Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
2005-08-30
2005-08-30
Horlick, Kenneth R. (Department: 1634)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C536S023100, C536S024300
Reexamination Certificate
active
06936702
ABSTRACT:
The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.
REFERENCES:
patent: 4415732 (1983-11-01), Caruthers et al.
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 4863849 (1989-09-01), Melamede
patent: 4962037 (1990-10-01), Jett et al.
patent: 4996143 (1991-02-01), Heller et al.
patent: 5013831 (1991-05-01), Stavrianopoulos
patent: 5047519 (1991-09-01), Hobbs, Jr. et al.
patent: 5241060 (1993-08-01), Engelhardt et al.
patent: 5260433 (1993-11-01), Engelhardt et al.
patent: 5332666 (1994-07-01), Prober et al.
patent: 5405747 (1995-04-01), Jett et al.
patent: 5608063 (1997-03-01), Hobbs, Jr. et al.
patent: 5635608 (1997-06-01), Haugland et al.
patent: 5714330 (1998-02-01), Brenner et al.
patent: 5723591 (1998-03-01), Livak et al.
patent: 5800996 (1998-09-01), Lee et al.
patent: 5846737 (1998-12-01), Kang
patent: 5863727 (1999-01-01), Lee et al.
patent: 5866336 (1999-02-01), Nazarenko et al.
patent: 5872243 (1999-02-01), Gee et al.
patent: 6001567 (1999-12-01), Brow et al.
patent: 6191266 (2001-02-01), Wang
patent: 6210891 (2001-04-01), Nyren et al.
patent: 6232075 (2001-05-01), Williams
patent: 6287821 (2001-09-01), Shi et al.
patent: 6323186 (2001-11-01), Klaubert et al.
patent: 0272007 (1992-03-01), None
patent: WO 98/28440 (1998-07-01), None
patent: WO 00/06770 (2000-02-01), None
patent: WO 00/27521 (2000-05-01), None
patent: WO 00/58507 (2000-10-01), None
patent: WO 00/70073 (2000-11-01), None
U.S. Appl. No. 09/876,375, John G.K. Williams.
Haugland, “Handbook of Fluorescent Probes and Research Chemicals,”Nucleic Acid Detection,8:143-178 (1996).
Agrawal et al., “Site-Specific Functionalization of Oligodeoxynucleotides For Non-Radioactive Labelling,”Tetrahedron Letters,31:1543-1546 (1990).
Ambrose et al., “Single-Molecule Detection With Total Internal Reflection Excitation: Comparing Signal-to-Background and Total Signals in Different Geometries,”Cytometry,36:224-231 (1999).
Araki et al., “Allosteric Regulation of a Ribozyme Activity Through Ligand-Induced Conformational Change,”Nucleic Acids Res.,26:3379-3384 (1998).
Armstrong et al., “Interaction of Substrate Analogues withEscherichia coliDNA-Dependent RNA Polymerase,”Eur. J. Biochem.,70:33-38 (1976).
Asanov et al., “Regenerable Biosensor Platform: A Total Internal Reflection Fluorescence Cell with Electrochemical Control,”Anal. Chem.,70:1156-1163 (1998).
Bergstrom et al., “Palladium-Mediated Coupling between Organic Disulfides and Nucleic Acid Constituents,”JACS,111:374-375 (1989).
Bonnaffe et al., “Potential Lipophilic Nucleotide Prodrugs: Synthesis, Hydrolysis, and Antiretroviral Activity of AZT and d4T Acyl Nucleotides,”J. Org. Chem.,61:895-902 (1996).
Castro et al., “Single-Molecule Detection of Specific Nucleic Acid Sequences in Unamplified Genomic DNA,”Anal. Chem.,69:3915-3920 (1997).
Church et al., “Multiplex DNA Sequencing,”Science,240:185-188 (1988).
Davis et al., “Rapid DNA Sequencing Based Upon Single Molecule Detection,”GAA,8(1):1-7 (1991).
Eckstein et al., “Phosphate Analogs for the Study of DNA Polymerases,”Methods in Enzymology,262:189-217 (1995).
Edman et al., “Conformational transitions monitored for single molecules in solution,”Proc. Natl. Acad. Sci. USA,93:6710-6715 (1996).
Fleischmann et al., “Whole-Genome Random Sequencing and Assembly ofHaemophilus influenzaeRd,”Science,269:496-511 (1995).
Garcia, “Determination of Ion Permeability by Fluorescence Quenching,”Meth. Enzymol.,207:501-511 (1992).
Gebeyehu et al., “Novel biotinylated nucleotide—analogs for labeling and colorimetric detection of DNA,”Nucleic Acids Research,15:4513-4535 (1987).
Gibson et al., “Synthesis and application of derivatizable oligonucleotides,”Nucleic Acids Research,15: 6455-6467(1987).
Giusti et al, “Synthesis and Characterization of 5'-Fluorescent-dye-labeled Oligonucleotides,”PCR Methods and Applications,2: 223-227 (1993).
Goody et al., “The Enzymatic Synthesis of Thiophosphate Analogs of Nucleotides,”Biochem. Biophys. Acta.,276:155-161 (1972).
Grachev et al., “ATP γ-Anilidate; A Substrate of DNA-Dependent RNA-Polymerase ofEscherichia Coli,” FEBS Lett.,49:163-166 (1974).
Grachev et al., “Studies on the functional topography ofEscherichia coliRNA polymerase,”Eur. J. Biochem.,163:113-121 (1987).
Griffin et al., “Specific Covalent Labeling of Recombinant Protein Molecules Inside Live Cells,”Science,281:269-272 (1998).
Gupta et al., “A general method for the synthesis of 3'-sulfhydryl and phosphate group containing oligonucleotides,”Nucleic Acids Research,19:3019-3025 (1991).
Gyllensten et al., “PCR-based HLA Class II Typing,”PCR Methods and Applications,1: 91-98 (1991).
Haralambidis et al., “Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides,”Nucleic Acids Research,15: 4856-4876 (1987).
Hobbs, “Palladium-Catalyzed Synthesis of Alkynylamino Nucleosides. A Universal Linker for Nucleic Acids,”J. Org. Chem.,54: 3420-3422 (1989).
Hunkapiller et al., “Large-Scale and Automated DNA Sequence Determination,”Science,254: 59-67 (1991).
Hyman, “A New Method of Sequencing DNA,”DNA Biochemistry,174:423-436 (1988).
Jett et al., “High-Speed DNA Sequencing: An Approach Based Upon Fluorescence Detection of Single Molecules,”J. Biomol. Struct. Dyn.,7:301-309 (1989).
Kadokura, M. et al., “Efficient Synthesis of γ-Methyl-Capped Guanosine 5'-Triphosphate as a 5'-Terminal Unique Structure of U6 RNA via a New Triphosphate Bond Formation Involving Activation of Methyl Phosphorimidazolidate Using ZnCl2as a Catalyst in DMF under Anhydrous Conditions,”Tetrahedron Letters,38:8359-8362 (1997).
Kinjo et al., “Ultrasensitive hybridization analysis using fluorescence correlation spectroscopy,”Nucleic Acids Res.,23:1795-1799 (1995).
Köster et al., “A strategy for rapid and efficient DNA sequencing by mass spectrometry,”Nature Biotechnology,14:1123-1128 (1996).
Kreimeyer et al., “Transmembrane Transport of Adenosine 5'-Triphosphate Using a Lipophilic Cholesterol Derivative,”Angew. Chem. Int. Ed.,37:2853-2855 (1998).
Kreimeyer et al., “Synthesis of Acylphosphates of Purine Ribonucleosides,”Tetrahedron Letters,37:8739-8742 (1006).
Laws et al., “Fluorescence Quenching Studies: Analysis of Nonlinear Stern—Volmer Data,”Meth. Enzymol.,210:448-463 (1992).
Li et al., “Design, Synthesis, and Spectroscopic Properties of Peptide-Bridged Fluorescence Energy-Transfer Cassettes,”Bioconjugate Chem.,10:241-245 (1999).
Luo et al., “Fluorous Mixture Synthesis: A Fluorous-Tagging Strategy for the Synthesis and Separation of Mixtures of Organic Compounds,”Science,291:1766-769 (2001).
Marshall, “Rules for the visible absorption spectra of halogenated Fluorescein dyes,”Histochemical J.,7:299-303 (1975).
Maxam et al., “A new method for sequencing DNA,”Proc. Natl. Acad. Sci. USA,74: 560-564 (1977).
Narasimhan et al., “p-Benzoquinone activation of metal oxide electrodes for attachment of enzymes,”Enzyme Microb. Technol.,7:283-286 (1985).
Nelson et al., “Bifunction
Bashford Gregory R.
Chen Jiyan
Draney Dan
Narayanan Nara
Reynolds Bambi L.
Horlick Kenneth R.
LI-COR, Inc.
Lu Frank
LandOfFree
Charge-switch nucleotides does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Charge-switch nucleotides, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Charge-switch nucleotides will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3468636