Methods for determining nucleic acid methylation

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Reexamination Certificate

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C435S091100, C435S091200

Reexamination Certificate

active

07470511

ABSTRACT:
The present invention provides methods for detecting the presence of a target molecule by generating multiple detectable oligonucleotides through reiterative enzymatic oligonucleotide synthesis events on a defined polynucleotide sequence. The methods generally comprise using a nucleoside, a mononucleotide, and oligonucleotide, or a polynucleotide, or analog thereof, to initiate synthesis of an oligonucleotide product that is substantially complementary to a target site on the defined polynucleotide sequence; optionally using nucleotides or nucleotide anologs as oligonucleotide chain elongators; using a chain terminator to terminate the polymerization reaction; and detecting multiple oligonucleotide products that have been synthesized by the polymerase. In one aspect, the invention provides a method for detecting a target protein, DNA or RNA by generating multiple detectable RNA oligoribonucleotides by abortive transcription.

REFERENCES:
patent: 3996345 (1976-12-01), Ullman et al.
patent: 4351760 (1982-09-01), Khanna et al.
patent: 4582788 (1986-04-01), Erlich
patent: 4683194 (1987-07-01), Saiki et al.
patent: 4739044 (1988-04-01), Stabinsky
patent: 4757141 (1988-07-01), Fung et al.
patent: 4786600 (1988-11-01), Kramer et al.
patent: 5130238 (1992-07-01), Malek et al.
patent: 5169766 (1992-12-01), Schuster et al.
patent: 5194370 (1993-03-01), Berninger et al.
patent: 5215899 (1993-06-01), Dattagupta
patent: 5246866 (1993-09-01), Nasu et al.
patent: 5399491 (1995-03-01), Kacian et al.
patent: 5503979 (1996-04-01), Kramer et al.
patent: 5508178 (1996-04-01), Rose et al.
patent: 5554516 (1996-09-01), Kacian et al.
patent: 5571669 (1996-11-01), Lu et al.
patent: 5595891 (1997-01-01), Rose et al.
patent: 5597694 (1997-01-01), Munroe et al.
patent: 5648211 (1997-07-01), Fraiser et al.
patent: 5654142 (1997-08-01), Kievits et al.
patent: 5679512 (1997-10-01), Laney et al.
patent: 5683879 (1997-11-01), Laney et al.
patent: 5744308 (1998-04-01), Guillou-Bonnici et al.
patent: 5766849 (1998-06-01), McDonough et al.
patent: 5824517 (1998-10-01), Cleuziat et al.
patent: 5837459 (1998-11-01), Berg et al.
patent: 5846723 (1998-12-01), Kim et al.
patent: 5858801 (1999-01-01), Brizzolara
patent: 5888729 (1999-03-01), Kacian et al.
patent: 5888819 (1999-03-01), Goelet et al.
patent: 6008334 (1999-12-01), Hanna
patent: 6107037 (2000-08-01), Sousa et al.
patent: 6107039 (2000-08-01), Hanna
patent: 6114519 (2000-09-01), Cole et al.
patent: 6251594 (2001-06-01), Gonzalgo et al.
patent: 6268131 (2001-07-01), Kang et al.
patent: 7045319 (2006-05-01), Hanna
patent: 7226738 (2007-06-01), Hanna
patent: 2002/0168641 (2002-11-01), Mortensen et al.
patent: 2003/0099950 (2003-05-01), Hanna
patent: 2004/0054162 (2004-03-01), Hanna
patent: 2004/0137461 (2004-07-01), Hanna
patent: 2004/0157257 (2004-08-01), Hanna
patent: 2004/0175724 (2004-09-01), Hanna
patent: 2004/0234996 (2004-11-01), Hanna
patent: 2005/0214796 (2005-09-01), Hanna
patent: 2006/0204964 (2006-09-01), Hanna
patent: 0 369 775 (1990-05-01), None
patent: WO 89/01050 (1989-02-01), None
patent: WO 03/038042 (2003-05-01), None
Herman et al., “Inactivation of the CDKN2/p16/MTS1 Gene is Frequently Associated with Aberrant DNA Methylation in All Common Human Cancers,” Cancer Research, 1995, vol. 55, pp. 4525-4530.
Frommer et al., “A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands,” PNAS, 1992, vol. 89, pp. 1827-1831.
Sasaki et al., “Transcriptional sequencing: A method for DNA sequencing using RNA polymerase,” PNAS, 1998, vol. 95, pp. 3455-3460.
Agrawal, S., and Tang, J.-Y., “Site-specific functionalization of oligodeoxynucleotides for non-radioactive labeling,”Tetrahedron Lett. 31:1543-1546, Pergamon Press (1990).
Chamberlin, M.J., “Bacterial DNA-Dependent RNA Polymerases,” inThe Enzymes, Boyer, P.D., ed., Academic Press, New York, N.Y. pp. 61, 84-86 (1982).
Costas, C., et al., “RNA-protein crosslinking to AMP residues at internal positions in RNA with a new photocrosslinking ATP analog,”Nucleic Acids Res. 28:1849-1858, Oxford University Press (May 2000).
Daube, S.S., and von Hippel, P.H., “Functional Transcription Elongation Complexes from Synthetic RNA-DNA Bubble Duplexes,”Science258:1320-1324, American Association for the Advancement of Science (1992).
Dunn, J.J., and Studier, F.W., “Complete Nucleotide Sequence of Bacteriophage T7 DNA and the Locations of T7 Genetic Elements,”J. Mol. Biol. 166:477-535, Academic Press, Inc. (1983).
Gait, M.J., et al., “Oligoribonucleotide synthesis,” inOligonucleotides and Analogues, Eckstein, F., ed., Oxford University Press, Oxford, Great Britain, pp. 25-31 (1992).
Gait, M.J., “An Introduction to Modern Methods of DNA Synthesis,” inOligonucleotide synthesis: a practical approach, Gait, M.J., ed., Oxford University Press, Oxford, Great Britain, pp. 1-22 (1984).
Geider, K., et al., “An RNA transcribed from DNA at the origin of phage fd single strand to replicative form conversion,”Proc. Natl. Acad. Sci. USA75:645-649, National Academy Press (1978).
Guatelli, J.C., et al., “Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication,”Proc. Natl. Acad. Sci. USA87:1874-1878, National Academy Press (1990).
Gupta, K.C., et al., “A general method for the synthesis of 3□-sulfhydryl and phosphate group containing oligonucleotides,”Nucleic Acids Res. 19:3019-3025, Oxford University Press (1991).
Gurevich, V.V., et al., “Preparative in Vitro mRNA Synthesis Using SP6 and T7 RNA Polymerases,”Anal. Biochem. 195:207-213, Academic Press, Inc. (1991).
Hanna, M.M., “Photoaffinity Cross-Linking Methods for Studying RNA-Protein Interactions,”Methods Enzymol. 180:383-409, Academic Press, Inc. (1989).
Hanna, M.M., et al., “Probing the environment of nascent RNA inEscherichia colitranscription elongation complexes utilizing a new fluorescent ribonucleotide analog,”Nucleic Acids Res. 27:1369-1376, Oxford University Press (1999).
Hanna, M.M., et al., “Synthesis and characterization of a new photocrosslinking CTP analog and its use in photoaffinity labelingE. coliand T7 RNA polymerases,”Nucleic Acids Res. 21:2073-2079, Oxford University Press (1993).
He, B., et al., “Preparation of probe-modified RNA with 5-mercapto-UTP for analysis of protein-RNA interactions,”Nucleic Acids Res. 23:1231-1238, Oxford University Press (1995).
Kwoh, D.Y., et al., “Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format,”Proc. Natl. Acad. Sci. USA86:1173-1177, National Academy Press (1989).
Lewis, M.K., and Burgess, R.R., “Transcription of Simian Virus 40 DNA by Wheat Germ RNA Polymerase II,”J. Biol. Chem. 255:4928-4936, American Society for Biochemistry and Molecular Biology (1980).
Martin, C.T., et al., “Processivity in Early Stages of Transcription by T7 RNA Polymerase,”Biochemistry27:3966-3974, American Chemical Society (1988).
Meyer, K.L., and Hanna, M.M., “Synthesis and Characterization of a New 5-Thiol-Protected Deoxyuridine Phosphoramidite for Site-Specific Modification of DNA,”Bioconjugate Chem. 7:401-412, American Chemical Society (1996).
Milligan, J.F., and Uhlenbeck, O.C., “Synthesis of Small RNAs Using T7 RNA Polymerase,”Methods Enzymol. 180:51-62, Academic Press, Inc. (1989).
Montemagno, C., and Bachand, G., “Constructing nanomechanical devices powered by biomolecular motors,”Nanotechnology10:225-231, IOP Publishing, Ltd. (1999).
Mullis, K., et al., “Specific Enzymatic Amplification of DNA In Vitro: The Polymerase Chain Reaction,”Cold Spring Harb. Symp. Quant. Biol. 51:263-273, Cold Spring Harbor Laboratory (1986).
Mullis, K.B., et al., “The Polymerase Chain Reaction: Why It

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