DNA sequencing by mass spectrometry via exonuclease degradation

Details DNA sequencing by mass spectrometry via exonuclease degradation DNA sequencing by mass spectrometry via exonuclease degradation

1995-05-30

1998-12-22

Horlick, Kenneth R.

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

435 912, 536 221, 536 243, 250281, 250282, 935 77, C12Q 168, C12P 1934, C07H 1900, C07H 2104

Patent

active

058517650

ABSTRACT:
Methods for determining the sequence of nucleic acids by cleaving the nucleic acid unilaterally from a first end with an exonuclease activity to sequentially release individual nucleotides, identifying each of the sequentially release nucleotides by mass spectrometry, and determining the sequence of the nucleic acid from the identified nucleotides are disclosed. The method is amenable to multiplexing for simulataneously determining more than one nuleic acid sequence.

REFERENCES:
patent: 4997928 (1991-03-01), Hobbs, Jr.
patent: 5002868 (1991-03-01), Jacobson et al.
patent: 5288644 (1994-02-01), Beavis et al.
Brennan et al, New Methods to sequence DNA by mass spectrometry, 1990. New technologies in Cytometry and Molecular biology, vol. 1206 pp. 60-67.
Miller et al. Synthesis of oligo-2'-deoxyribonucleoside methyl phosphonate M oligonucleotides and analogues a practical approach, Eskstein ed, 1991 IRL Press.
Nakamaye et al. Direct sequencing of polymerase chain reaction amplified DNA fragments through the incorporation if deoxynucleotide 60 -thiotriphosphate, Nucleic Acids Research 1988, vol. 16(21) pp. 9947-9959.
Ardrey, "Electrospray Mass Spectrometry," Spectroscopy Europe, vol. 4, No. 4, 11-18, 1992.
Arlinghaus et al., "Applications of resonance ionization spectroscopy for semiconductor, environmental and biomedical analysis, and for DNA sequencing," SPIE, vol. 1435, 26-35, 1991.
Axelrod et al., "Transcription from Bacteriophage T7 and SP6 RNA Polymerase Promoters in the Presence of 3'-Deoxyribonucleoside 5'-Triphosphate Chain Terminators," Biochemistry, vol. 24, 5716-5723, 1985.
Bains, "DNA Sequencing by Mass Spectrometry. Outline of a Potential Future Application," CHIMICAOGGI Reiew, Oct. 1991.
Bains, "Setting a Sequence to Sequence a Sequence," Bio/Technology, vol. 10, 757-758, 1992.
Barrell, "DNA sequencing: present limitations and prospects for the future," The FASEB Journal, vol. 5, 40-45, 1991.
Beck and Koster, "Applications of dioxetane Chemiluminescent Probes to Molecular Biology," Analytical Chemistry, vol. 62, No. 21, 2258-2270, 1990.
Beck et al., "Chemiluminescent detection of DNA: application for DNA sequencing and hybridization," Nucleic Acids Research, vol. 17, No. 13, 5115-5123, 1989.
Brennen, et al., "New Methods to Sequence DNA by Mass Spectrometry," SPIE/New Technologies in Cytometry and Molecular Biology, vol. 1206, 60-67, 1990.
Brumbaugh et al., "Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores," PNAS USA, vol. 85, 5610-5614, 1988.
Chu et al., "Synthesis of an amplifiable reporter RNA for bioassays," Nucleic Acids Research, vol. 14, No. 14, 5591-5603, 1986.
Church et al., "Multiplex DNA Sequencing," Science, Research Articles, vol. 240, 185-188, 1988.
Covey et al., "The Determination of Protein, Oligonucleotide and Peptide Molecular Weights by Ion-spray Mass Spectrometry," Rapid Communications in Mass Spectrometry, vol. 2, No. 11, 249-256, 1988.
Crain, "Mass spectrometric techniques in nucleic acid research," Mass Spectrometry Reviews, vol. 9, 505-554, 1990.
Eckstein, ed., Oligonucleotides and Analogues: A Practical Approach, (IRL Press at Oxford University Press) 56-57, 137-139, 256-259.
Eckstein, "Nucleoside Phosphorothioates," Ann. Rev. Biochem., vol. 54, 367-402, 1985.
Eckstein, "Phosphorothioate Analogues of Nucleotides," Accounts of Chemical Research, vol. 12, 204-210, 1978.
Eckstein and Goody, "Synthesis and Properties of Diastereoisomers of Adenosine 5'-(O-1-Thiotriphosphate) and Adenosine 5'-(O-2-Thiotriphosphate)," Biochemistry, vol. 15, No. 8, 1685-1691, 1976.
Edmonds and Smith, "Electrospray Ionization Mass Spectrometry," Methods in Enzymology, vol. 193, 412-431, 1990.
Frank et al., "DNA chain length and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamine-gels," Nucleic Acids Research, vol. 6, No. 6, 2069-2087, 1979.
Gildea et al., "A versatile acid-labile linker for modification of synthetic biomolecules," Tetrahedron, Letters, vol. 31, No. 49, 7095-7098, 1990.
Green and Jorgenson, "Variable-wavelength on-column fluorescence detector for open-tubular zone electrophoresis," Journal of Chromatography, vol. 352, 337-343, 1986.
Haralambidis et al., "Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oliodexyribonucleotides," Nucleic Acids Research, vol. 15, No. 12, 4857-4876, 1987.
Higuchi et al., "A general method of in iro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions," Nucleic Acids Research, ol. 16, No. 15, 7351-7367, 1988.
Hillenkamp et al., "Matrix Assisted UV-Laser Desorption/Ionization: A New Approach to Mass Spectrometry of Large Biomolecules," Biological Mass Spectrometry, 49-61, 1987.
Hobbs and Eckstein, "A General Method for the Synthesis of 2'-Azido-2'-deoxy-and 2'-Amino-2'-deoxyribofuranosyl Purines," Journal Organic Chemistry, vol. 42, No. 4, 714-719, 1977.
Huth-Fehre et al., "Matrix-assisted Laser Desorption Mass Spectrometry of Oligodeoxythymidylic Acids," Rapid Communications in Mass Spectrometry, vol. 6, 209-213, 1992.
Hymen, "A New Method of Sequencing DNA," Analytical Biochemistry, vol. 174, 423-436, 1988.
Ikehara and Maruyama, "Studies of Nucleosides and Nucleotides. LXXIX. Purine Cyclonucleosides. (37). The Total Synthesis of an Antibiotic 2'-Amino-2'-deoxyguanosine," Chem. Pharm. Bull., vol. 26, No. 1, 240-244, 1978.
Imazawa and Eckstein, "Facile Synthesis of 2'-Amino-2'-deoxyribofuranosyl Purines," Journal Organic Chemistry, vol. 44, No. 12, 2039-2041, 1979.
Jacobson et al., "Applications of Mass Spectrometry to DNA Sequencing," GATA, vol. 8, No. 8, 223-229, 1991.
Jett et al., "High-Speed DNA Sequencing: An Approach Based Upon Fluorescence Detection of Single Molecules," Journal of Bimolecular Structure & Dynamics, vol. 7, No. 2, 301-309, 1989.
Khrapko et al., "An oligonucleotide hybridization approach to DNA sequencing," FEBS, Letters, vol. 256, No. 1, 2, 118-122, 1989.
Koster et al., "N-Acyl Protecting Groups for Deoxynucleosides, a Quantitative and Comparative Study," Tetrahedron, vol. 37, No. 2, 363-369, 1981.
Koster et al., "Oligonucleotide synthesis and multiplex DNA sequencing using chemiluminescent detection," Nucleic Acids Research, Symposium Series, No. 24, 318-321, 1991.
Lim and Pene, "Optimal conditions for Supercoil DNA Sequencing with the Escherichia coli DNA Polymerase I Large Fragment," Gene. Anal. Tech., vol. 5, 32-39, 1988.
Nakamaye et al., "Direct sequencing of polymerase chain reaction amplified DNA fragments through the incorporation of deoxynucleoside .alpha.-thiototrip0hosphates," Nucleic Acids Research, vol. 16, No. 21, 9947-9959, 1988.
Nelson, et al., "Time-of-Flight Mass Spectrometry of Nucleic Acids by Laser Ablation and Ionization from a Frozen Aqueous Matrix," Rapid Communications in Mass spectrometry, vol. 4, No. 9, 348-351, 1990.
Nelson et al., "Volatilization of High Molecular Weight DNA by Pulsed Laser Ablation of Frozen Aqueous Solutions," Science, Reports, vol. 246, 1585-1587, 1989.
Perrouault et al., "Sequence-specific artificial photo-induced endonucleases based on triple helix-forming oligonucleotides," Nature (Letters), vol. 344, 358-360, 1990.
Pitulle et al., "Initiator oligonucleotides for the combination of chemical and enzymatic RNA synthesis," Gene, ol. 112, 101-105, 1992.
Prober et al., "A System for Rapid DNA Sequencing with Fluorescent Chain-Terminating Dedeoxynucleotides," Science, Research Articles, vol. 238, 336-341, 1987.
Ruth, "Oligodeoxynucleotides with Reporter Groups Attached to the Base," Practical appraoch Series: Oligonucleotides and Analogues, 255-282, 1991.
Schram, "Mass Spectrometry of Nucleic Acid Components," Biomedical Applications of Mass Spectrometry, vol. 34, 203-287, 1990.
Seela and Gumbiowski, "98. 1,7-Dideaza-2',3'-dideoxyadenosine: Syntheses of of Purine N(1) during HIV-1 Reverse Transcriptase Inhibition," Helvetica Chimica Acta, vol. 74, 1048-1058, 1991.
Singh et al., "Oligonucleotides, part 5+: synthesis and fluorescence studie

Affiliated with

Also associated with

Rating

DNA sequencing by mass spectrometry via exonuclease degradation does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with DNA sequencing by mass spectrometry via exonuclease degradation, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and DNA sequencing by mass spectrometry via exonuclease degradation will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-2045715