Methods and compositions for nucleic acid analysis

Details Methods and compositions for nucleic acid analysis Methods and compositions for nucleic acid analysis

2007-10-16

2007-10-16

Whisenant, Ethan (Department: 1634)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S091200, C536S022100, C536S023100, C536S024300

Reexamination Certificate

active

10969032

ABSTRACT:
The present invention relates to improved methods and composition for nucleic acid analysis. In particular, the present invention provides improved methods and compositions for carrying out nucleic acid analysis using modified nucleotides.

REFERENCES:
patent: 5216141 (1993-06-01), Benner
patent: 5432272 (1995-07-01), Benner
patent: 5565340 (1996-10-01), Chenchik et al.
patent: 5912340 (1999-06-01), IKutyavin et al.
patent: 5958702 (1999-09-01), Benner
patent: 5965364 (1999-10-01), Benner
patent: 6001983 (1999-12-01), Benner
patent: 6037120 (2000-03-01), Benner
patent: 6140496 (2000-10-01), Benner
patent: 6270967 (2001-08-01), Whitcombe et al.
patent: 7056703 (2006-06-01), Callen et al.
patent: 2002/0150900 (2002-10-01), Marshall et al.
patent: 2004/0106108 (2004-06-01), Grenier et al.
Newton et al., The Production of PCR Products with 5′ Single-Stranded Tails Using Primers That Incorporate Novel Phosphoramidite Intermediates. Nucleic Acids Res 21:1155-1162 (1993).
ABI Prism Dye Terminator Cycle Sequencing Core Kit with AmpliTaq DNA Polymerase, FS : Protocol published by Applied Biosystems (Copyright 2001).
U.S. Appl. No. 09/415,966, filed Oct. 12, 1999, Benner.
U.S. Appl. No. 09/538,338, filed Mar. 29, 2000, Benner.
U.S. Appl. No. 09/993,757, filed Nov. 27, 2001, Thorson.
U.S. Appl. No. 60/205,712, filed May 19, 2000, Marshall.
U.S. Appl. No. 60/240,398, filed Oct. 14, 2000, Marshall.
U.S. Appl. No. 60/282,831, filed Apr. 10, 2001, Marshall.
U.S. Appl. No. 60/240,397, filed Oct. 14, 2000, Grenier.
U.S. Appl. No. 60/252,783, filed Nov. 22, 2000, Prudent et al.
U.S. Appl. No. 60/253,382, filed Nov. 27, 2000, Thorson.
Allawi, H.T. & SantaLucia, J. Jr. Thermodynamics of Internal G-T Mismatches, Biochemistry 36(34):10581-94 (1997).
Lin, PKT. and Brown,D.M., Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues. Nucleic Acids Res. 17 10373-10383 (1989).
Lin, PKT. and Brown,D.M., Synthesis of oligodeoxyribonucleotides containing degenerate bases and their use as primers in the polymerase chain reaction, Nucleic Acids Res. 20 (19):5149-52 (1992).
Brownie, et al., “The elimination of primer-dimer accumulation in PCR,” Nucleic Acids Res. 25(16): 3235-41 (1997).
Robinson, H., et al., 2′-Deoxyisoguanosine Adopts More Than One Tautomer To Form Base Pairs With Thymidine Observed by High-Resolution Crystal Structure Analysis, Biochemistry Aug. 4, 1998;37(31):10897-905.
Switzer, CY, et al., Enzymatic Recognition of the Base Pair Between Isocytidine and Isoguanosine, Biochemistry Oct. 5, 1993;32(39):10489-96).
Roberts, C., et al., Synthesis of Oligonucleotides Bearing the Non-Standard Bases Iso0C and Iso-G. Comparison of iso-C-isoG, C-G, and U-A Base-Pair Stabilities in RNA/DNA Duplexes, Tetrahedron Letters 36 (21):3601-3604 (1995).
McMinn, DL, et al., Efforts toward the Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base, J. Am Chem. Soc. 121:11585-11586 (1999).
Moran, S., et al., Difluorotoluene, a Nonpolar Isotere for Thymine, Codes Specifically and Efficiently for Adenine in DNA Replication, J. Am Chem. Soc. 119:2056-2057 (1997).
Moser, MJ, et al., Exploiting the Enzymatic Recognition of an Unnatural Base Pair to Develop a Universal Genetic Analysis System, Clinical Chemistry 49(3):407-414 (2003.
Ren, R X -F., et al., Naphthalene, Phenanthrese, and Pyrine as DNA Base Analogs: Synthesis, Structure, and Fluorescence in DNA, J. Am Chem. Soc. 118:7671-7678 (1996).
Wilhelm J and A. Pingoud, Real Time Polymerase Chain Reaction, Chem BioChem 4:1120-1128 (2003).
Rice, KP, et al., RecA Protein Promotes Strand Exchange with DNA Substrates Containing Isoguanine and 5-Methyl Isocytosine, Biochemistry 39:10177-10188 (2000).
Kool, E., “Synthetically modified DNAs as substrates for polymerases,” Current Opinions in Chemical Biology 2000 4:802-808.
Kainz et al., “Specificity-Enhanced Hot-Start PCR: Addition of Double-Stranded DNA Fragments Adapted to the Annealing Temperature,” BioTechniques 28:278.
Kamiya et al., “Formation of 2-Hydroxydeoxyadenosine Triphosphate, an oxidatively Damaged Nucleotide, and Its Incorporation by DNA Polymerases,” J. of Biol. Chem 270:19446-194.
Whitcomb et al., “A homogeneous fluorescence assay for PCR amplicons: its application to real-time, single-tube genotyping,” Clinical Chemistry 44:918-923 (1998).

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