In vitro recombination method

Young, Lei; Smith, Hamilton O.; Gibson, Daniel Glenn

Title: In vitro recombination method

Patent · Tue May 25 00:00:00 EDT 2010

OSTI ID:1531636

Young, Lei; Smith, Hamilton O.; Gibson, Daniel Glenn

The present invention relates, e.g., to in vitro method, using isolated protein reagents, for joining two double stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity, comprising contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5′ exonculease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.

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Research Organization:: Synthetic Genomics, Inc., San Diego, CA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: FG02-02ER63453

Assignee:: Synthetic Genomics, Inc. (San Diego, CA)

Patent Number(s):: 7,723,077

Application Number:: 11/502,746

OSTI ID:: 1531636

Resource Relation:: Patent File Date: 2006-08-11

Country of Publication:: United States

Language:: English

References (76)

TempliPhi, ⌽29 DNA Polymerase Based Rolling Circle Amplification of Templates for DNA Sequencing Nelson, John R.; Cai, Yuyang Christine; Giesler, Theresa L. BioTechniques, Vol. 32, Issue 6S https://doi.org/10.2144/jun0208	journal	June 2002
Process for in vitro creation of recombinant polynucleotide sequences by oriented ligation Dupret, Daniel; Lefevre, Fabrice; Masson, Jean-Michel https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6991922 US Patent Document 6,991,922	patent	January 2006
Watermark Systems and Methods Anglin, Hugh W.; Brunk, Hugh L.; Cattone, Jeremy https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20030032033 US Patent Application 10/122141; 20030032033	patent-application	February 2003
In vitro recombination of bacteriophage T7 DNA detected by a direct physical assay Lee, D.; Sadowski, P. D. Journal of Virology, Vol. 48, Issue 3 https://doi.org/10.1128/jvi.48.3.647-653.1983	journal	December 1983
The enzymatic basis of processivity in lambda exonuclease Subramanian, K. Nucleic Acids Research, Vol. 31, Issue 6 https://doi.org/10.1093/nar/gkg266	journal	March 2003
An alternative pathway of recombination of chromosomal fragments precedes recA-dependent recombination in the radioresistant bacterium Deinococcus radiodurans. Daly, M. J.; Minton, K. W. Journal of bacteriology, Vol. 178, Issue 15 https://doi.org/10.1128/jb.178.15.4461-4471.1996	journal	January 1996
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC Li, Mamie Z.; Elledge, Stephen J. Nature Methods, Vol. 4, Issue 3 https://doi.org/10.1038/nmeth1010	journal	February 2007
Method for amplification of nucleic acids in solid media Chetverin, Alexander B.; Chetverina, Helena Vladimirovna https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/5616478 US Patent Document 5,616,478	patent	April 1997
Seamless gene engineering using RNA- and DNA-overhang cloning Coljee, Vincent W.; Murray, Heather L.; Donahue, William F. Nature Biotechnology, Vol. 18, Issue 7 https://doi.org/10.1038/77363	journal	July 2000
In Vivo Gene Transfer Elledge, Stephen J.; Li, Mamie Z. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20030224481 US Patent Application 10/345523; 20030224481	patent-application	December 2003
Yeast artificial chromosomes (YACs) and the analysis of complex genomes Anand, Rakesh Trends in Biotechnology, Vol. 10 https://doi.org/10.1016/0167-7799(92)90165-R	journal	January 1992
Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template Cello, J. Science, Vol. 297, Issue 5583 https://doi.org/10.1126/science.1072266	journal	July 2002
Method of amplifying whole genomes without subjecting the genome to denaturing conditions Dean, Frank B.; Lasken, Roger https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6617137 US Patent Document 6,617,137	patent	September 2003
Biochemical effects of molecular crowding Chebotareva, N. A.; Kurganov, B. I.; Livanova, N. B. Biochemistry (Moscow), Vol. 69, Issue 11 https://doi.org/10.1007/s10541-005-0070-y	journal	November 2004
Method for the complete chemical synthesis and assembly of genes and genomes Evans, Glen A. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6521427 US Patent Document 6,521,427	patent	February 2003
Rolling Circle DNA Synthesis: Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases Liu, Dongyu; Daubendiek, Sarah L.; Zillman, Martin A. Journal of the American Chemical Society, Vol. 118, Issue 7 https://doi.org/10.1021/ja952786k	journal	January 1996
Stimulation of enzymatic ligation of DNA by high concentrations of nonspecific polymers Zimmerman, Steven B.; Pheiffer, Barbara H. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/4582802 US Patent Document 4,582,802	patent	April 1986
Cell-free cloning using φ29 DNA polymerase Hutchison, C. A.; Smith, H. O.; Pfannkoch, C. Proceedings of the National Academy of Sciences, Vol. 102, Issue 48, p. 17332-17336 https://doi.org/10.1073/pnas.0508809102	journal	November 2005
High-throughput, genome-scale protein production method based on the wheat germ cell-free expression system Endo, Yaeta; Sawasaki, Tatsuya Biotechnology Advances, Vol. 21, Issue 8 https://doi.org/10.1016/S0734-9750(03)00105-8	journal	November 2003
Recombinase Polymerase Amplification Piepenburg, Olaf; Williams, Colin H.; Armes, Niall A. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20050112631 US Patent Application 10/931916; 20050112631	patent-application	May 2005
Rolling replication of short DNA circles. Fire, A.; Xu, S. Q. Proceedings of the National Academy of Sciences, Vol. 92, Issue 10 https://doi.org/10.1073/pnas.92.10.4641	journal	May 1995
General Method for Plasmid Construction Using Homologous Recombination Raymond, Christopher K.; Pownder, Tracey A.; Sexson, Shannon L. BioTechniques, Vol. 26, Issue 1 https://doi.org/10.2144/99261rr02	journal	January 1999
Effects of abasic sites and DNA single-strand breaks on prokaryotic RNA polymerases. Zhou, W.; Doetsch, P. W. Proceedings of the National Academy of Sciences, Vol. 90, Issue 14 https://doi.org/10.1073/pnas.90.14.6601	journal	July 1993
Defining the minimal length of sequence homology required for selective gene isolation by TAR cloning Noskov, V. N. Nucleic Acids Research, Vol. 29, Issue 6 https://doi.org/10.1093/nar/29.6.e32	journal	March 2001
In situ localized amplification and contact replication of many individual DNA molecules Mitra, R. Nucleic Acids Research, Vol. 27, Issue 24 https://doi.org/10.1093/nar/27.24.e34	journal	December 1999
Composition and Method for Hot Start Nucleic Acid Amplification Ankenbauer, Waltraud; Heindl, Dieter; Laue, Frank https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20030119150 US Patent Application 10/192902; 20030119150	patent-application	June 2003
Joining of long double-stranded RNA molecules through controlled overhangs Dekker, N. H. Nucleic Acids Research, Vol. 32, Issue 18 https://doi.org/10.1093/nar/gnh138	journal	October 2004
Directional cloning of PCR products using exonuclease III Kaluz, Stefan; Kölble, Konrad; Reid, Kenneth B. M. Nucleic Acids Research, Vol. 20, Issue 16 https://doi.org/10.1093/nar/20.16.4369	journal	January 1992
Method for generating a library of oligonucleotides comprising a controlled distribution of mutations Caldwell, Robert M.; Schellenberger, Volker https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6582914 US Patent Document 6,582,914	patent	June 2003
Convergent DNA synthesis: a non-enzymatic dimerization approach to circular oligodeoxynucleotides Rubin, Ethel; Rumney, Squire; Wang, Shaohui Nucleic Acids Research, Vol. 23, Issue 17 https://doi.org/10.1093/nar/23.17.3547	journal	January 1995
Ligation independent cloning irrespective of restriction site compatibility Li, C. Nucleic Acids Research, Vol. 25, Issue 20 https://doi.org/10.1093/nar/25.20.4165	journal	October 1997
Construction of recombinant DNA by exonuclease recession Yang, Yih-Sheng; Watson, William J.; Tucker, Philip W. Nucleic Acids Research, Vol. 21, Issue 8 https://doi.org/10.1093/nar/21.8.1889	journal	January 1993
T7 Single Strand DNA Binding Protein but Not T7 Helicase Is Required for DNA Double Strand Break Repair Yu, Man; Masker, Warren Journal of Bacteriology, Vol. 183, Issue 6 https://doi.org/10.1128/JB.183.6.1862-1869.2001	journal	March 2001
Evolution of whole cells and organisms by recursive sequence recombination del Cardayre, Stephen; Tobin, Matthew; Stemmer, Willem P. C. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6379964 US Patent Document 6,379,964	patent	April 2002
Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification Dean, F. B. Genome Research, Vol. 11, Issue 6 https://doi.org/10.1101/gr.180501	journal	June 2001
Linker-Mediated Recombinational Subcloning of Large DNA Fragments Using Yeast Raymond, C. K. Genome Research, Vol. 12, Issue 1 https://doi.org/10.1101/gr.205201	journal	January 2002
Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome Gibson, D. G.; Benders, G. A.; Andrews-Pfannkoch, C. Science, Vol. 319, Issue 5867 https://doi.org/10.1126/science.1151721	journal	February 2008
Method for nucleic acid hybridization using single-stranded DNA binding protein Tabor, Stanley; Richardson, Charles C. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/5534407 US Patent Document 5,534,407	patent	July 1996
A mammalian protein complex that repairs double-strand breaks and deletions by recombination Jessberger, R.; Podust, V.; Hübscher, U. Journal of Biological Chemistry, Vol. 268, Issue 20 https://doi.org/10.1016/S0021-9258(18)82439-5	journal	July 1993
Mechanisms of overlap formation in nonhomologous DNA end joining. Pfeiffer, P.; Thode, S.; Hancke, J. Molecular and Cellular Biology, Vol. 14, Issue 2 https://doi.org/10.1128/MCB.14.2.888	journal	February 1994
Single-molecule PCR using water-in-oil emulsion Nakano, Michihiko; Komatsu, Jun; Matsuura, Shun-ichi Journal of Biotechnology, Vol. 102, Issue 2, p. 117-124 https://doi.org/10.1016/S0168-1656(03)00023-3	journal	April 2003
Repair of double-strand breaks by incorporation of a molecule of homologous DNA Lai, Ying-Ta; Masker, Warren Molecular Microbiology, Vol. 36, Issue 2 https://doi.org/10.1046/j.1365-2958.2000.01861.x	journal	April 2000
Method for Preparing Water-Insoluble Alpha-1, 4-Glucans Quanz, Martin; Provart, Nicholas; Banasiak, Ronald https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20020052029 US Patent Application 09/740824; 20020052029	patent-application	May 2002
Isothermal Strand-Displacement Amplification Applications for High-Throughput Genomics Detter, John C.; Jett, Jamie M.; Lucas, Susan M. Genomics, Vol. 80, Issue 6 https://doi.org/10.1006/geno.2002.7020	journal	December 2002
Method for the complete chemical synthesis and assembly of genes and genomes Evans, Glen A. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20030165946 US Patent Application 10/322360; 20030165946	patent-application	September 2003
Nucleic Acid Cloning Jarrell, Kevin A.; Coljee, Vincent W.; Donahue, William https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20050191623 US Patent Application 09/897712; 20050191623	patent-application	September 2005
Compositions and Methods for Reverse Transcription Arezi, Bahram https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20050272074 US Patent Application 11/100183; 20050272074	patent-application	December 2005
Directional cloning Hagen, Frederick S. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/5075227 US Patent Document 5,075,227	patent	December 1991
Heirarchical Assembly Methods For Genome Engineering Church, George; Baynes, Brian M.; Pitcher, Edmund R. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20070004041 US Patent Application 11/331927; 20070004041 A1	patent-application	January 2007
Synthetic genomes Venter, J. Craig; Smith, Hamilton O.; Hutchison, III, Clyde A. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20070264688 US Patent Document 11/635355; 20070264688	patent-application	November 2007
A “Double Adaptor” Method for Improved Shotgun Library Construction Andersson, Björn; Wentland, Meredith A.; Ricafrente, Jennifer Y. Analytical Biochemistry, Vol. 236, Issue 1 https://doi.org/10.1006/abio.1996.0138	journal	April 1996
Essential Amino Acid Residues in the Single-stranded DNA-binding Protein of Bacteriophage T7 Rezende, Lisa F.; Hollis, Thomas; Ellenberger, Tom Journal of Biological Chemistry, Vol. 277, Issue 52 https://doi.org/10.1074/jbc.M207359200	journal	December 2002
A Sequence-Independent Strategy for Detection and Cloning of Circular DNA Virus Genomes by Using Multiply Primed Rolling-Circle Amplification Rector, Annabel; Tachezy, Ruth; Van Ranst, Marc Journal of Virology, Vol. 78, Issue 10 https://doi.org/10.1128/JVI.78.10.4993-4998.2004	journal	May 2004
Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors Burke, D.; Carle, G.; Olson, M. Science, Vol. 236, Issue 4803 https://doi.org/10.1126/science.3033825	journal	May 1987
Synthesis of Error-Minimized Nucleic Acid Molecules Young, Lei https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20070128649 US Patent Application 11/633686; 20070128649	patent-application	June 2007
An improved ligase-free method for directional subcloning of PCR amplified DNA Zhou, Meixia; Hatahet, Zafer Nucleic Acids Research, Vol. 23, Issue 6 https://doi.org/10.1093/nar/23.6.1089	journal	January 1995
Recombineering with overlapping single-stranded DNA oligonucleotides: Testing a recombination intermediate Yu, D.; Sawitzke, J. A.; Ellis, H. Proceedings of the National Academy of Sciences, Vol. 100, Issue 12 https://doi.org/10.1073/pnas.1232375100	journal	May 2003
Visualization of Repair of Double-Strand Breaks in the Bacteriophage T7 Genome without Normal DNA Replication Lai, Ying-Ta; Masker, Warren Journal of Bacteriology, Vol. 182, Issue 2 https://doi.org/10.1128/JB.182.2.327-336.2000	journal	January 2000
From The Cover: Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome Itaya, M.; Tsuge, K.; Koizumi, M. Proceedings of the National Academy of Sciences, Vol. 102, Issue 44 https://doi.org/10.1073/pnas.0503868102	journal	October 2005
Method for In Vitro Recombination Gibson, Daniel Glenn; Smith, Hamilton O. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20070037196 US Patent Application 11/502624; 20070037196	patent-application	February 2007
In Vitro Recombination Method Young, Lei; Smith, Hamilton O.; Gibson, Daniel Glenn https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20070037197 US Patent Application 11/502746; 20070037197	patent-application	February 2007
RecE/RecT and Redα/Redβ initiate double-stranded break repair by specifically interacting with their respective partners Muyrers, Joep P. P.; Zhang, Youming; Buchholz, Fraenk Genes & Development, Vol. 14, Issue 15 https://doi.org/10.1101/gad.14.15.1971	journal	August 2000
Methods and kits for recombining nucleic acids Tseng, Hung-Hsu https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6150111 US Patent Document 6,150,111	patent	November 2000
Microbial Reductase Useful for the Stereoselective Reduction of a Racemic Tetralone Brown, Maria S.; Fedechko, Ronald W.; Wong, John W. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20010044142 US Patent Application 09/834098; 20010044142	patent-application	November 2001
In Vitro Repair of Gaps in Bacteriophage T7 DNA Lai, Ying-Ta; Masker, Warren Journal of Bacteriology, Vol. 180, Issue 23 https://doi.org/10.1128/JB.180.23.6193-6202.1998	journal	December 1998
Efficient Initiation of HCV RNA Replication in Cell Culture Blight, K. J. Science, Vol. 290, Issue 5498 https://doi.org/10.1126/science.290.5498.1972	journal	December 2000
Essential genes of a minimal bacterium Glass, J. I.; Assad-Garcia, N.; Alperovich, N. Proceedings of the National Academy of Sciences, Vol. 103, Issue 2 https://doi.org/10.1073/pnas.0510013103	journal	January 2006
Functional cloning vectors for use in directional cDNA cloning using cohesive ends produced with T4 DNA polymerase Kuijper, Joseph L.; Wiren, Kristine M.; Mathies, Laura D. Gene, Vol. 112, Issue 2 https://doi.org/10.1016/0378-1119(92)90370-5	journal	March 1992
Structure and Function of the Escherichia coli RecE Protein, a Member of the RecB Nuclease Domain Family Chang, Hoshing Wan; Julin, Douglas A. Journal of Biological Chemistry, Vol. 276, Issue 49 https://doi.org/10.1074/jbc.M108627200	journal	December 2001
Rapid generation of long synthetic tandem repeats and its application for analysis in human artificial chromosome formation Ebersole, T.; Okamoto, Y.; Noskov, V. N. Nucleic Acids Research, Vol. 33, Issue 15 https://doi.org/10.1093/nar/gni129	journal	September 2005
Thermostable DNA ligase mutants Barany, Francis; Luo, Jianying; Khanna, Marilyn https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6576453 US Patent Document 6,576,453	patent	June 2003
Cloning of PCR products after defined cohesive termini are created with T4 DNA polymerase Stoker, Andrew W. Nucleic Acids Research, Vol. 18, Issue 14 https://doi.org/10.1093/nar/18.14.4290	journal	January 1990
Bacteriophage T7 Deoxyribonucleic Acid Replication in Vitro Hinkle, David C.; Richardson, Charles C. Journal of Biological Chemistry, Vol. 249, Issue 9 https://doi.org/10.1016/S0021-9258(19)42726-9	journal	May 1974
Efficient total gene synthesis of 1.35-kb hybrid alpha-lytic protease gene using the polymerase chain reaction. Bambot, S. B.; Russell, A. J. Genome Research, Vol. 2, Issue 3 https://doi.org/10.1101/gr.2.3.266	journal	February 1993
Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides Smith, H. O.; Hutchison, C. A.; Pfannkoch, C. Proceedings of the National Academy of Sciences, Vol. 100, Issue 26, p. 15440-15445 https://doi.org/10.1073/pnas.2237126100	journal	December 2003
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Stemmer, Willem P. C.; Crameri, Andreas; Ha, Kim D. Gene, Vol. 164, Issue 1 https://doi.org/10.1016/0378-1119(95)00511-4	journal	October 1995

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