De novo or “universal” sequencing array

Details De novo or “universal” sequencing array De novo or “universal” sequencing array

2005-09-20

2005-09-20

Horlick, Kenneth R. (Department: 1637)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S091200, C435S287200, C536S024300

Reexamination Certificate

active

06946249

ABSTRACT:
The present invention describes a novel nucleic acid sequencing reagent which consists of a capture moiety, a spacer region and a sequence specific hybridizing region of 4-8 bases. The nucleic acid sequencing reagent of the present invention can also contain an attachment moiety. The nucleic acid sequencing reagent can be arranged into a nested array. This array configuration can then be used to sequence a given template without prior knowledge (de novo) of the wild type or expected sequence in conjunction with primer extension in the presence of a labeled chain terminating nucleotide.

REFERENCES:
patent: 4521509 (1985-06-01), Benkovic et al.
patent: 4656127 (1987-04-01), Mundy
patent: 4812856 (1989-03-01), Wallace
patent: 4851331 (1989-07-01), Vary et al.
patent: 4981783 (1991-01-01), Augenlicht
patent: 5002867 (1991-03-01), Macevicz
patent: 5053100 (1991-10-01), Hayes et al.
patent: 5151507 (1992-09-01), Hobbs et al.
patent: 5302509 (1994-04-01), Cheeseman
patent: 5445933 (1995-08-01), Eadie et al.
patent: 5445934 (1995-08-01), Fodor et al.
patent: 5503980 (1996-04-01), Cantor
patent: 5518900 (1996-05-01), Nikiforov et al.
patent: 5547839 (1996-08-01), Dower et al.
patent: 5599695 (1997-02-01), Pease et al.
patent: 5691141 (1997-11-01), Köster
patent: 5700637 (1997-12-01), Southern et al.
patent: 5759779 (1998-06-01), Dehlinger
patent: 5795714 (1998-08-01), Cantor et al.
patent: 6265155 (2001-07-01), Meade et al.
patent: 6322968 (2001-11-01), Head et al.
patent: 6337188 (2002-01-01), Head et al.
patent: 8910414 (1989-11-01), None
patent: WO 91/02087 (1991-02-01), None
patent: 9215712 (1992-09-01), None
patent: 9500669 (1995-01-01), None
patent: WO 95/03401 (1995-02-01), None
patent: 9511995 (1995-05-01), None
patent: WO 96/13609 (1996-05-01), None
patent: WO 96/17957 (1996-06-01), None
patent: WO 97/26368 (1997-07-01), None
patent: WO 97/27317 (1997-07-01), None
patent: WO 98/49341 (1998-11-01), None
Spiegelman, S., “Hybrid Nucleic Acids,” Scientific American, 210:48-56 (1964).
Sanger, F. et al., “A Rapid Method for Determining the Sequences in DNA by Primed Synthesis with DNA Polymerase,” J. Mol. Bio., 94: 441-448 (1975).
Maxam, A.M. et al., “A New Method for Sequencing DNA,” Proc. Natl. Acad. Sci. USA, 74:560-564 (1977).
Matteucci, M.D. et al., “Synthesis of Deoxyoligonucleotides on a Polymer Support,” J. Am. Chem. Soc., 103:3185-3191 (1981).
Sliwkowski, M.X. et al, “Resolution of Sulphydryl Oxidase from γglutamyltransferase in Bovine Milk by Covalent Chromatography on Cysteinylsuccinamidopropyl-glass,” Biochem J., 209:731-739 (1983).
Messing, J., “New M13 Vectors for Cloning,” Methods in Enzymology, 101:20-78 (1983).
Mitsuya, H. et al., “Inhibition of the In Vitro infectivity and Cytopathic Effect of Human T-lymphotrophic Virus Type III/Lymphadenopathy-associatedVirus (HTLV-III/LAV) by 2′,3′-dideoxynucleosides,” Proc. Natl. Acad. Sci. USA, 83:1911-1915 (1986).
Antrazhev et al., “3′ Substituted Nucleoside Phosphorothioates Terminate DNA Synthesis Catalyzed by Various DNA Polymerases,” Bio Org Khim, 13:1045-1052 (1987) ( Russian Article, English abstract).
Wong, C. et al., “Characterization of β-thalassaemia Mutations Using Direct Genomic Sequencing of Amplified Single Copy DNA,” Nature, 330:384-386 (1987).
Ott, J. et al., “Protection of Oligonucleotide Primers Agaisnt Degradation by DNA Polymerase I,” Biochemistry, 26:8237-8241 (1987).
White, R. et al., “Chromosome Mapping with DNA Markers,” Scientific American, 258:40-48, (1988).
Sayers, J.R. et al., “5′-3′Exonucleases in Phosphorothioate-Based Oligonucleotide-Directed Mutagenesis,” Nucleic Acids Research, 16:791-802 (1988).
Gyllensten, U.B. et al., “Generation of Single-Stranded DNA by the Polymerase Chain Reaction and Its Application to Direct Sequencing of the HLA-DQA locus,” Proc. Natl. Acad. Sci., U.S.A., 85:7652-7656 (1988).
Engelke, D.R. et al., “Direct Sequencing of Enzymatically Amplified Human Genomic DNA,” Proc. Natl. Acad. Sci. U.S.A., 85:544-548 (1988).
Higuchi, R.G. et al., “Production of Single-Stranded DNA Templates by Exonuclease Digestion Following the Polymerase Chain Reaction,” Nucleic Acids Reaseach, 17:5865 (1989).
Miholovic, M. et al., “An Efficient Method for Sequncing PCR Amplified DNA,” BioTechniques, 7:14-16 (1989).
Nickerson, D.A. et al., “Automated DNA Diagnostics Using an ELISA-based oligonucleotide Ligation Assay,” Proc. Natl. Acad. Sci. USA, 87:8923-8927 (1990).
Running, J.A. et al., “A Procedure for Productive Coupling of Synthetic Oligonucleotides to the Polystyrene Microtiter Wells for Hybridization Capture,” BioTechniques, 8:276-277 (1990).
Rasmussen, S.R. et al., “Covalent Immobilization of DNA onto Polystyrene Microwells: The Molecules Are Only Bound at the 5′ End,” Analytical Biochemistry, 198:138-142 (1991).
Jalanko, A. et al., “Screening for Defined Cystic Fibrosis Mutations by Solid-Phase Minisequencing,” Clin. Chem., 38:39-43 (1992).
Maskos, U. et al., “Oligonucleotide Hybridisations on Glass Supports: A Novel Linker for OIigonucleotide Synthesis and Hybridisation Properties of Oligonucleotides Synthesised in situ,” Nucleic Acids Research, 20:1679-1684 (1992).
Yuzhakov, A.A., et al., “3′-Mercapto-2′, 3′-Dideoxynucleotides are High Effective Terminators of DNA Synthesis Catalyzed by HIV Reverse Transciptase,” FEBS Letters, 306:185-188 (1992).
Kawai, S. et al., “A Simple Method of Detecting Amplified DNA with Immobilized Probes on Microtiter Wells,” Analytical Biochemistry, 209:63-69 (1993).
Fahy, et al., “Design and Synthesis of Polyacrylamide Based Oligonucleotide Supports for Use in Nucleic Acid Diagnostics,” Nucleic Acids Research, 21:1819-1826 (1993).
Newton, C.R. et al, “The Production of PcR Products with 5′ Single-Stranded Tails Using Primers that Incorporate Novel Phosphoramidite Intermediates,” Nucleic Acids Research, 21:1155-1162 (1993).
Holmstrom, K. et al., “A Highly Sensitive and Fast Nonradioactive Method for Detection of Polymerase Chain Reaction Products,” Analytical Biochemistry, 209:278-283 (1993).
Lamture, J.B. et al., “Direct Detection of Nucleic Acid Hybridization on the Surface of a Charge Coupled Device,” Nucleic Acids Research, 22:2121-2125 (1994).
Southern, E.M. et al., “Arrays of Complementary Oligonucleotides for Analysing the Hybridisation behaviour of Nucleic Acids,” Nucleic Acids Research, 22:1368-1373 (1994).
Herrlein, M.K. et al., “3′-Amino-Modified Nucleotides Useful as Potent Chain Terminators for Current DNA Sequencing Methods,” Helvetica Chimica Acta, 77:586-596 (1994).
Beattie, W.G. et al., “Hybridization of DNA Targets to Glass-Tethered Oligonucleotide Probes,” Molecular Biotechnology, 4:213-225 (1995).
Haff, L.A. et al., “Single-Nucleotide Polymorphism Identification Assays Using a Thermostable DNA Polymerase and Delayed Extraction MALDI-TOF Mass Spectrometry,” Genome Research, 97:378-388 (1997).
Landegren, U. et al., “A Ligase-Mediated Gene Detection Technique,” Science, 241:1077-1080 (1998).
Guo, Z. et al., “Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports,”Nucleic Acids Research,22: 5456-5465 (1994).
Chetverin, A.B., et al., “Oligonucleotide Arrays: New Concepts and Possibilities,” BioTechnology, 12:1093-1099 (1994).
Kornher, J.S., et al., “Mutation Detection Using Nucleotide Analogs that Alter Electrophoretic Mobility,” Nucleic Acids Research, 17:7779-7784 (1989).
Sokolov, B.P., “Primer Extension Technique for the Detection of Single Nucleotide in Genomic DNA,” Nucleic Acids Research

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