METHODS FOR IDENTIFYING SETS OF OLIGONUCLEOTIDES FOR USE IN AN IN VITRO RECOMBINATION PROCEDURE

• US 20100056385A1
• Filed: 09/10/2009
• Published: 03/04/2010
• Est. Priority Date: 01/19/1999
• Status: Active Grant

• Current Assignee: Codexis, Inc.
• Original Assignee: Maxygen Inc.
• Inventors: del Cardayre, Stephen, Tobin, Matthew, Patten, Phillip A., Giver, Lorraine J., Selifonov, Sergey A., Gustafsson, Claes, Minshull, Jeremy, Stemmer, Willem P.C.
• Granted Patent: US 7,957,912 B2
• Time in Patent Office: Days
• US Class Current: 506/8
• CPC Class Codes: B01J 2219/007 Simulation or vitual synthesis
• CPC Class Codes: G16B 10/00 ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/20 Protein or domain folding
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/30 Detection of binding sites or motifs
• CPC Class Codes: G16B 20/50 Mutagenesis
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/20 Screening of libraries
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided.

Claims

1. A method of identifying a set of oligonucleotides for use in an in vitro recombination procedure, the method comprising:

(a) receiving data identifying sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides;

(b) selecting one or more cross-over sites on the sequences based on structural information about the parental polypeptides or polypeptides encoded by the parental nucleic acids;

thereby defining one or more recombinant polypeptides or recombinant nucleic acids that result from cross-overs between the parental polypeptides or nucleic acids at the one or more cross-over sites;

(c) selecting at least one of the recombinant polypeptides or recombinant nucleic acids;

(d) identifying one or more oligonucleotides for in vitro recombination by choosing at least one portion of at least one of the recombinant polypeptides or recombinant nucleic acids selected in (c) which at least one portion identifies the one or more oligonucleotides for in vitro recombination; and

(e) outputting the identities of the one or more oligonucleotides for in vitro recombination,

wherein each of operations (a) through (e) is performed via a suitably programmed computer system.