RNA detection assays

Chemistry: natural resins or derivatives; peptides or proteins; – Proteins – i.e. – more than 100 amino acid residues

Reexamination Certificate

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C435S069100

Reexamination Certificate

active

08063184

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: 6228628 (2001-05-01), Gelfand 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
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 from Methanococcus 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 of Thermus acquaticus and Thermus thermophilus DNA polymerases” J. Biol. Chem., 2000, 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. “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 a Thermus thermophilus DNA 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” Eur J Biochem. May 15, 1993;214(1):59-65.
Patel, et al. “DNA polymerase active site is highly mutable: Evolutionary consequences” PNAS, vol. 97 No. 10, pp. 5095-5100 (2000).
Pelletier, et al. “Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP” Science. Jun. 24, 1994;264(5167):1891-903.
Perenboom, et al. “Cytokine profiles in bronchoalveolar lavage fluid and blood in HIV-seronegative patients with Pneumocystis carinii pneumonia” Eur J Clin Invest. Feb. 1996;26(2)159-66
Polesky, et al. “Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I fromEscherichia coli” J Biol Chem. Aug. 25, 1990;265(24):14579-91.
Polesky, et al. “Side chains involved in catalysis of the polymerase reaction of DNA polymerase I fromEscherichia coli” J Biol Chem. Apr. 25, 1992;267(12):8417-28.
Saag, et al. “HIV viral load markers in clinical practice” Nature Medicine 2:625-9 (1996).
Saiki, et al. “Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia” Science. Dec. 20, 1985;230(4732):1350-4.
Sambrook, et al. “Molecular Cloning” Cold Spring Harbor Laboratory Press Cold Spring Harbor pp. 1.63-1.69 (1989).
Stark “Multicopy expression vectors carrying the lac repressor gene for regulated high-level expression of genes inEscherichia coli” Gene. 1987;51(2-3):255-67.
Studier, et al. “Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes” J Mol Biol. May 5, 1986;189(1):113-30.
Urs, et al. “Structure of tag DNA polymerase shows a new orientation for the structure-specific nuclease domain” Acta Crystallogr D Biol Crystallogr. Dec. 1999;55(Pt 12):1971-7.
Van Deuren, et al. “Cytokine production in whole blood cultures” J. Int. Fed. Clin. Chem. 5:216 (1993).
Van Deuren, et al. “Differential expression of proinflammatory cytokines a

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