Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2000-12-08
2008-10-07
Benzion, Gary (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091100, C435S091200
Reexamination Certificate
active
07432048
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 solid support 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: 5011769 (1991-04-01), Duck et al.
patent: 5118605 (1992-06-01), Urdea
patent: 5210015 (1993-05-01), Gelfand et al.
patent: 5403711 (1995-04-01), Walder et al.
patent: 5422253 (1995-06-01), Dahlberg et al.
patent: 5424186 (1995-06-01), Fodor et al.
patent: 5472881 (1995-12-01), Beebe et al.
patent: 5516663 (1996-05-01), Backman et al.
patent: 5541311 (1996-07-01), Dahlberg et al.
patent: 5609907 (1997-03-01), Natan
patent: 5614402 (1997-03-01), Dahlberg et al.
patent: 5691142 (1997-11-01), Dahlberg et al.
patent: 5719028 (1998-02-01), Dahlberg et al.
patent: 5744305 (1998-04-01), Fodor et al.
patent: 5795763 (1998-08-01), Dahlberg et al.
patent: 5807682 (1998-09-01), Grossman 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: 5874283 (1999-02-01), Harrington et al.
patent: 5882867 (1999-03-01), Ullman et al.
patent: 5888780 (1999-03-01), Dahlberg 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: 6060288 (2000-05-01), Adams et al.
patent: 6090543 (2000-07-01), Prudent et al.
patent: 6090606 (2000-07-01), Kaiser et al.
patent: 6280950 (2001-08-01), Lipshutz et al.
patent: 6348314 (2002-02-01), Prudent et al.
patent: 6372424 (2002-04-01), Brow et al.
patent: 6372813 (2002-04-01), Johnson et al.
patent: 6375903 (2002-04-01), Cerrina et al.
patent: 6458535 (2002-10-01), Hall et al.
patent: 6500622 (2002-12-01), Bruchez, Jr. et al.
patent: 6692917 (2004-02-01), Neri et al.
patent: 6872816 (2005-03-01), Hall et al.
patent: 6875572 (2005-04-01), Prudent et al.
patent: 2002/0187486 (2002-12-01), Hall et al.
patent: 2002/0197623 (2002-12-01), Prudent et al.
patent: 2003/0096245 (2003-05-01), Prudent et al.
patent: 94/29482 (1994-12-01), None
patent: 95/11995 (1995-05-01), None
patent: 97/27214 (1997-07-01), None
patent: 99/42813 (1999-08-01), None
patent: 02/04597 (2002-01-01), None
Ryan et al. Molecular Diagnosis vol. 4:135-144. 1999.
Shen et al. TIBS. 1998.
Drmanac et al., Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nature Biotechnology, 16:54 (1998].
Chee et al., Science, 274:610 [1996].
Sosnowski et al., PNAS, 94:1119 [1997].
Pastinen et al., Genome Research, 7:606 [1997].
Shuber et al., Human Molecular Genetics, 6:337 [1997].
Kwok et al., Nuc. Acid. Res., 18:999 [1990].
Landegren et al., Science, 241:1077 [1988].
Livak et al., PCR Methods and Applications, 4:357 [1995].
Shafer et al., J. clinical Microbiology, 34:1849 [1996].
Wang et al., Science, 280:1077 [1998].
Collins et al., Science, 278:1580 [1997].
Chernukhin and Klenova, Anal. Biochem., 280:178 [2000].
Bilkova et al., J. Chromatogr. A, 852:141 [1999].
Guo et al., Nucleic Acids Res., 22:5456 [1994].
Maskos and Southern, Nucleic Acids Res., 20:1679 [1992].
Frutos et al., Nuc. Acid. Res., 25:4748 [1997].
Frey and Corn, Analytical Chem. 68-3187 (1996).
Jordan et al., Analytical Chem. 694939 [1997].
Shchepinov et al., Nucleic Acids Research 25: 1155 [1997].
Ostroff et al., Cleinical Chem., 45:1659 [1999].
Bambara et al., “Enzymes and Reactions at the Eukaryotic DNA Replication Fork,”J. Biol. Chem.272:4647-4650 (1997.
Harrington et al., “DNA Structural Elements Required for FEN-1 Binding,”J. Biol. Chem.270:4503-4508 (1995).
Harrington et al., “The characterization of a mammalian DNA structure-specific endonuclease,”EMBO Journ.13:1235-1246 (1994).
Harrington and Lieber, “Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair,”Genes and Develop. 8:1344-1355 (1994).
Lyamichev et al.“Structure-Specific Endonucleolytic Cleavage of Nucleic Acids by Eubacterial DNA Polymerases,”Science260:778-783 (1993).
Murante et al., “Calf 5′ to 3′ Exo/Endonuclease Must Slide from a 5′ End of the Substrate to Perform Structure-specific Cleavage,”J. Biol. Chem. 270:30377-30383 (1995).
Murante et al., “The Calf 5′- to 3′-Exonuclease Is Also an Endonuclease with Both Activities Dependent on Primers Annealed Upstream of the Point of Cleavage,”J. Biol. Chem. 269:1191-1196 (1994).
Hessner et al., Genotyping of Factor V G1691A (Leiden) without the Use of PCR by Invasive Cleavage of Oligonucleotide Probes,Clinical Chemistry46:1051-1056 (2000).
Lyamichev et al., Experimental and Theoretical Analysis of the Invasive Signal Amplification Reaction,Biochemistry39:9523-9532 (2000).
Neri et al., Transferring Automation for Large-scale Development and Production of Invader™ SNP Assays,Progress in Biomedical Optics1:117-125 (2000).
Newlin et al., The Invader Assay: An Alternative To PCR-Based Testing For The Detection Of Point Mutations Associated With Venous Thrombosis,Clinical Hemostasis Review, 14:10-12 (2000).
Hall et al., Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction, PNAS 97:8272-8277 (2000).
Ledford et al., A Multi-Site Study for Detection of the Factor V (Leiden) Mutation from Genomic DNA Using Homogeneous Invader Microtiter Plate Fluorescence Resonance Energy Transfer (FRET) Assay,J. Molecular Diagnostics2:97-104 (2000).
Ma et al., RNA Template-dependent 5′ Nuclease Activity ofThermus aquaticusandThermus thermophilusDNA Polymerases,J. Biol. Chem., 275:24693-24700 (2000).
Fors et al., Large-scale SNP scoring from unamplified genomic DNA,Pharmacogenomics1(2):219-229 (2000).
Agarwal et al., Comparison Study For Identifying Promoter Allelic Polymorphism in Interleukin 10 and Tumor Necrosis Factor á Genes,Diagn Mol Pathol9(3):158-164 (2000).
Cooksey et al., Evaluation of the Invader Assay, a Linear Signal Amplification Method, for Identification of Mutation Associated with Resistance to Rifampin and Isoniazid inMycobacterium tuberculosis, Antimicrobial Agents and Chemotherapy, 44:1296-1301 (2000).
Mein et al., Evaluation of Single Nucleotide Polymorphism Typing with Invader or PCR Amplicons and Its Automation,Genome Research10:330-343 (2000).
Lieder, Excitement Builds in Molecular Biology,Advance for Administrators of the Laboratory50-52 (1999).
Lieder, Invader Technology Provices Alternative to PCR,Advance for Administrators of the Laboratory, 70-71 (2000).
Treble et al., Invader ? technology for SNP detection,Gene&Medicine4:68-72 (2000).
Kwiatkowski et al., Clinical, Genetic, and Pharmacogenetic Applications of the Invader Assay,Molecular Diagnosis, 4:353-364 (1999).
Check, Labs home in on mutant alleles,College of American Pathologists Today, 1-5 Sep. 1999.
Griffin et al., Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry,PNAS96:6301-6306 (1999).
Ryan et al., Non-PCR-Dependent Detection of the Factor V Leiden Mutation From Genomic DNA Using a Homogeneous Invader Microtiter Plate Assay,Molecular Diagnosis, :135-144 (1999).
Kaiser et al., A Comparison of Eubacterial and Archaeal Structure-specific 5′-Exonucleases,J. Biol. Chem., 274:21387-21394 (1999).
Lyamichev et al., Polymorphism indentification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes,Nature Biotech. 17:292-296-(1999).
Harrington, The Characterization of the Fen-1 Family of Structure-Specific Endonucleases: Im
Hall Jeff G.
Lyamichev Victor
Neri Bruce P.
Smith Lloyd M.
Benzion Gary
Calamita Heather G.
Casimir Jones S.C.
Third Wave Technologies Inc.
LandOfFree
Reactions on a solid surface does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Reactions on a solid surface, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Reactions on a solid surface will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4008089