Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
2007-10-30
2010-10-05
Chunduru, Suryaprabha (Department: 1637)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C530S350000
Reexamination Certificate
active
07807806
ABSTRACT:
The present invention provides novel cleavage agents and polymerases for the cleavage and modification of nucleic acid. The cleavage agents and polymerases find use, for example, for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. In some embodiments, the 5′ nuclease activity of a variety of enzymes is used to cleave a target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.
REFERENCES:
patent: 5244797 (1993-09-01), Kotewicz et al.
patent: 5268289 (1993-12-01), Dahl et al.
patent: 5459055 (1995-10-01), Jendrisak et al.
patent: 5466591 (1995-11-01), Abramson et al.
patent: 5500370 (1996-03-01), Jendrisak et al.
patent: 5541311 (1996-07-01), Dahlberg et al.
patent: 5614402 (1997-03-01), Dahlberg et al.
patent: 5795762 (1998-08-01), Abramson et al.
patent: 5795763 (1998-08-01), Dahlberg et al.
patent: 5837450 (1998-11-01), Brow et al.
patent: 5837458 (1998-11-01), Minshull et al.
patent: 5843669 (1998-12-01), Kaiser et al.
patent: 5846717 (1998-12-01), Prudent et al.
patent: 5874283 (1999-02-01), Harrington et al.
patent: 5972603 (1999-10-01), Tabor et al.
patent: 5985557 (1999-11-01), Prudent et al.
patent: 5994069 (1999-11-01), Hall et al.
patent: 6001567 (1999-12-01), Brow et al.
patent: 6090606 (2000-07-01), Kaiser et al.
patent: 7150982 (2006-12-01), Allawi et al.
patent: 0892058 (1999-01-01), None
patent: WO97/27214 (1997-07-01), None
patent: WO98/23774 (1998-06-01), None
patent: WO 98/27230 (1998-06-01), None
patent: WO 98/31837 (1998-07-01), None
patent: WO98/42873 (1998-10-01), None
patent: WO 99/65927 (2000-01-01), None
patent: WO 00/18906 (2000-04-01), None
patent: WO01/01823 (2001-01-01), None
patent: WO01/90337 (2001-11-01), None
Beese, et al. “Structure of DNA polymerase I Klenow fragment bound to duplex DNA” Science. Apr. 16, 1993;260 (5106):352-5.
Brautigam, et al. “Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes” Curr Opin Struct Biol. Feb. 1998;8(1):54-63.
Ceska, et al. “A helical arch allowing single-stranded DNA to thread through T5 5′-exonuclease” Nature. Jul. 4, 1996;382(6586):90-3.
Database UNIPROT Accession No. O08307.
Database UNIPROT Accession No. P52028.
Del Rio, et al. “Combinatorial libraries of proteins: analysis of efficiency of mutagenesis techniques” Biotechniques. Dec. 1994;17(6):1132-9.
Doherty, et al. “The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA” Nucl. Acid. Res. 24, pp. 2488-2497 (1996).
Doty, et al. “strand separation and specific recombination in deoxyribonucleic acids: physical chemical studies” Proc Natl Acad Sci U S A. Apr. 1960;46(4):461-76.
Doublie, et al. “Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution” Nature. Jan. 15, 1998;391(6664):251-8.
Engelke, et al. “Purification of Thermus aquaticus DNA polymerase expressed inEscherichia coli” Anal Biochem. Dec. 1990;191(2):396-400.
Eom, et al. “Structure of Taq polymerase with DNA at the polymerase active site” Nature. Jul. 18, 1996;382 (6588):278-81.
Grant, et al. “Expression of cytokine messenger RNA after heart transplantation: relationship with rejection and serum cytokines” Transplantation. Oct. 15, 1996;62(7):910-6.
Guidotti, et al. “Intracellular inactivation of the hepatitis B virus by cytotoxic T lymphocytes” Immunity. Jan. 1996;4 (1):25-36.
Hall, et al. “Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction” Proc Natl Acad Sci U S A. Jul. 18, 2000 vol. 97(15):8272-7.
Higuchi in PCR Technology H. A. Erlich ed. Stockton Press New York. pp. 6170 (1989).
Holm, et al. “Mapping the protein universe” Science. Aug. 2, 1996;273(5275):595-603.
Holm, et al. “Protein structure comparison by alignment of distance matrices” J Mol Biol. Sep. 5, 1993;233(1):123-38.
Hwang, et al. “The crystal structure of flap endonuclease-1 fromMethanococcus jannaschii” Nat Struct Biol. Aug. 1998;5(8):707-13.
Johnson, et al. “Requirement of the yeast RTH1 5′ to 3′ exonuclease for the stability of simple repetitive DNA” Science. Jul. 14, 1995;269(5221):238-40.
Joyce, et al. “DNA polymerase I: from crystal structure to function via genetics” Trends in Biochemical Science 12:288 (1987).
Kaiser, et al. “A comparison of eubacterial and archaeal structure-specific 5′-exonucleases” J. Biol. Chem. 274:21387 (1999).
Kiefer, et al. “Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal” Nature. Jan. 15, 1998;391(6664):304-7.
Kim, et al. “Crystal structure of Thermus aquaticus DNA polymerase” Nature. Aug. 17, 1995;376(6541):612-6.
Korolev, et al. “Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability” Proc Natl Acad Sci U S A. Sep. 26, 1995;92(20):9264-8.
Kwiatkowski, et al. “Clinical, genetic, and pharmacogenetic applications of the Invader assay” Molec. Diagn. 4:353-64 (1999).
Li, et al. “Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation” EMBO J. Dec. 15, 1998;17 (24):7514-25.
Li, et al. “Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates” Protein Sci. May 1998;7(5):1116-23.
Lyamichev, et al. “Comparison of the 5′ nuclease activities of taq DNA polymerase and its isolated nuclease domain” Proc Natl Acad Sci U S A. May 25, 1999;96(11):6143-8.
Lyamichev, et al. “Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes” Nat. Biotechnol. 17:292-6 (1999).
Lyamichev, et al. “Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases” Science 260:778-83 (1993).
Ma, et al. “RNA template-dependent 5′ nuclease activity ofThermus acquaticusandThermus thermophilusDNA polymerases” J. Biol. Chem., vol. 275, No. 32, pp. 24693-24700.
Marmur, et al. “Strand separation and specific recombination in deoxyribonucleic acids: biological studies” Proc Natl Acad Sci U S A. Apr. 1960;46(4):453-61.
May, et al. “Anti-beta-interferon antibodies inhibit the increased expression of HLA-B7 mRNA in tumor necrosis factor-treated human fibroblasts: structural studies of the beta 2 interferon involved” Proc Natl Acad Sci U S A. Dec. 1986;83 (23):8957-61.
Mellors, et al. “Prognosis in HIV-1 infection predicted by the quantity of virus in plasma” Science. May 24, 1996;272 (5265):1167-70.
Minnick, et al. “A thumb subdomain mutant of the large fragment ofEscherichia coliDNA polymerase I with reduced DNA binding affinity, processivity, and frameshift fidelity” J Biol Chem. Oct. 4, 1996;271(40):24954-61.
Mullis,et al. “Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction” Methods Enzymol. 1987;155:335-50.
Myers, et al. “Reverse transcription and DNA amplification by aThermus thermophilusDNA polymerase” Biochemistry. Aug. 6, 1991;30(31):7661-6.
Nielsen, et al. “Peptide nucleic acids (PNAs): potential antisense and anti-gene agents” Anticancer Drug Des. Feb. 1993;8(1):53-63.
Ollis, et al. “Structure of large fragment ofEscherichia coliDNA polymerase I complexed with dTMP” Nature. Feb. 28-Mar. 6, 1985;313(6005):762-6.
Pandey, et al. “Site directed mutagenesis of DNA polymerase I (Klenow) fromEscherichia coli. The significance of Arg682 in catalysis&
Allawi Hatim T.
Argue Brad T.
Bartholomay Christian Tor
Chehak LuAnne
Curtis Michelle L.
Casimir Jones S.C.
Chunduru Suryaprabha
Third Wave Technologies Inc.
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