Solid phase sequencing of double-stranded nucleic acids

Fu, Dong-Jing; Cantor, Charles R; Koster, Hubert; Smith, Cassandra L

Title: Solid phase sequencing of double-stranded nucleic acids

Patent · Tue Jan 01 00:00:00 EST 2002

OSTI ID:874666

Fu, Dong-Jing ^[1]; Cantor, Charles R ^[2]; Koster, Hubert ^[3]; Smith, Cassandra L ^[2]

Waltham, MA
Boston, MA
Concord, MA

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

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Research Organization:: Boston University

DOE Contract Number:: FG02-93ER61609

Assignee:: Boston University (Boston, MA); Sequenom, Inc. (San Diego, CA)

Patent Number(s):: US 6436635

OSTI ID:: 874666

Country of Publication:: United States

Language:: English

References (23)

An Algorithm for the DNA Sequence Generation from k-Tuple Word Contents of the Minimal Number of Random Fragments Drmanac, R.; Labat, I.; Crkvenjakov, R. Journal of Biomolecular Structure and Dynamics, Vol. 8, Issue 5 https://doi.org/10.1080/07391102.1991.10507867	journal	April 1991
Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation Maskos, Uwe; Southern, Edwin M. Nucleic Acids Research, Vol. 20, Issue 7 https://doi.org/10.1093/nar/20.7.1675	journal	January 1992
Improved Chips for Sequencing by Hybridization Pevzner, P. A.; Lysov, Yu. P.; Khrapko, K. R. Journal of Biomolecular Structure and Dynamics, Vol. 9, Issue 2 https://doi.org/10.1080/07391102.1991.10507920	journal	October 1991
Optical properties of specific complexes between complementary oligoribonucleotides Gennis, Robert B.; Cantor, Charles R. Biochemistry, Vol. 9, Issue 24 https://doi.org/10.1021/bi00826a014	journal	November 1970
A method for DNA sequencing by hybridization with oligonucleotide matrix Khrapko, K. R.; Lysov, Yu. P.; Khorlin, A. A. DNA Sequence, Vol. 1, Issue 6 https://doi.org/10.3109/10425179109020793	journal	January 1991
An oligonucleotide hybridization approach to DNA sequencing Khrapko, K. R.; P. Lysov, Yu; Khorlyn, A. A. FEBS Letters, Vol. 256, Issue 1-2, p. 118-122 https://doi.org/10.1016/0014-5793(89)81730-2	journal	October 1989
Oligonucleotide hybridisations on glass supports: a novel linker for oligonucleotide synthesis and hybridisation properties of oligonucleotides synthesised in situ Maskos, Uwe; Southern, Edwin M. Nucleic Acids Research, Vol. 20, Issue 7 https://doi.org/10.1093/nar/20.7.1679	journal	January 1992
Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models Southern, E. M.; Maskos, U.; Elder, J. K. Genomics, Vol. 13, Issue 4, p. 1008-1017 https://doi.org/10.1016/0888-7543(92)90014-J	journal	August 1992
Report on the sequencing by Hybridization workshop Cantor, C. R.; Mirzabekov, A.; Southern, E. Genomics, Vol. 13, Issue 4 https://doi.org/10.1016/0888-7543(92)90079-8	journal	August 1992
A versatile acid-labile linker for modification of synthetic biomolecules Oildea, Brian D.; Coull, James M.; Köster, Hubert Tetrahedron Letters, Vol. 31, Issue 49, p. 7095-7098 https://doi.org/10.1016/S0040-4039(00)97249-6	journal	January 1990
Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide Nielsen, P.; Egholm, M.; Berg, R. Science, Vol. 254, Issue 5037 https://doi.org/10.1126/science.1962210	journal	December 1991
Reliable Hybridization of Oligonucleotides as Short as Six Nucleotides Drmanac, R.; Strezoska, Z.; Labat, I. DNA and Cell Biology, Vol. 9, Issue 7 https://doi.org/10.1089/dna.1990.9.527	journal	September 1990
Negative ion FAB mass spectrometric analysis of non-charged key intermediates in oligonucleotide synthesis: Rapid identification of partially protected dinucleoside monophosphates Wolter, A.; Möhringer, C.; Köster, H. Biological Mass Spectrometry, Vol. 14, Issue 3, p. 111-116 https://doi.org/10.1002/bms.1200140304	journal	March 1987
Electrospray ion source. Another variation on the free-jet theme Yamashita, Masamichi; Fenn, John B. The Journal of Physical Chemistry, Vol. 88, Issue 20 https://doi.org/10.1021/j150664a002	journal	September 1984
Analytical strategies for the use of DNA probes Matthews, Jayne A.; Kricka, Larry J. Analytical Biochemistry, Vol. 169, Issue 1, p. 1-25 https://doi.org/10.1016/0003-2697(88)90251-5	journal	February 1988
Volatilization of high molecular weight DNA by pulsed laser ablation of frozen aqueous solutions Nelson, R.; Rainbow, M.; Lohr, D. Science, Vol. 246, Issue 4937 https://doi.org/10.1126/science.2595370	journal	December 1989
1-Tuple DNA Sequencing: Computer Analysis Pevzner, Pavel A. Journal of Biomolecular Structure and Dynamics, Vol. 7, Issue 1 https://doi.org/10.1080/07391102.1989.10507752	journal	August 1989
New developments in biochemical mass spectrometry: electrospray ionization Smith, Richard D.; Loo, Joseph A.; Edmonds, Charles G. Analytical Chemistry, Vol. 62, Issue 9 https://doi.org/10.1021/ac00208a002	journal	May 1990
DNA sequencing by hybridization: 100 bases read by a non-gel-based method. Strezoska, Z.; Paunesku, T.; Radosavljevic, D. Proceedings of the National Academy of Sciences, Vol. 88, Issue 22 https://doi.org/10.1073/pnas.88.22.10089	journal	November 1991
Encoded combinatorial chemistry. Brenner, S.; Lerner, R. A. Proceedings of the National Academy of Sciences, Vol. 89, Issue 12 https://doi.org/10.1073/pnas.89.12.5381	journal	June 1992
Electrospray ionization mass spectrometry of biomolecules Jardine, Ian Nature, Vol. 345, Issue 6277 https://doi.org/10.1038/345747a0	journal	June 1990
Mass spectrometric techniques in nucleic acid research Crain, Pamela F. Mass Spectrometry Reviews, Vol. 9, Issue 5 https://doi.org/10.1002/mas.1280090504	journal	September 1990
Rapid detection and sequencing of specific in vitro amplified DNA sequences using solid phase methods Wahlberg, Johan; Lundeberg, Joakim; Hultman, Thomas Molecular and Cellular Probes, Vol. 4, Issue 4, p. 285-297 https://doi.org/10.1016/0890-8508(90)90020-Z	journal	August 1990

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Title: Solid phase sequencing of double-stranded nucleic acids

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