Methods and kits for methylation detection

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

Reexamination Certificate

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C536S023100, C536S024300

Reexamination Certificate

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11119985

ABSTRACT:
Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.

REFERENCES:
patent: 4988617 (1991-01-01), Landegren et al.
patent: 5494810 (1996-02-01), Barany et al.
patent: 5700672 (1997-12-01), Mathur et al.
patent: 6027889 (2000-02-01), Barany et al.
patent: 6331393 (2001-12-01), Laird et al.
patent: 2003/0119025 (2003-06-01), Olek et al.
patent: 2005/0053957 (2005-03-01), Rosenblum
patent: 2005/0272071 (2005-12-01), Lao et al.
patent: 2006/0121492 (2006-06-01), Zon
patent: 0 976 835 (2000-02-01), None
patent: WO 91/17239 (1991-11-01), None
patent: WO 96/15271 (1996-05-01), None
patent: WO 01/62961 (2001-08-01), None
patent: WO 03/057909 (2003-07-01), None
patent: WO 2004/048614 (2004-06-01), None
patent: WO 2005/024053 (2005-03-01), None
Conner et al.., Detection of βs-globin allele by hybridization with synthetic oligonucleotides. PNAS 80 : 278-282(1983).
Saiki et al. , Analysis of enzymatically amplified β-globin and HLA-DQα DNA with allele-specific oligonucleotide probes. Nature 324: 163-166 (1986).
Heid et al., Real Time quantitative PCR. Genome Research 6 :986-994 (1996).
McGrew et al., Quantitation of genomic methylation using ligation-mediated PCR. Biotechniques 15(4) : 722-729 (1993).
S. Steigerwald 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, Feb. 11, 1990, pp. 1435-1439.
Z. Xiong et al., COBRA: A Sensitive And Quantitative DNA Methylation Assay, Nucleic Acids Research, vol. 25, No. 12, Apr. 18, 1997, pp. 2532-2534.
International Search Report mailed Feb. 14, 2006 issued in PCT/US2005/015152, 12 pages.
M. Angers et al., “Optimal Conditions To Use Pfu exo DNA Polymerase For Highly Efficient Ligation-Mediated Polymerase Chain Reaction Protocols”, Nucleic Acids Research, 2001, vol. 29, No. 16 e83, pp. 1-11.
F. Barany, “Genetic Disease Detection And DNA Amplification Using Cloned Thermostable Ligase”, Proc. Natl. Acad. Sci. USA, vol. 88, Jan. 1991, pp. 189-193.
W. Bi et al., “CCR: A Rapid And Simple Approach For Mutation Detection”, Nucleic Acids Research, 1997, vol. 25, No. 14, pp. 2949-2951.
W. Cao, “Recent Developments In Ligase-Mediated Amplification And Detection”, Trends in Biotechnology, vol. 22, No. 1, Jan. 2004, pp. 38-44.
C. Eads et al., “MethyLight: A High-Throughput Assay To Measure DNA Methylation”, Nucleic Acids Research, 2000, vol. 28, No. 8 e32, pp. i-viii.
D. Faulhammer et al., “Fidelity Of Enzymatic Ligation For DNA Computing”, Journal of Computational Biology, vol. 7 No. 6, 2000, pp. 839-848.
M. Fraga et al., “DNA Methylation: A Profile Of Methods And Applications” BioTechniques, vol. 33, Sep. 2002, pp. 632-649.
J. Herman et al., “Methylation-Specific PCR: A Novel PCR Assay For Methylation Status Of CpG Islands”, Proc. Natl. Acad. Sci. USA, vol. 93, Sep. 1996, pp. 9821-9826.
J. N. Housby et al., “Optimised Ligation Of Oligonucleotides By Thermal Ligases: Comparison OfThermus scotoductusAndRhodothermus marinusDNA Ligases To Other Thermophilic Ligases”, Nucleic Acids Research, 2000, vol. 28, No. 3 e10, pp. i-v.
J. N. Housby et al., “Fidelity Of DNA Ligation: A Novel Experimental Approach Based On The Polymerisation Of Libraries Of Oligonucleotides”, Nucleic Acids Research, 1998, vol. 26, No. 18, pp. 4259-4266.
S. Jeon et al., “A Novel ADP-Dependent DNA Ligase FromAeropyrum pernixK1”, FEBS Letters 550, Jul. 2003, pp. 69-73.
H. Klenk et al., “The Complete Genome Sequence Of The Hyperthermophilic, Sulphate-Reducing Archaeon Archaeoglobus Fulgidus”, Nature, vol. 390, Nov. 1997, pp. 364-375.
H. Klenk et al., “The Complete Genome Sequence Of The Hyperthermophilic, Sulphate-Reducing Archaeon Archaeoglobus Fulgidus”, Nature, vol. 394, Jul. 2, 1998, pp. 101.
P. Laird, “The Power And The Promise Of DNA Methylation Markers”, Nature Reviews, Cancer, vol. 3, Apr. 2003, pp. 253-266.
U. Landegren et al., “A Ligase-Mediated Gene Detection Technique”, Science, New Series, vol. 241, No. 4869, Aug. 26, 1988, pp. 1077-1080.
J. Luo et al., “Improving The Fidelity OfThermus thermophilusDNA Ligase”, Nucleic Acids Research, 1996, vol. 24, No. 14, pp. 3071-3078.
I. Martin et al., “ATP-Dependent DNA Ligases”, Genome Biology 2002, vol. 3(4) :Reviews, pp. 3005.1-3005.7.
M. Nakatani et al., “Substrate Recognition And Fidelity Of Strand Joining By An Archaeal DNA Ligase”, Eur. J. Biochem. vol. 269, 2002, pp. 650-656, FEBS 2002.
O. Okochi et al., “Detection Of Mitochondrial DNA Alterations In The Serum Of Hepatocellular Carcinoma Patients1”, Clinical Cancer Research, vol. 8, Sep. 2002, pp. 2875-2878.
C. Pritchard et al., “Effects Of Base Mismatches On Joining Of Short Oligodeoxynucleotides By DNA Ligases”, Nucleic Acids Research, 1997, vol. 25, No. 17, pp. 3403-3407.
T. Rein et al., “Indentifying 5-Methylcytosine And Related Modifications In DNA Genomes”, Nucleic Acids Research, 1998, vol. 26, No. 10, pp. 2255-2264.
S. Shuman, “Vaccinia Virus DNA Ligase: Specificity, Fidelity, And Inhibition”, Biochemistry 1995, vol. 34, pp. 16138-16147.
V. Sriskanda et al., “Characterization Of An ATP-Dependent DNA Ligase From The Thermophilic Archaeon Methanobacterium Thermoautotrophicum”, Nucleic Acids Research, 2000, vol. 28, No. 11, pp. 2221-2228.
V. Sriskanda et al., “Chlorella Virus DNA Ligase: Nick Recognition And Mutational Analysis”, Nucleic Acids Research, 1998, vol. 26, No. 2, pp. 525-531.
V. Sriskanda et al., “Specificity And Fidelity Of Strand Joining By Chlorella Virus DNA Ligase”, Nucleic Acids Research, 1998, vol. 26, No. 15, pp. 3536-3541.
J. Tong et al., “Biochemical Properties Of A High Fidelity DNA Ligase From Thermus Species AK16D”, Nucleic Acids Research, 1999, vol. 27, No. 3, pp. 788-794.
J. Tong et al., “Ligation Reaction Specificities Of An NAD+-Dependent DNA Ligase From The Hyperthermophile Aquifex Aeolicus”, Nucleic Acids Research 2000, vol. 28, No. 6, pp. 1447-1454.
G. Weller et al., “A Family Of DNA Repair Ligases In Bacteria?”, FEBS:Letters 505, 2001, pp. 340-342.
M. Zirvi et al, “Improved Fidelity Of Thermostable Ligases For Detection Of Microsatellite Repeat Sequences Using Nucleoside Analogs”, Nucleic Acids Research, 1999, vol. 27, No. 24 e41, pp. i-vii.
M. Zirvi et al., “Ligase-Based Detection Of Mononucleotide Repeat Sequences”, Nucleic Acids Research, 1999, vol. 27, No. 24 e40, pp. i-viii.
U.S. Appl. No. 11/119,069, filed Apr. 29, 2005.
U.S. Appl. No. 11/118,973, filed Apr. 29, 2005.

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