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1. WO2011035105 - REDUCED CODON MUTAGENESIS

Publication Number WO/2011/035105
Publication Date 24.03.2011
International Application No. PCT/US2010/049251
International Filing Date 17.09.2010
IPC
C40B 50/06 2006.01
CCHEMISTRY; METALLURGY
40COMBINATORIAL TECHNOLOGY
BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
50Methods of creating libraries, e.g. combinatorial synthesis
06Biochemical methods, e.g. using enzymes or whole viable microorganisms
C40B 40/06 2006.01
CCHEMISTRY; METALLURGY
40COMBINATORIAL TECHNOLOGY
BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
40Libraries per se, e.g. arrays, mixtures
04Libraries containing only organic compounds
06Libraries containing nucleotides or polynucleotides, or derivatives thereof
C12P 19/34 2006.01
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
PFERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
19Preparation of compounds containing saccharide radicals
26Preparation of nitrogen-containing carbohydrates
28N-glycosides
30Nucleotides
34Polynucleotides, e.g. nucleic acids, oligoribonucleotides
CPC
C12N 15/102
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
10Processes for the isolation, preparation or purification of DNA or RNA
102Mutagenizing nucleic acids
C12N 15/1027
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
10Processes for the isolation, preparation or purification of DNA or RNA
102Mutagenizing nucleic acids
1027by DNA shuffling, e.g. RSR, STEP, RPR
C12N 15/67
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
63Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
67General methods for enhancing the expression
C40B 40/06
CCHEMISTRY; METALLURGY
40COMBINATORIAL TECHNOLOGY
BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
40Libraries per se, e.g. arrays, mixtures
04Libraries containing only organic compounds
06Libraries containing nucleotides or polynucleotides, or derivatives thereof
C40B 50/06
CCHEMISTRY; METALLURGY
40COMBINATORIAL TECHNOLOGY
BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
50Methods of creating libraries, e.g. combinatorial synthesis
06Biochemical methods, e.g. using enzymes or whole viable microorganisms
Applicants
  • CODEXIS, INC. [US]/[US] (AllExceptUS)
  • FOX, Richard [US]/[US] (UsOnly)
  • GIVER, Lorraine J. [US]/[US] (UsOnly)
  • HELD, Daniel [US]/[US] (UsOnly)
  • HATTENDORF, Douglas [US]/[US] (UsOnly)
  • CHOUDHARY, Trish [US]/[US] (UsOnly)
Inventors
  • FOX, Richard
  • GIVER, Lorraine J.
  • HELD, Daniel
  • HATTENDORF, Douglas
  • CHOUDHARY, Trish
Agents
  • QUINE, Jonathan, Alan
Priority Data
12/562,98818.09.2009US
61/283,87709.12.2009US
PCT/US2009/05750718.09.2009US
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) REDUCED CODON MUTAGENESIS
(FR) MUTAGENÈSE DE CODON RÉDUITE
Abstract
(EN)
Methods and compositions that reduce complexity of libraries of variant biological molecules, that reduce oversampling of these libraries during screening and that improve screening efficiency are provided. Sets of efficient degenerate codon sets are provided that efficiently encode all, or nearly all canonical amino acids. Degenerate oligonucleotides comprising these codons are provided, as are polynucleotide variants. Variant pooling strategies are used during library construction. Logical filtering is applied to select codon sites for mutagenesis, or to select amino acid sets to be incorporated at such sites. Methods for reducing non-optimal oversampling during screening are provided.
(FR)
L'invention porte sur des méthodes et des compositions qui réduisent la complexité de bibliothèques de variants de molécules biologiques, qui réduisent le suréchantillonnage de ces bibliothèques durant le criblage et qui améliorent l'efficacité du criblage. Des ensembles d'ensembles de codon dégénérés efficaces sont proposés, lesquels codent de manière efficace pour la totalité ou presque la totalité des acides aminés canoniques. L'invention porte également sur les oligonucléotides dégénérés comprenant ces codons ainsi que sur les variants polynucléotidiques. Des stratégies de regroupement de variants sont utilisées durant la construction de la bibliothèque. Un filtrage logique est appliqué pour choisir les sites de codon pour la mutagenèse, ou pour sélectionner les ensembles d'acides aminés devant être incorporés dans de tels sites. L'invention porte également sur des méthodes pour réduire le suréchantillonnage non optimal durant un criblage.
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