Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
2004-04-01
2010-10-26
Bowman, Amy (Department: 1635)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C536S023100, C514S04400A
Reexamination Certificate
active
07820808
ABSTRACT:
The present invention provides nucleic acid based polymerase inhibitors and methods for reducing non-specific polymerase extension and amplification in nucleic acid amplification reactions. The polymerase inhibitors provide a double stranded nucleic acid portion that is recognized by a polymerase enzyme as a template for extension but is incapable of being extended by the polymerase enzyme. The polymerase binds to the polymerase inhibitor which sequesters the enzyme until the temperature achieves a level that denatures the double stranded portion of the inhibitor after which the polymerase is released and can then catalyze nucleic acid extension.
REFERENCES:
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis
patent: 4800159 (1989-01-01), Mullis et al.
patent: 4996143 (1991-02-01), Heller et al.
patent: 5126439 (1992-06-01), Rappaport
patent: 5177064 (1993-01-01), Bodor
patent: 5210015 (1993-05-01), Gelfand et al.
patent: 5412088 (1995-05-01), Jones et al.
patent: 5432272 (1995-07-01), Benner
patent: 5470974 (1995-11-01), Summerton et al.
patent: 5604097 (1997-02-01), Brenner
patent: 5605794 (1997-02-01), Rust et al.
patent: 5679524 (1997-10-01), Nikiforov et al.
patent: 5681702 (1997-10-01), Collins et al.
patent: 5705621 (1998-01-01), Ravikumar
patent: 5736330 (1998-04-01), Fulton
patent: 5843669 (1998-12-01), Kaiser et al.
patent: 5846717 (1998-12-01), Brow et al.
patent: 5856092 (1999-01-01), Dale et al.
patent: 5928869 (1999-07-01), Nadeau et al.
patent: 5958784 (1999-09-01), Benner
patent: 5965364 (1999-10-01), Benner
patent: 6001983 (1999-12-01), Benner
patent: 6007984 (1999-12-01), Wang et al.
patent: 6037120 (2000-03-01), Benner
patent: 6046807 (2000-04-01), Chandler
patent: 6054270 (2000-04-01), Southern
patent: 6057107 (2000-05-01), Fulton
patent: 6140496 (2000-10-01), Benner
patent: 6200757 (2001-03-01), Kurn et al.
patent: 6232462 (2001-05-01), Collins et al.
patent: 6287766 (2001-09-01), Nolan et al.
patent: 6294336 (2001-09-01), Boyce-Jacino et al.
patent: 6444798 (2002-09-01), Benner
patent: 6509157 (2003-01-01), Martinez
patent: 6548250 (2003-04-01), Sorge
patent: 6617106 (2003-09-01), Benner
patent: 6627456 (2003-09-01), Benner
patent: 6833257 (2004-12-01), Lee et al.
patent: 6977161 (2005-12-01), Grenier et al.
patent: 2002/0055104 (2002-05-01), Michelotti
patent: 2002/0132221 (2002-09-01), Chee et al.
patent: 2002/0150900 (2002-10-01), Marshall et al.
patent: 2003/0194705 (2003-10-01), Schroth
patent: 2004/0106108 (2004-06-01), Grenier et al.
patent: 2005/0014163 (2005-01-01), Dong et al.
patent: 2005/0084894 (2005-04-01), Brow et al.
patent: 2006/0078936 (2006-04-01), Grenier et al.
patent: 0 382 433 (1990-08-01), None
patent: 0 416 817 (1991-03-01), None
patent: 0 742 287 (1996-11-01), None
patent: 0 915 174 (1999-05-01), None
patent: 64-034300 (1989-02-01), None
patent: 09-511149 (1997-11-01), None
patent: WO 90/06042 (1990-06-01), None
patent: WO 92/11389 (1992-07-01), None
patent: WO 94/21820 (1994-09-01), None
patent: WO-96/23079 (1996-08-01), None
patent: WO 96/31622 (1996-10-01), None
patent: WO 97/46711 (1997-12-01), None
patent: WO 98/14610 (1998-04-01), None
patent: WO-00/52207 (2000-09-01), None
patent: WO 01/75139 (2001-10-01), None
patent: WO 01/90417 (2001-11-01), None
patent: WO 03/046149 (2003-06-01), None
Chung et al., Biochemical studies on capped RNA primers identify a class of oligonucleotide inhibitors of the influenza virus RNA polymerase, 1994, 91(6), pp. 2372-2376.
Kaboev, O. et al., “PCR hot start using primers with the structure of molecular beacons (hairpin-like structures),”Nucleic Acids Research, Oxford University Press, Surrey, GB, vol. 28, No. 21, Nov. 1, 2000, p. E94.
Kainz. P. et al., “Specificity-enhanced hot-start PCR: Addition of double-stranded DNA fragments adapted to the annealing temperature,”Biotechniques, Informa Life Sciences Publishing, Westborough, MA, US, vol. 28, No. 2, pp. 278-282, Feb. 1, 2000.
Supplementary European Search Report for European Patent Application No. 04 75 8726 dated Feb. 16, 2009.
PCT International Search Report based on International Application No. PCT/US04/10029, date of mailing of the International Search Report Apr. 5, 2005 (1 p.).
Australian Examiner's Report for Patent Application No. 2004227353 dated Sep. 24, 2009.
Biggins et al., “A continuous assay for DNA cleavage: The application of “break lights” to enediynes, iron-dependent agents, and nucleases”,PNAS, vol. 97, No. 25, Dec. 5, 2000 (pp. 13537-13542).
Cobianchi et al., “Enzymes for Modifying and Labeling DNA and RNA”,Methods in Enzymology, vol. 152, Copyright © 1987 by Academic Press, Inc., (pp. 94-110).
Hall et al., “Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction”,PNAS, vol. 97, No. 15, Jul. 18, 2000 (pp. 8272-8277).
Horlacher et al., “Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns”,Proc. Natl. Acad. Sci., vol. 92, Jul. 1995 (pp. 6329-6333).
Johnson et al., “A third base pair for the polymerase chain reaction: inserting isoC and isoG”,Nucleic Acids Research, vol. 32, No. 6, 2004, (pp. 1937-1941).
Jurczyk et al., “Synthesis of 2′-Deoxyisoguanosine 5′-Triphosphate and 2′-Deoxy-5-methylisocytidine 5′Triphosphate”,Helvetica Chimica Acta, vol. 82, 1999 (pp. 1005-1015).
Lutz, Michael J. et al., “Differential discrimination of DNA polymerases for variants of the non-standard nucleobase pair between xanthosine and 2,4-diaminopyrimidine, two components of an expanded genetic alphabet”,Nucleic Acids Research, vol. 24, No. 7, 1996 (pp. 1308-1313).
Lutz, Stefan et al., “An in vitro screening technique for DNA polymerases that can incorporate modified nucleotides. Pseudothymidine as a substrate for thermostable polymerases”,Nucleic Acids Research, vol. 27, No. 13, 1999 (pp. 2792-2798).
Moser et al., “Quantifying Mixed Populations of Drug-Resistant Human Immunodeficiency Virus type 1”,Antimicrobial Agents and Chemotherapy, vol. 49, No. 8, Aug. 2005 (pp. 3334-3340).
Moser et al., “Enzymatic repair of an expanded genetic information system”,Nucleic Acids Research, vol. 31, No. 27, 2003 (pp. 5048-5053).
Newton et al., “The production of PCR products with 5′ single-stranded tails using primers that incorporate novel phosphoramidite intermediates”,Nucleic Acids Research, vol. 21, No. 5, 1993 (pp. 1155-1162).
Piccirilli et al., “Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet”, Reprinted fromNature, vol. 343, No. 6253, Jan. 4, 1990 (pp. 33-37).
Randerath et al., “3H and32P Derivative Methods for Base Composition and Sequence Analysis of RNA”,Methods in Enzymology, vol. 65, Copyright © 1980 by Academic Press, Inc., (pp. 638-681).
Sepiol et al., “Tautomerism of Isoguanosine and Solvent-Induced Keto-Enol Equilibrium”,Z. Naturforsch, 1976 (pp. 361-370).
Sismour et al., “The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system”,Nucleic Acids Research, vol. 33, No. 17, 2005 (pp. 5640-5646).
Sismour et al., “PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1”,Nucleic Acids Research, vol. 32, No. 2, 2004 (pp. 728-735).
Switzer et al., “Enzymatic Recognition of the Base Pair between Isocytidine and Isoguanosine”,Biochemistry, vol. 32, No. 39, 1993 (pp. 10489-10496).
Tabrizi et al., “Evaluation of real time polymerase chain reaction assays for confirmation ofNeisseria gonorrhoeaein clinical samples tested positive in the Roche Cobas Amplicor assay”,Sex Transm Infect, vol. 80, 2004 (pp. 68-71).
Tor et al., “Site-Specific Enzymatic Indorporation of
Larsen Christine A.
Marshall David J.
Moser Michael James
Prudent James R.
Van Hout Christopher V.
Bowman Amy
EraGen Biosciences, Inc.
Foley & Lardner LLP
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