Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Preparing compound containing saccharide radical
Reexamination Certificate
2007-06-25
2010-11-16
Lu, Frank W (Department: 1634)
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Preparing compound containing saccharide radical
C435S006120, C435S091100, C536S023100, C536S024300, C536S024330, C536S025300
Reexamination Certificate
active
07833759
ABSTRACT:
We describe here an in vitro method of increasing complementarity in a heteroduplex polynucleotide sequence. The method uses annealing of opposite strands to form a polynucleotide duplex with mismatches. The heteroduplex polynucleotide is combined with an effective amount of enzymes having strand cleavage activity, 3′ to 5′ exonuclease activity, and polymerase activity, and allowing sufficient time for the percentage of complementarity to be increased within the heteroduplex. Not all heteroduplex polynucleotides will necessarily have all mismatches resolved to complementarity. The resulting polynucleotide is optionally ligated. Several variant polynucleotides result. At sites where either of the opposite strands has templated recoding in the other strand, the resulting percent complementarity of the heteroduplex polynucleotide sequence is increased. The parent polynucleotides need not be cleaved into fragments prior to annealing heterologous strands. Therefore, no reassembly is required.
REFERENCES:
patent: 4994368 (1991-02-01), Goodman et al.
patent: 5459039 (1995-10-01), Modrich et al.
patent: 5556747 (1996-09-01), Kumar
patent: 5679522 (1997-10-01), Modrich et al.
patent: 5683877 (1997-11-01), Lu-Chang et al.
patent: 5723323 (1998-03-01), Kauffman et al.
patent: 5795747 (1998-08-01), Henco et al.
patent: 5861482 (1999-01-01), Modrich et al.
patent: 5869245 (1999-02-01), Yeung
patent: 5922539 (1999-07-01), Modrich et al.
patent: 6057103 (2000-05-01), Short
patent: 6165793 (2000-12-01), Stemmer
patent: 6376246 (2002-04-01), Crameri et al.
patent: 6391557 (2002-05-01), Yeung
patent: 6537746 (2003-03-01), Arnold et al.
patent: 6783941 (2004-08-01), Vind
patent: 6821758 (2004-11-01), Koltermann
patent: 6846655 (2005-01-01), Wagner et al.
patent: 7056740 (2006-06-01), Padgett et al.
patent: 7217514 (2007-05-01), Padgett et al.
patent: 7235386 (2007-06-01), Padgett et al.
patent: 2002/0045175 (2002-04-01), Wang et al.
patent: 2003/0017477 (2003-01-01), Vind
patent: 2004/0048268 (2004-03-01), Delcourt et al.
patent: 4112440 (1992-10-01), None
patent: 19953854 (2001-05-01), None
patent: 2789696 (2000-08-01), None
patent: WO 92/18645 (1992-10-01), None
patent: WO 93/20233 (1993-10-01), None
patent: WO 96/40902 (1996-12-01), None
patent: WO 97/37011 (1997-10-01), None
patent: WO 97/46701 (1997-12-01), None
patent: WO 99/28451 (1999-06-01), None
patent: WO 99/29902 (1999-06-01), None
patent: WO 00/71730 (2000-11-01), None
patent: WO 01/34835 (2001-05-01), None
patent: WO 01/62974 (2001-08-01), None
patent: WO 02/24953 (2002-03-01), None
patent: WO 02/079468 (2002-10-01), None
patent: WO 2004/035771 (2004-04-01), None
Abastado, et al., “Processing of complex heteroduplexes inEscherichia coliandCos-1 monkey cells”,Proc. Natl. Acad. Sci. USA, Sep. 1984, vol. 81, pp. 5792-5796.
Cami, et al., “Correction of complex heteroduplexes made of mouse H-2 gene sequences inEscherichia coliK-12”,Proc. Natl. Acad. Sci. USA, Jan. 1984, vol. 81, pp. 503-507.
Chang, et al., “Recombination following transformation ofEscherichia coliby heteroduplex plasmid DNA molecules”,Gene, 1984, vol. 29, pp. 255-261, Elsevier.
Cotton, “Slowly but surely towards better scanning for mutations”,TIG, Feb. 1997, vol. 13, No. 2, pp. 43-46, Elsevier Science Ltd.
Joyce, “Directed Molecular Evolution”,Scientific American, Dec. 1992, pp. 90-97.
Kulinski, et al., “CEL I Enzymatic Mutation Detection Assay”,Biotechniques, Jul. 2000, vol. 29, pp. 44-48.
Lahue, et al., “Requirement for d(GATC) sequences inEscherichia coli mutHLSmismatch correction”,Proc. Natl. Acad. Sci. USA, Mar. 1987, vol. 84, pp. 1482-1486.
Modrich, “Strand-specific Mismatch Repair in Mammalian Cells”,The Journal of Biological Chemistry, Oct. 3, 1997, vol. 272, No. 4, pp. 24727-24730, The American Society of for Biochemistry and Molecular Biology, Inc., Bethesda, MD.
Oleykowski, et al., “Mutation detection using a novel plant endonuclease”,Nucleic Acids Research, 1998, vol. 26, No. 20, pp. 4597-4602, Oxford University Press, United Kingdom.
Oleykowski, et al., “Incision at Nucleotide Insertions/Deletions and Base Pair Mismatches by the SP Nuclease of Spinach”,Biochemistry, 1999, vol. 38, pp. 2200-2205, American Chemical Society. Columbus. OH.
Robertson, “Directed evolution patent could have major impact”,Nature Biotechnology, May 1998, vol. 16, p. 411.
Solaro, et al., “Endonuclease VII of Phage T4 Triggers Mismatch Correction in Vitro”,J. Mol. Biol., 1993, vol. 230, pp. 868-877, Academic Press Limited.
Volkov, et al., “Random Chimeragenesis by Heteroduplex Recombination”,Methods in Enzymology, 2000, vol. 328, pp. 456-463, Academic Press.
Volkov, et al., “Recombination and chimeragenesis by in vitro heteroduplex formation and in vivo repair”,Nucleic Acids Research, 1999, vol. 27, No. 18, pp. e18 (i-vi), Oxford Univeristy Press.
Yang, et al., “Purification, Cloning, and Characterization of the CEL I Nuclease”,Biochemistry, 2000, vol. 39, pp. 3533-3541, American Chemical Society.
Birkenkamp and Kemper, “In vitro processing of heteroduplex loops and mismatches by Endonuclease VII”,DNA Research, 1995, vol. 2, pp. 9-14.
Biswas and Hsieh, “Identification and characterization of a thermostable MutS homolog fromThermus aquaticus”, J. Biol. Chem. (1996) 271(9):5040-5048.
Kraemer and Digiovanna, “Topical enzyme therapy for skin diseases?”,J. Am. Acad. Dermatol. (2002) 46:463-6.
O'Grady, et al., “DNA repair in thermophiles: investigation of DNA-binding activities inThermus aquaticus”, Biochem. Soc. Tranactions (1997) 25:319-22.
Sugahara, et al., “Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile,Thermus thermophilusHB8”,EMBO J(2000) 19(15):3857-3869.
Wang, “Creating hybrid genes by homologous recombination”,Disease Markers(2000) 16:3-13.
Fishel, R. and R. Kolodner, Gene conversion in Escherichia coli: the recF pathway for resolution of heteroduplex DNA. J Bacteriol, 1989. 171(6): p. 3046-52.
Fishel, R.A. and R. Kolodner, An Escherichia coli cell-free system that catalyzes the repair of symmetrically methylated heteroduplex DNA. Cold Spring Harb Symp Quant Biol, 1984. 49: p. 603-9.
Glaser, P.M., et al., DNA mismatch repair detected in human cell extracts. Mol Cell Biol, 1987. 7(1): p. 218-24.
Paabo, S., D.M. Irwin, and A.C. Wilson, DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem, 1990. 265(8): p. 4718-21.
Su, S.S., et al., Mispair specificity of methyl-directed DNA mismatch correction in vitro. J Biol Chem, 1988. 263(14): p. 6829-35.
Sung, W.L., et al., Simultaneous synthesis of human-, mouse- and chimeric epidermal growth factor genes via ‘hybrid gene synthesis’ approach. Nucleic Acids Res, 1986. 14(15): p. 6159-68.
Weber, H. and C. Weissmann, Formation of genes coding for hybrid proteins by recombination between related, cloned genes in E. coll. Nucleic Acids Res, 1983. 11(16): p. 5661-9.
Borts, R.H. and Haber, J.E., “Meiotic Recombination in Yeast: Alteration by Multiple Heterozygosities”, Science 237 (1987) 1459-1465.
Wagner et al., “Involvement of Escherichia coli Mismatch Repair in DNA Replication and Recombination”, Cold Spring Harb Symp Quant Biol 49 (1984) 611-615.
Doutriaux et al., “Mismatch-stimulated Killing”, Proc Natl Acad Sci USA 83 (1986) 2576-2578.
Fitzmaurice Wayne P.
Lindbo John A.
Padgett Hal S.
Fitzmaurice Wayne P.
Lu Frank W
Novici Biotech LLC
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