5-methylcytosine detection, compositions and methods therefor

Details 5-methylcytosine detection, compositions and methods therefor 5-methylcytosine detection, compositions and methods therefor

2004-06-30

2008-07-15

Riley, Jezia (Department: 1637)

Chemistry: molecular biology and microbiology

Micro-organism, tissue cell culture or enzyme using process...

Preparing compound containing saccharide radical

C435S006120, C435S091200, C536S023100, C536S024300, C536S024330, C536S026600

Reexamination Certificate

active

07399614

ABSTRACT:
Compositions and methods for detecting 5-methylcytosine in a nucleic acid are disclosed. A 5-methylcytosine discriminator, which is a deoxyribonucleosidetriphosphate comprising a cytosine-pairing moiety such as a guanosine and a moiety which hinders hydrogen bonding between the cytosine-pairing moiety and a 5-methylcytosine is described. The discriminator is able to base pair with a cytosine but not a 5-methylcytosine. A 5-methylcytosine comprised by a target nucleotide can be detected in a reaction using a DNA polymerase and a primer hybridized immediately adjacent to the target nucleotide. In the reaction, pyrophosphate released upon incorporation of a dNTP complementary to a target nucleotide is detected. Lack of incorporation of the discriminator, but incorporation of a dGTP, can indicate that the target nucleotide is a 5-methylcytosine.

REFERENCES:
patent: 5210015 (1993-05-01), Gelfand et al.
patent: 5436149 (1995-07-01), Barnes
patent: 6210891 (2001-04-01), Nyren
patent: 6258568 (2001-07-01), Nyren
patent: 7118868 (2006-10-01), Berlin
patent: WO 90/01069 (1990-02-01), None
Royer, R. E. et al.; “Reactivity-Selectivity Properties of Reactions of Carcinogenic Electrophiles with Biomolecules;” Journal of Organic Chemistry, vol. 44, No. 18 (Aug. 31, 1979); pp. 3202-3207.
Szejnwald, Brown H. et al.; “Preparation and Enzymatic Hydrolysis of Dinucleoside Monophosphates and DNA Modified with Aromatic Residues;” Nucleic Acids and Protein Synthesis, vol. 475, No. 2 (Mar. 18, 1977); pp. 241-253.
Scribner, J. D. et al.; “Adducts Between the Carcinogen 2 Acetamido Phenanthrene and Adenine and Guanine of DNA;” Cancer Research, vol. 35, No. 6 (1975); pp. 1416-1421.
Pochon, F. et al.; “Action of the Carcinogen 7 Bromomethyl Benz Anthracene on Synthetic Poly Nucleotides;” European Journal of Biochemistry, vol. 21, No. 1 (Jul. 1971); pp. 144-153.
Che, Y. et al.; “A Multiplexing Single Nucleotide Polymorphism Typing Method Based on Restriction-Enzyme-Mediated Single-Base Extension and Capillary Electrophoresis;” Analytical Biochemistry, Academic Press, New York, NY, vol. 329, No. 2 (Jun. 15, 2004); pp. 220-229.
Rein et al.; “Identifying 5-Methylcytosine and Related Modifications in DNA Genomes;” Nucleic Acids Research, Oxford University Press, vol. 26, No. 10 (May 15, 1998); pp. 2255-2264.
Balog, Robert P. et al.; “Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays”; Analytical Biochemistry 309 (2002) 301-310.
Benhattar, Jean et al.; “Methylation-Sensitive Single-Strand Conformation Analysis”; Methods in Molecular Biology, vol. 287, pp. 181-193; Epigenetics Protocols; Edited by: T.O. Tollefsbol.
Colasanti, Joseph et al.; “Cytosine Methylated DNA synthesized by Taq polymerase used to assay methylation sensitivity of restriction endonuclease Hinfl”; Nucleic Acids Research; (Dec. 4, 1990); vol. 19, No. 2; pp. 391-394.
Cook, Lindsey et al.; “Methylated DNA labels for marking objects”; Biotechnology Letters 25: 89-94; (2003).
Cottrell, Susan E.; “A real-time PCR assay for DNA-methylation using methylation-specific blockers”; Nucleic Acids Research; vol. 32, No. 1; 2004; pp. 1-8.
Derks, Sarah et al.; “Methylation-specific PCR unraveled”; Cellular Oncology 26 (2004); pp. 291-299.
Fackler, Mary Jo et al.; “Quantitative Multiplex Methylation-Specific PCR Assay for the Detection of Promoter Hypermethylation in Multiple Genes in Breast Cancer”; Cancer Research 64, 4442-4452, Jul. 1, 2004.
Fraga, Mario F. et al.; “DNA Methylation: A Profile of Methods and Applications”; BioTechniques 33:632-649 (Sep. 2002).
Gitan, Raad S. et al.; “Methylation-Specific Oligonucleotide Microarray: A New Potential for High Throughput Methylation Analysis”; Genome Research; (Sep. 20, 2001) pp. 158-164.
Guldberg, Per et al.; “Profiling DNA methylation by melting analysis”; Methods 27 (2002) 121-127.
Laird, Charles D. et al.; “Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules”; PNAS (Jan. 6, 2004); vol. 101, No. 1; pp. 204-209.
Lewin, Jörn et al.; “Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates”; Bioinformatics; vol. 20, No. 17 (2004); pp. 3005-3012.
Li, Long-Cheng; “MethPrimer: designing primers for methylation PCRs”; Bioinformatics; vol. 18, No. 11 (2002); pp. 1427-1431.
Liu, Liang et al.; “Profiling DNA Methylation by Bisulfite Genomic Sequencing”; Methods in Molecular Biology, vol. 287; pp. 169-179; Epigentics Protocols; Edited by Trygve O. Tollefsbol.
Liu, Ze-Jun et al.; “Polymerase chain reaction-based methods of DNA methylation analysis”; Analytical Biochemestry 317 (2003) 259-265.
Maekawa, Masato et al.; DNA Methylation Analysis Using Bisulfite Treatment and PCR-Single-Strand Conformation Polymorphism in Colorectal Cancer Showing Microsatellite Instability; Biochemical and Biophysical Research Communications 262, 671-676 (1999).
Makrigiorgos, Mike G. et al.; :A PCR-based amplification method retaiing the quantitative differnce between two complex genomes; Nature Biotechnology; vol. 20; Sep. 2002; pp. 936-939.
Nagane, Yuriko et al.; “PCR amplification in bisulfite methylcytosine mapping in the GC-rich promoter region of amyloid precursor protein gene in autopsy human brain”; Brain Research Protocols 5 (2000) 167-171.
Ohashi, Haruhiko; “Methylation-Specific PCR”; Methods in Molecular Biology, vol. 192, pp. 91-97; PCR Cloning Protocols, 2nd Edition; Edited by B-Y Chen and H.W. Janes.
Ohmori, Haruo et al.; “Detection of 5-methylcytosine in DNA sequences”; Nucleic Acids Research; vol. 5, No. 5; (May 1978); pp. 1479-1485.
Panagopoulos, Ioannis et al.; “A Methylation PCR Approach for Detection of Fragile X Syndrome”; Methods; Human Mutation 14: 71-79 (1999).
Sasaki, Masahiro et al.; “Bisulfite conversion-specific and methylation-specific PCR: a sensitive technique for accurate evaluation of CpG methylation”; Biochemical and Biophysical Research Communications 309 (2003) 305-309.
Steigerwald, Sabine D. et al.; “Ligation-mediated PCR improves the sensitivity of methylation analysis by restriction enzymes and detection of specific DNA strand breaks”; Nucleic Acids Research; vol. 18, No. 6; pp. 1435-1439 (Feb. 11, 1990).
Thomassin, Helene et al.; “Identification of 5-Methylcytosine in Complex Genomes”; Methods 19, 465-475 (1999).
Thomassin, Helene et al.; “MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome”; Nucleic Acids Research (2004); vol. 32, No. 21; pp. 1-9.
Towers, Greg J. et al; “One Step Screening of Retroviral Producer Clones by Real Time Quantitative PCR”; The Journal of Gene Medicine 1999; 1: 352-359.
Toyota, Minoru et al.; “Identification of Differentialy Methylated Sequences in Colorectal Cancer by Methylated CpG Island Amplification”; Cancer Research 59; May 15, 1999; pp. 2307-2312.
Trinh, Binh N. et al; DNA Methylation Analysis by MethyLight Technology; Methods 25, 456-462 (2001).
Tusnady, Gabor E. et al.; “BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes”; Nucleic Acids Research; vol. 33, No. 1; 2005; pp. 1-6.
van Dijk, Jeroen P. et al.; “A Novel, Essential Control for Clonality Analysis with Human Androgen Receptor Gene Polymerase Chain Reaction”; American Journal of Pathology; vol. 161, No. 3; Sep. 2002; pp. 807-812.
Warnecke, Peter M. et al.; “Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA”; Nucleic Acids Research; vol. 25, No. 21; 1997; pp. 4422-4426.
Worm, Jesper et al.; “In-Tube DNA Methylation Profiling by Fluorescence Meltin

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