Methods and kits for identifying target nucleotides in mixed...

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

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C435S091200

Reexamination Certificate

active

07427479

ABSTRACT:
Ligation-based methods and kits are disclosed for identifying at least two target nucleotides in a mixed population sample, that is a sample that contains or potentially contains target nucleic acid sequences from more than one source. Typically, two ligation reaction compositions are formed, ligation products generated, and the ligation products or their surrogates are analyzed to identify target nucleotides in the mixed population sample. In certain embodiments, the target nucleic acid sequences, the ligation products, or both are amplified. In certain embodiments, multiplex amplification and/or ligation reactions are performed.

REFERENCES:
patent: 4988617 (1991-01-01), Landegren et al.
patent: 5700672 (1997-12-01), Mathur et al.
patent: 6130073 (2000-10-01), Eggerding
patent: 6331393 (2001-12-01), Laird et al.
patent: WO 91/17239 (1991-11-01), None
patent: WO 96/15271 (1996-05-01), None
patent: WO 98/03673 (1998-01-01), None
M. Khanna et al., “Multiplex PCR/LDR for Detection of K-ras Mutations in Primary Colon Tumors”, Oncogene (1999), vol. 18, pp. 27-38, XP009006346.
Partial International Search Report issued in International Application No. PCT/US2005/015027 on Dec. 12, 2006, 10 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.
L. Aravind et al., “Prokaryotic Homologs Of The Eukatyotic DNA-End-Binding Protein Ku, Novel Domains In The Ku Protein And Prediction Of A Prokaryotic Double-Strand Break Repair System”, Genome Research, 2001, vol. 11, pp. 1365-1374.
F. Barany, “Genetic Disease Detection And DNA Amplifcation 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.
C. Goffin et al., “Nicks 3′ 5′ To AP Sites Or To Mispaired Bases, And One-Nucleotide Gaps Can Be Sealed By T4 DNA Ligase”, Nucleic Acids Research, 1987, vol. 15, No. 21, pp. 8755-8771
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 Of Thermus Scotoductus And Rhodothermus Marinus DNA 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.
I. Husain et al., “Purification And Characterization Of DNA Ligase III From Bovine Testes”, The Journal of Biological Chemistry, vol. 270, No. 16, Apr. 21, 1995, pp. 9683-9690.
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 Archeaoglobus Fulgidus”, Nature, vol. 390, Nov. 1997, pp. 364-375.
H. Klenk et al., “The Complete Genome Sequence Of the Hyperthermiphilic 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. Lou et al., “Improving The Fidelity Of Thermus Thermophilus DNA 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 Patients”, 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., “Identifying 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.
V. Sriskanda et al., “NAD+-Dependent DNA Ligase Encoded By A Eukaryotic Virus”, The Journal of Biological Chemistry, vol. 276, No. 39, Sep. 28, 2001, pp. 36100-36109.
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. 11/119,985, filed May 2, 2005.

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Methods and kits for identifying target nucleotides in mixed... does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Methods and kits for identifying target nucleotides in mixed..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods and kits for identifying target nucleotides in mixed... will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3980959

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.