Methods of detecting an amplified nucleic acid

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(12) United States Patent

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(io) Patent No.: (45) Date of Patent:

US 7,846,661 B2 *Dec. 7, 2010

5,403,711 A 4/1995 Walder

5,422,253 A 6/1995 Dahlberg

5,424,413 A 6/1995 Hogan etal 536/24.31

5,466,591 A 11/1995 Abramson et al.

5,487,972 A 1/1996 Gelfand etal 435/6

5,538,848 A 7/1996 Livaketal 435/5

5,541,311 A 7/1996 Dahlberg

5,556,772 A 9/1996 Sorge etal.

5,618,703 A 4/1997 Gelfand

5,624,802 A 4/1997 Urdea

5,654,143 A 8/1997 Mallet

5,691,142 A 11/1997 Dahlberg

5,710,264 A 1/1998 Drdea

5,719,028 A 2/1998 Dahlberg et al 435/6

5,792,614 A 8/1998 Western

5,795,763 A 8/1998 Dhalberg

5,804,375 A 9/1998 Gelfand etal.

5,837,450 A 11/1998 Dahlberg et al 435/6

5,837,464 A 11/1998 Capon etal.

5,843,654 A 12/1998 Heisler

5,843,669 A 12/1998 Kaiser etal.

5,846,717 A 12/1998 Brow etal 435/6

5,849,481 A 12/1998 Urdea

5,853,990 A 12/1998 Winger et al.

5,854,033 A 12/1998 Lizardi

5,874,283 A 2/1999 Harrington et al.

(Continued)
FOREIGN PATENT DOCUMENTS
WO WO91/09950 11/1991

(Continued)

OTHER PUBLICATIONS

A Practical Guide to Molecular Cloning (B. Perbal, 1984).
Ausubel et al., 1995, Short Protocols in Molecular biology, 3rd Edi-
tion, John Wiley & Sons.

Barany, PCRMethods and Applications 1:5-16 (1991).
Beaucage et al., 1981, Tetrahedron Letters, 22:1859.
Brown et al., 1979, Methods in Enzymology, 68:109.
Chirgwin et al., 1979, Biochemistry, 18:5294.
International search report. (PCT/US00/29663).
International Search Report. (PCT/US01/31670).
Derbershire et al., 1995, Methods. Enzymolo. 262:363.
Ehricht R., et al., Nucleic Acids Res. 25L4697-4699 (1997).
Fahy etal, PCRMEthods and Applications 1:25-33 (1991).
Hosfield et al., 1998a, Cell., 95:135.
Hosfieldetaf, 1998b, J. Biol. Chem., 273:27154.

(Continued)

Primary Examiner—Ethan Whisenant

(74) Attorney, Agent, or Firm—Theodore Allen; Paul Muzzi

U.S. PATENT DOCUMENTS

5,874,293 A 2/1999 Miettinen-Oinonen et al.

5,888,780 A 3/1999 Dahlberg et al 435/91.53

5,925,517 A 7/1999 Tyagietal.

5,942,391 A 8/1999 Zhang etal.

5,948,649 A 9/1999 Stewart etal.

5,981,183 A 11/1999 Takarada

5,985,557 A 11/1999 Prudent etal.

5,994,069 A 11/1999 Hall etal.

6,001,567 A 12/1999 Brow

6,090,543 A 7/2000 Prudent

6,110,677 A 8/2000 Western

6,150,097 A 11/2000 Tyagietal 435/6

6,277,570 Bl 8/2001 Wood

6,350,580 Bl 2/2002 Sorge 435/6

6,458,535 Bl 10/2002 Hall

6,528,254 Bl * 3/2003 Sorge 435/6

6.548.250 Bl* 4/2003 Sorge 435/6

6,589,743 B2 * 7/2003 Sorge 435/6

6,893,819 Bl* 5/2005 Sorge 435/6

7,118,860 B2* 10/2006 Sorge et al 435/6

7,183,052 B2* 2/2007 Sorge 435/6

7,189,508 B2* 3/2007 Sorge et al 435/6

7,276,597 B2 * 10/2007 Sorge 536/24.3

7,309,573 B2* 12/2007 Sorge 435/6

7,361,467 B2* 4/2008 Sorge et al 435/6

7,361,469 B2* 4/2008 Sorge et al 435/6

7,381,532 B2* 6/2008 Sorge 435/6

7.468.251 B2* 12/2008 Sorge 435/6

7,482,121 B2* 1/2009 Sorge et al 435/6

7,504,218 B2* 3/2009 Happe et al 435/6

7,541,145 B2* 6/2009 Prudent etal 435/6

OTHER PUBLICATIONS

Hosfield, et al. (1998), Cell., 95:135-145.

International Search Report, PCT/US01/44215.

Kaiser et al., 1999, J. Biol. Chem. 274:21387-21394.

Kanehisa, M., 1984, Nucleic Acids Res. 12:203.

Kim et al., 1997, Mol. Cells, 7:468.

Kim et al., 1998, J. Biol. Chem. 273:8842-8.

Klenow et al., 1970, Proc. Natl. Acad. Sci., USA, 65:168.

Klenow et al., 1971, Eur. J. Biochem., 22:371.

Landegren et al., 1988, Science, 241: 1077.

Lawyer et al., 1993, PCR Methods Appl., 2:275.

Leone, etal., 1998, Nucleic Acids Res., 26:2150.

Lieber, 1997', BioEssays, 19:233.

Livak, et al, Oligonucleotides with Fluorescent Dyes at Opposite Ends Provide a Quenched Probe System Useful for Detecting PCR Product and Nucleic Acid Hybridization, PCR Methods and Applications, Cold Harbor Laboratory Press, 1995, p. 357-362. Lundbergetal., 1991 Gene, 108:1-6.

Lyamichev et al. Nature Biotechnology, vol. 17. Mar. 1999. pp. 292-296.

Lyamichev, et al, Polymorphism Identification And Quantitative Detection Of Genomic DNA by Invasive Cleavage Of Oligonucleotide Probes, Nature Biotechnology, vol. 17, 1999, p. 292-296.

Lyamichev, et al, Structure-Specific Endonucleolytic Cleavage of Nucleic Acids by Eubacterial DNA Polymerases, Science, vol. 260, 1993, p. 778-783.

Lyamichev, et al. (1999), Nature Biotechnology, I7L292-296.

Matsui et al., Thermostable Flap Endonuckease from the Archaeon,

Pyrococcus horeikoshii, Cleaves the Replication Fork-like Struture

Endo/Exonucleolytically, The Journal of Biological Chemistry,

1999, vol. 274, No. 26. pp. 18297-18309.

McHenry et al., 1997 J. Mol. biol, 272:178.

Mullis and Faloona, 1987'. Methods Enzymol, 155:335.

Narang et al., 1979, Methods in Enzymology, 68:90.

Nucleic Acid Hybridization (B.d. Harnes & S.JHiggins, eds., 1984.

Oligonucleotide Synthesis (M.J. Gail, ed., 1984).

Rumbaugh et al., 1999, J. Biol. Chem., 274:14602.

Sacchi etal, \9%l,Anal. Biochem., 162: 156).

Saiki et al, 1985, Science 230:1350.

Saiki et al, 1986, Nature 324:163.

Saiki, et al. (1985), Science, 230:1350-1354.

Sambrook, Fritsch & Maniatis, 1989, Molecular cloning: A Laboratory Manual, Second Edition.

Tabor and Richardson, 1985, Proc. Natl. Acad. Sci, USA, 82:1074.

Tyagi S and Kramer FR, Nature Biotechnology 14: 303-308 (1996).

Walker, 1992, Proc. Natl. Acad. Sci, USA, 89:392.

Wu et al., 1996, Nuc. Acids Res., 24:2036-2043.

Wyborski et al, 1997', Strategies, 10:1.

Xu et al., 1997, J. Mol. Biol, 268:294.

Yi-Ping et al., 1999, J. Mol. Evol, 48:756.

Agrawal (ed.)Methods in Molecular Biology, vol. 20 : Protocols for
Oligonucleotides and Analogs, Humana Press, pp. 165-189 (1993).
Agrawal, et al. "Modified oligonucleotides as therapeutic and diag-
nostic agents," Current Opinion in Biotechnology, 6:12-19 (1995).
Bambara, et al., "Enzymes and Reactions at the Eukaryotic DNA
Replication Fork," J. Biol. Chem. 272:4647-4650 (1997).
Bardwell, et al., "Specific Cleavage of Model Recombination and
Repair Intermediates by the Yeast Radl-RadlO DNA Endonuclease,"
Science 265:2082-2085 (1994).

Barnes, et al., "Mechanism of Tracking and Cleavage of Adduct-
damaged DNA Substrates by the Mammalian 5'-to 3'Exonuclease
/Endonuclease RAD2 Homologue 1 or Flap Endonuclease 1", J. Biol.
Chem. 271:29624-29632 (1996).

Bebenek, et al. "The effects of dNTP pool imbalances on frameshift fidelity during DNA replication" J Biol Chem. 267 (6):3589-96 (1992).

Bergseid, et al., "A High Fidelity Thermostable DNA Polymerase Isolated from Pyrococcus Furiosus" Strategies 4:34-35 (1991). Bhagwat, et al. "The 5'-Exonuclease Activity of Bacteriophage T4 RNase H is Stimulated by the T4 Gene 32 Single-stranded DNAbinding Protein, but Its Flap Endonuclease Is Inhibited," J. Biol. Chem. 272:28523-28530 (1997).

Bonch-Osmolovskaya, et al. "Charachteristies of Desulfurococcus Amylolyticas N. SP.—A New Extremely Thermophilic Archaebacterium Isolated From Thermal Springs of Kamchatka and Kunashir Island" Microbiology (Engl. Transl. of Mikrobiologiya) 57:78-85 (1988).

Brow, et al. "Differentitation of Bacterial 16SrRNA Genes and Intergenic Regions and Mycobacterium tuberculosis katG Genes by Structure-Specific Endonuclease Cleavage," J. of Clin. Micro. 34:3129-3137(1996).

Brutlag, et al. "Active Fragment of DNA Polymerase Produced By Proteoytic Cleavage," Biochem. Biophys. Res. Commun. 37:982989 (1968).

Carballeira, et al. "Purification of a Thermostable DNA Polymerase from Thermus thermophilus HB8, Useful in the Polymerase Chain Reaction," Biotechniques 9:276-281 (1990).

Cargill, et al. "Characterization of single-nucleotide polymorphisms in coding regions of human genes" Nature Genetics, 22: 231-8 (1999).

Ceska, et al. "Structure-specific DNA cleavage by 5' nucleases" TIPS 23 (1998).

Clark "Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases" Nucl. Acids Res. 16(20):9677-86 (1988).

Copley, et al. "Exonuclease Cycling Assay: An Amplified Assay for the Detection of Specific DNA Sequences" BioTechniques 13:888891 (1992).

Creighton, et al. "Base mispair extension kinetics. Binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini" J. Biol. Chem. 267(4):2633-39 (1992. Defrancesco "The Next New Wave in Genome Analysis" The Scientist, 12(21): 1-3 (1998).

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).

Duck, et al. "Probe Amplifier System Based on Chimeric Cycling
Oligonucleotides" BioTech., 9:142-147 (1990).
Erlich, et al., "Recent Advances in the Polymerase Chain Reaction,"
Science 252:1643-1651 (1991).

Francois, et al. "Recognition and cleavage of hairpin structures in nucleic acids by oligodeoxvnucleotides," Nucl Acids Res. vol. 22, pp. 3943-3950 (1994).

Gelfand "PCR Technology—Principles and Applications for DNA Amplification" (H.A. Erlich, Ed.) Stockton Press, New York, p. 19 (1989).

Guatelli, et al. "Isothermal in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication" Proc. Natl. Acad. Sci., 8 :1874-1878 (1990) with an erratum at Proc. Natl. Acad. Sci., 87; 7797 (1990).

Harrington, et al. "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).

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

strurcture-specific endonuclease," EMBO Journ. 13:1235-1246

(1994).

Harrington, The Characterization of the Fen-I Family of StructureSpecific Endonucleases: Implications For DNA Replication, Recombination, And Repair. Dissertation submitted to the Program in Cancer Biology and the Committee on Graduate Studies of Stanford University (1994).

Hiraoka, et al., "Sequence of human FEN-1, a structure specific

endonucleases, and chromosomal localization of the gene(FENl) in

mouse and human," Genomics 25:220-225 (1995).

Holland, et al., "Detection of specific polymerase chain reaction

product by utilizing the 5'-3' exonuclease activity of Thermus

aquaticus DNA polymerase," Proc. Natl. Acad. Sci. USA 88:7276

7280(1991).

Hosfield, et al. "Newly Discovered Archaebacterial Flap Endonucleases Show a Stucture-Specific Mechanism for DNA Substrate Binding and Catalysis Resembling Human Flap Endonuclease1," J. Biol Chem. 273:27154-1716 (1998)1.

Hosfield, et al., "Structure of the DNA Repair and Replication Endonuclease and Exonuclease FEN-1: Coupling DNA and PCNA Binding to FEN-1 Activity," Cell 95:135-146 (1998). Huang, et al. "Role of CalfRTH-1 Nuclease in Removal of 5'-Ribonucleotides during Okazaki Frament Processing," Biochemistry 35:9266-9277 (1996).

Kaiser, et al. "A Comparison of Eubacterial and Archaeal Structurespecific 5'-Exonucleases" J. Biol Chem 274: 21387-21394 (1999). Kaledin, et al. "Isolation and Properties of DNA Polymerase From the Extremely Thermophilic Bacterium Thermus flavus," Biokhimiya46(9):1576-1584 (1981).

Kwiatkowski, et al. "Clinical, Genetic, and Pharmacogenetic Applications of the Invader Assay" Molecular Diagnosis, 4:353-364 (1999).

Li, et al. "Lagging Strand DNA Synthesis at the Eukaryotic Replication Fork Involves Binding and Stimulation of FEN-1 by Proliferating Cell Nuclear Antigen" J. Biol. Chem. 270:22109-22112 (1995). Lieber "The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair" BioEssays 19:233-240 (1997).

Livak, et al., "Oligonucleotides With Flurescent Dyes at Opposite Ends Provide a Quenched Probe System, Useful for Detecting PCR Product and Nucleic Acid Hybridization," PCR Methods and Appln. 4:357-362(1995).

Longley, et al. "Characterization of the 5' to 3' exonuclease associated with Thermus aquaticus DNA polymerase," Nucl. Acids Res. 18:7317-7322(1990).

Lyamichev, et al. "Comparison of the 5' nuclease activities of Taq DNA polymerase and its isolated nuclease domain" Proc Natl Acad Sci: 96: 6143-6148(1999).

Lyamichev, et al. "Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes" Nat. Biotech., 17:292-6 (1999).

Lyamichev, et al. "Structure-Specific Endonucleoytic Cleavage of Nucleic Acids by Eubacterial DNA Polymerases," Science 260:778783 (1993).

Morris, et al. Rapid reverse transcription-PCR detection of hepatitis

C virus RNA in serum by using the TaqMan flurogenic detection

system J Clin Microbiol. Dec. 1996; 34(12):2933-6.

Myers, et al., "Reverse Transcription and DNA amplification by a

Thermus fhermophilus DNA polymerase," Biochem. 30:7661-7666

(1991).

Nolan, et al. "Kinetic Analysis of Human Flap Endonuclease-1 by
Flow Cytometry," Biochemistry 35: 11668-11677 (1996).
Rao, et al. "Mefhanococcus jannaschii Flap Endonuclease: Expres-
sion, Purification, and Substrate Requirements" J. of Bacteriology
180:5406-5412(1998).

Ryan, et al. "Non-PCR-Dependent Detection of the Factor V Leiden
Mutation From Genomic DNA Using a Homogeneous Invader
Microtiter ..." Molecular Diagnosis, 4:135-144 (1999).
Sambrook, et al., "Molecular Cloning. A Laboratory Manual" Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 1.63-1.69
(1989).

Selvin "Fluorescence resonance energy transfer" 1995, Methods
Enzymol., 246:300-34.

Turchi, et al. "Completion of Mammalian Lagging Strand DNA Replication Using Purified Proteins" J. Biol Chem. 268 (20): 15136141 (1993).

Turchi, et al., "Enzymatic completion of mammalian lagging-strand DNA replication," Proc. Natl. Acad. Sci. USA9L9803-9807 (1994). Urdea, et al. "A novel method for the rapid detection of specific nucleotide sequences in crude biological samples without blotting or radioactivity; application to the analysis if hepatitis B virus in human serum," Gene 61:253-264 (1987).

Xu, et al., "Biochemical and Mutational Studies of the 5'-3' Exonuclease of DNA Polymerase 1 of Escherichia coli," J. Mol. Biol. 268:284-302 (1997).

Behrens et al., Identification and properties of the RNA-dependent RNApolmerase of hepitis C Virus. EMBO J. 15 (1) 12-22 (1996).

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