority patent/AU2005203719A1/en

Links

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
    • C12N15/1058—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)

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 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
JP2000603365A JP2002537836A (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
EP00917887A EP1161529A2 (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

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/006497 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)

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US6326204B1 (en) 1997-01-17 2001-12-04 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
EP1119616A2 (en) 1998-10-07 2001-08-01 Maxygen, Inc. Dna shuffling to produce nucleic acids for mycotoxin detoxification
US6368861B1 (en) 1999-01-19 2002-04-09 Maxygen, Inc. Oligonucleotide mediated nucleic acid recombination
IL138206A (en) * 1999-02-04 2011-06-30 Verenium Corp Methods for non-stochastic generation of progeny polypeptides and hybrid polynucleotides
US6531316B1 (en) 1999-03-05 2003-03-11 Maxyag, Inc. Encryption of traits using split gene sequences and engineered genetic elements
US6686515B1 (en) 1999-11-23 2004-02-03 Maxygen, Inc. Homologous recombination in plants
WO2002000717A2 (en) 2000-06-23 2002-01-03 Maxygen, Inc. Novel co-stimulatory molecules
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 synthetase
US6958217B2 (en) 2001-01-24 2005-10-25 Genomic Expression Aps Single-stranded polynucleotide tags
EP1423529B1 (en) * 2001-01-24 2013-11-20 Genomic Expression APS Assay for analyzing gene expression
DE60239386D1 (en) 2001-01-25 2011-04-21 Evolva Ltd CELL LIBRARY
US8008459B2 (en) 2001-01-25 2011-08-30 Evolva Sa Concatemers of differentially expressed multiple genes
WO2002092780A2 (en) * 2001-05-17 2002-11-21 Diversa Corporation Novel antigen binding molecules for therapeutic, diagnostic, prophylactic, enzymatic, industrial, and agricultural applications, and methods for generating and screening thereof
WO2004073657A2 (en) * 2003-02-19 2004-09-02 Protein Design Labs, Inc. Methods of diagnosis of cancer and other diseases, composition and methods of screening for modulators of cancer and other diseases
EP2087107A2 (en) 2006-10-30 2009-08-12 Promega Corporation Mutant hydrolase proteins with enhanced kinetics and functional expression
EP2139515B2 (en) 2007-03-30 2023-12-20 The Research Foundation of the State University of New York Attenuated viruses useful for vaccines
US20110039722A1 (en) * 2007-12-31 2011-02-17 Xoma Technology Ltd. Libraries, arrays and their uses for targeted affinity enhancement
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
IL145165A0 (en) 2002-06-30
JP2002537836A (en) 2002-11-12
EP1161529A2 (en) 2001-12-12
WO2000053744A9 (en) 2001-06-28
CA2361927A1 (en) 2000-09-14
WO2000053744A2 (en) 2000-09-14
AU3879300A (en) 2000-09-28

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