High throughput nucleic acid sequencing by expansion

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

Reexamination Certificate

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C435S091200, C536S024310, C536S024320

Reexamination Certificate

active

07939259

ABSTRACT:
Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected. Corresponding products, including Xpandomers and oligomeric and monomeric substrate constructs are also disclosed.

REFERENCES:
patent: 4415732 (1983-11-01), Caruthers et al.
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 5378825 (1995-01-01), Cook et al.
patent: 5432272 (1995-07-01), Benner
patent: 5770713 (1998-06-01), Imbach et al.
patent: 5804375 (1998-09-01), Gelfand et al.
patent: 5844106 (1998-12-01), Seela et al.
patent: 6150510 (2000-11-01), Seela et al.
patent: 6242589 (2001-06-01), Cook et al.
patent: 6329178 (2001-12-01), Patel et al.
patent: 6395524 (2002-05-01), Loeb et al.
patent: 6465193 (2002-10-01), Akeson et al.
patent: 6602695 (2003-08-01), Patel et al.
patent: 6627067 (2003-09-01), Branton et al.
patent: 6723513 (2004-04-01), Lexow
patent: 6951720 (2005-10-01), Burgin, Jr. et al.
patent: 7060440 (2006-06-01), Kless
patent: 7060507 (2006-06-01), Akeson et al.
patent: 7371851 (2008-05-01), Lexow
patent: 2002/0028458 (2002-03-01), Lexow
patent: 2002/0182601 (2002-12-01), Sampson et al.
patent: 2005/0032053 (2005-02-01), Sampson
patent: 2007/0048748 (2007-03-01), Williams et al.
patent: 2007/0254280 (2007-11-01), Lexow et al.
patent: 2009/0181385 (2009-07-01), McKernan et al.
patent: WO 92/02258 (1992-02-01), None
patent: WO 93/10820 (1993-06-01), None
patent: WO 94/22892 (1994-10-01), None
patent: WO 94/24144 (1994-10-01), None
patent: WO 00/79257 (2000-12-01), None
patent: WO 2004/094663 (2004-11-01), None
Abramova et al., “A facile and effective synthesis of dinucleotide 5′-triphosphates”,Bioorg Med Chem15: 6549-6555, 2007.
Agrawal, “Functionalization of Oligonucleotides with Amino Groups and Attachment of Amino Specific Reporter Groups”,Methods in Molecular Biology, vol. 26:Protocols for Oligonucleotide Conjugates, Agrawal, ed., Humana Press Inc., Totowa, NJ, 1994, pp. 93-120.
Agrawal et al., “Oliogodeoxynucleoside phosphoramidates and phosphorothioates as inhibitors of human immunodeficiency virus”,PNAS 85: 7079-83, Oct. 1988.
Agrawal et al., “Site specific functionalization of oligonucleotides for attaching two different reporter groups”,Nucleic Acids Research18(18): 5419-5423, 1990.
Benoiton, “Chemistry of Peptide Synthesis”, CRC Press, Ottawa, Ontario, Canada, 2005.
Branton et al., “The potential and challenges of nanopore sequencing,”Nature Biotechnology26(10): 1146-1153, Oct. 2008.
Burgess and Cook, “Syntheses of Nucleoside Triphosphates”,Chem. Rev. 100(6): 2047-2059, 2000.
de Lange et al., “Cell biology beyond the diffraction limit: near-field scanning optical microscopy,”J. Cell Sci. 114: 4153-60, 2001.
DeMattei et al., “Designed Dendrimer Syntheses by Self-Assembly of Single-Site, ssDNA Functionalized Dendrons”,Nano Letters4(5): 771-77, 2004.
De Mesmaeker et al., “Amide Backbone Modifications for Antisense Oligonucleotides Carrying Potential Intercalating Substituents: Influence on the Thermodynamic Stability of the Corresponding Duplexes with RNA- and DNA-Complements”,Bioorganic&Medicinal Chemistry Letters7(14): 1869-1874, 1997.
Efimov et al., “Synthesis of polyacrylamidesN-substituted with PNA-like oligonucleotide mimics for molecular diagnostic applications,”Nucleic Acids Res. 27(22): 4416-4426, 1999.
Fathi et al., “Oligonucleotides with novel, cationic backbone substituents: aminoethylphosphonates”,Nucleic Acids Research22(24): 5416-5424, 1994.
Ferree et al., “Electrokinetic Stretching of Tethered DNA”,Biophysical Journal85: 2539-2546, Oct. 2003.
Gellman, “Foldamers: a manifesto”,Acc Chem Res31(4): 173-80, 1998.
Gish et al., “DNA and RNA Sequence Determination Based on Phosphorothioate Chemistry”,Science240(4858): 1520-1522, Jun. 10, 1988.
Holmes et al., “Reagents for Combinatorial Organic Synthesis: Development of a Newo-Nitrobenzyl Photolabile Linker for Solid Phase Synthesis”,J Org Chem, 60(8): 2318-19, 1995.
Hong et al., “DNA microarrays on nanoscale-controlled surface”,Nucleic Acids Research33(12): e106(1-8), 2005.
Igloi et al., “Enzymatic Addition of Fluorescein- or Biotin-RiboUTP to Oligonucleotides Results in Primers Suitable for DNA Sequencing and PCR”,BioTechniques15(3): 486-497, 1993.
Jo et al., “A single-molecule barcoding system using nanoslits for DNA analysis”,PNAS104(8): 2673-2678, Feb. 20, 2007.
Ju et al., “Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators”,PNAS103(52): 19635-19640, Dec. 26, 2006.
Kayushin et al., “A convenient approach to the synthesis of trinucleotide phosphoramidites—synthons for the generation of oligonucleotide/ peptide libraries,”Nucl Acids Res24(19): 3748-55, 1996.
Kenney et al., “Mutation Typing Using Electrophoresis and Gel-Immobilized Acrydite™ Probes”,BioTechniques25(3): 516-21, 1998.
Lee, “Ligase Chain Reaction”,Biologicals24(3): 197-199, 1996.
Lee, “Nanoelectrode-Gated Detection of Individual Molecules with Potential for Rapid DNA Sequencing”,Solid State Phenomena121-123: 1379-1386, 2007.
Lee and Meller, “Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA Chains,” Chapter 8 inNew High Throughput Technologies for DNA Sequencing and Genomics, vol. 2 (Perspectives in Bioanalysis), Mitchelson, ed., Elsevier B.V., Amsterdam, The Netherlands, 2007, pp. 245-263.
Levene et al., “Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations,”Science299: 682-86, Jan. 31, 2003.
Mag et al., “Synthesis and selective cleavage of an oligodeoxynucleotide containing a bridged internucleotide 5′-phosphorothioate linkage”,Nucleic Acids Research19(7): 1437-1441, 1991.
Mag et al., “Synthesis and selective cleavage of oligodeoxyribonucleotides containing non-chiral internucleotide phosphoramidate linkages”,Nucleic Acids Research17(15): 5973-5988, 1989.
Matsukura et al., “Phosphorothioate analogs of oligodeoxynucleotides: Inhibitors of replication and cytopathic effects of human immunodeficiency virus”,PNAS84: 7706-7710, Nov. 1987.
Meagher et al., “End-labeled free-solution electrophoresis of DNA”,Electrophoresis26: 331-350, 2005.
Merrifield, “Solid Phase Peptide Synthesis. I. The Synthesis of a Tetrapeptide”,J. Am. Chem. Soc.85: 2149-2154, Jul. 20, 1963.
Metzker et al., “Termination of DNA synthesis by novel 3′-modified-deoxyribonucleoside 5′-triphosphates,”Nucleic Acids Res. 22(20): 4259-4267, 1994.
Miles, “Scanning Probe Microscopy—Probing the Future,”Science277: 1845-1847, Sep. 19, 1997.
Montoliu et al., “Visualization of Large DNA Molecules by Electron Microscopy with Polyamines: Application to the Analysis of Yeast Endogenous and artificial Chromosomes”,J. Mol. Biol. 246: 486-92, 1995.
Nauwelaerts et al., “Cleavage of DNA without loss of genetic information by incorporation of a disaccha

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