Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2007-03-27
2007-03-27
Kim, Young J. (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091100, C435S091200
Reexamination Certificate
active
10290386
ABSTRACT:
The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. For example, in some embodiments, a 5′ nuclease activity from any of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.
REFERENCES:
patent: 4511502 (1985-04-01), Builder et al.
patent: 4511503 (1985-04-01), Olson et al.
patent: 4512922 (1985-04-01), Jones et al.
patent: 4518526 (1985-05-01), Olson
patent: 4683194 (1987-07-01), Saiki et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis
patent: 4775619 (1988-10-01), Urdea
patent: 4818680 (1989-04-01), Collins et al.
patent: 4876187 (1989-10-01), Duck et al.
patent: 5001050 (1991-03-01), Blanco et al.
patent: 5011769 (1991-04-01), Duck et al.
patent: 5030557 (1991-07-01), Hogan et al.
patent: 5108892 (1992-04-01), Burke et al.
patent: 5118605 (1992-06-01), Urdea
patent: 5124246 (1992-06-01), Urdea et al.
patent: 5144019 (1992-09-01), Rossi
patent: 5198543 (1993-03-01), Blanco et al.
patent: 5210015 (1993-05-01), Gelfand et al.
patent: 5248618 (1993-09-01), Haces
patent: 5288609 (1994-02-01), Engelhardt et al.
patent: 5380833 (1995-01-01), Urdea
patent: 5403711 (1995-04-01), Walder et al.
patent: 5407795 (1995-04-01), Kolberg et al.
patent: 5409818 (1995-04-01), Davey et al.
patent: 5422253 (1995-06-01), Dahlberg et al.
patent: 5427930 (1995-06-01), Birkenmeyer et al.
patent: 5487972 (1996-01-01), Geland et al.
patent: 5494810 (1996-02-01), Barany et al.
patent: 5541311 (1996-07-01), Dahlberg et al.
patent: 5545729 (1996-08-01), Goodchild et al.
patent: 5601976 (1997-02-01), Yamane et al.
patent: 5614402 (1997-03-01), Dahlberg et al.
patent: 5624802 (1997-04-01), Urdea et al.
patent: 5660988 (1997-08-01), Duck et al.
patent: 5691142 (1997-11-01), Dahlberg et al.
patent: 5698400 (1997-12-01), Cotton et al.
patent: 5710264 (1998-01-01), Urdea et al.
patent: 5719028 (1998-02-01), Dahlberg et al.
patent: 5783392 (1998-07-01), Seibl et al.
patent: 5792614 (1998-08-01), Western et al.
patent: 5795763 (1998-08-01), Dahlberg et al.
patent: 5830664 (1998-11-01), Rosemeyer et al.
patent: 5837450 (1998-11-01), Dahlberg et al.
patent: 5843654 (1998-12-01), Heisler et al.
patent: 5843669 (1998-12-01), Kaiser et al.
patent: 5846717 (1998-12-01), Brow et al.
patent: 5849481 (1998-12-01), Urdea et al.
patent: 5851770 (1998-12-01), Babon et al.
patent: 5874283 (1999-02-01), Harrington et al.
patent: 5882867 (1999-03-01), Ullman et al.
patent: 5888780 (1999-03-01), Dahlberg et al.
patent: 5914230 (1999-06-01), Liu et al.
patent: 5958692 (1999-09-01), Cotton 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: 6013170 (2000-01-01), Meade
patent: 6063573 (2000-05-01), Kayyem
patent: 6110677 (2000-08-01), Western et al.
patent: 6110684 (2000-08-01), Kemper et al.
patent: 6121001 (2000-09-01), Western et al.
patent: 6150097 (2000-11-01), Tyagi et al.
patent: 6183960 (2001-02-01), Lizardi
patent: 6210884 (2001-04-01), Lizardi
patent: 6221583 (2001-04-01), Kayyem et al.
patent: 6235502 (2001-05-01), Weissman et al.
patent: 6248229 (2001-06-01), Meade
patent: 6291187 (2001-09-01), Kingsmore et al.
patent: 6323009 (2001-11-01), Lasken et al.
patent: 0 411 186 (1991-02-01), None
patent: 0 482 714 (1991-10-01), None
patent: 89/09284 (1989-10-01), None
patent: 90/01069 (1990-02-01), None
patent: 90/15157 (1990-12-01), None
patent: 91/09950 (1991-07-01), None
patent: 92/02638 (1992-02-01), None
patent: 92/06200 (1992-04-01), None
patent: 94/29482 (1994-12-01), None
patent: 95/14106 (1995-05-01), None
patent: 96/20287 (1996-07-01), None
patent: 96/40999 (1996-12-01), None
patent: WO 01/88190 (2001-11-01), None
patent: WO 02/00934 (2002-01-01), None
Abrams et al., “Comprehensive Detection of Single Base Changes in Human Genomic DNA Using Denaturing Gradient Electrophoresis and a GC Clamp,”Genomics7:463-475 (1990).
Akhmetzjanov and Vakhitov, “Molecular cloning and nucleotide sequence of the DNA polymerase gene fromThermus flavus,” Nucl. Acids Res. 20:5839 (1992).
Altamirano et al., “Identification of Hepatitis C Virus Genotypes among Hospitalized Patients in British Columbia, Canada,”J. Infect. Dis. 171:1034-1038 (1995).
Anderson and Young, “Quantitative Filter Hybridization”,in Nucleic Acid Hybridization, Eds Hames & Higgins, IRL Press, Washington, DC, pp. 73-111 (1985).
Electrophoresis, 2nd Edition, ed. Anthony T. Andrews, Clarendon Press, New York, New York (1986), pp. 153-154.
Antao et al. “A thermodynamic study of unusually stable RNA and DNA hairpins,”Nucl. Acids Res. 19:5901-5905 (1991).
Bambara et al., “Enzymes and Reactions at the Eukaryotic DNA Replication Fork,”J. Biol. Chem. 272:4647-4650 (1997).
Barany, “Genetic disease detection and DNA amplification using cloned thermostable ligase,”Proc. Natl. Acad. Sci., 88:189-193 (1991).
Barany, “The Ligase Chain Reaction in a PCR World,”PCR Methods and Applic., 1:5-16 (1991).
Bardwell et al., “Specific Cleavage of Model Recombination and Repair Intermediates by the Yeast Rad1-Rad10 DNA Endonuclease,”Science265:2082-2085 (1994).
Barnes et al., “Mechanism of Tracking and Cleavage of Adduct-damaged DNA Substrates by the Mammalian 5′-to3′Exonuclease/Endonuclease RAD2 Homologue 1 or Flap Endonuclease 1”,J. Biol. Chem. 271:29624-29632 (1996).
Bergseid et al., “A High Fidelity Thermostable DNA Polymerase Isolated fromPyrococcus furiosus,” Strategies4:34-35 (1991).
Bhagwat et al., “The 5′-Exonuclease Activity of Bacteriophage T4 RNase H is Stimulated by the T4 Gene 32 Single-stranded DNA-binding Protein, but Its Flap Endonuclease Is Inhibited,”J. Biol. Chem.272:28523-28530 (1997).
Bonch-Osmolovskaya, et al.,Microbiology(Engl. Transl. of Mikrobiologiya) 57:78-85 (1988).
Brutlag et al., “An Active Fragment of DNA Polymerase Produced By Proteolytic Cleavage,”Biochem. Biophys. Res. Commun.37:982-989 (1969).
Brow et al., “Differentiation of Bacterial 16S rRNA Genes and Intergenic Regions andMycobacterium tuberculosis katGGenes by Structure-Specific Endonuclease Cleavage,”J. of Clin. Micro.34:3129-3137 (1996).
Carballeira et al., “Purification of a Thermostable DNA Polymerase fromThermus thermophilusHB8, Useful in the Polymerase Chain Reaction,”Biotechniques9:276-281 (1990).
Ceska et al., “A helical arch allowing single-stranded DNA to thread through T5 5′-exonuclease,”Nature382:90-93 (1996).
Ceska et al., “Structure-specific DNA cleavage by 5′ nucleases,”TIPS 23(1998).
Copley and Boot, “Exonuclease Cycling Assay: An Amplified Assay for the Detection of Specific DNA Sequences,”BioTechniques13:888-891 (1992).
Cuthbert, “Hepatitis C:Progress and Problems,”Clin. Microbiol. Rev.7:505-532 (1994).
DeMott et al., “Human RAD2 Homolog 1 5′-3′-Exo/Endonuclease Can Efficiently Excise a Displaced DNA Fragment Containing a 5′-Terminal Abasic Lesion by Endonuclease Activity,”J. Biol. Chem.271:30068-30076 (1996).
Doty et al., “Strand Separation and Specific Recombination in Deoxyribonucleic Acids: Physical Chemical Studies,”Proc. Natl. Acad. Sci. USA46:461-476 (1960).
Duck et al., “Probe Amplifier System Based on Chimeric Cycling Oligonucleotides,”BioTech., 9:142-147 (1990).
Dunn et al., “Complete Nucleotide Sequence of Bacteriophage T7 DNA and the Locations of T7 Genetic Elements,”J. Mol. Biol.166:477-535 (1983).
Engelke, “Purification ofThermus aquaticusD
Hall Jeff
Lukowiak Andrew A.
Lyamichev Victor
Neri Bruce P.
Kim Young J.
Medlen & Carroll LLP
Third Wave Technologies, Inc
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