Methods and compositions for efficient nucleic acid sequencing

Drmanac, Radoje

Methods and compositions for efficient nucleic acid sequencing

Patent · 04 July 2006

OSTI ID:1175815

Drmanac, Radoje

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

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Research Organization:: The University Of Chicago, Chicago, IL (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: W-31109-ENG-38

Assignee:: University of Chicago (Chicago, IL)

Patent Number(s):: 7,070,927

Application Number:: 10/068,301

OSTI ID:: 1175815

Country of Publication:: United States

Language:: English

References (55)

A novel method for nucleic acid sequence determination Bains, William; Smith, Geoff C. Journal of Theoretical Biology, Vol. 135, Issue 3 https://doi.org/10.1016/S0022-5193(88)80246-7	journal	December 1988
Quantification of picogram levels of specific DNA immobilized in microtiter wells Nagata, Yoshiho; Yokota, Hiroshi; Kosuda, Osamu FEBS Letters, Vol. 183, Issue 2 https://doi.org/10.1016/0014-5793(85)80814-0	journal	April 1985
Worldwide Distribution of a Common Methylenetetrahydrofolate Reductase Mutation Schneider, Julie A.; Rees, David C.; Liu, Yan-Tat The American Journal of Human Genetics, Vol. 62, Issue 5 https://doi.org/10.1086/301836	journal	May 1998
Covalent immobilization of DNA onto polystyrene microwells: The molecules are only bound at the 5′ end Rasmussen, Søren Richard; Larsen, Mette Ravn; Rasmussen, Svend Erik Analytical Biochemistry, Vol. 198, Issue 1, p. 138-142 https://doi.org/10.1016/0003-2697(91)90518-X	journal	October 1991
DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing Drmanac, R.; Drmanac, S.; Strezoska, Z. Science, Vol. 260, Issue 5114 https://doi.org/10.1126/science.8503011	journal	June 1993
Fluorescent-labeled oligonucleotide probes: detection of hybrid formation in solution by fluorescence polarization spectroscopy Murakami, Akira; Nakaura, Misuzu; Nakatsuji, Yuna Nucleic Acids Research, Vol. 19, Issue 15 https://doi.org/10.1093/nar/19.15.4097	journal	January 1991
Labelling oligonucleotides to high specific activity (I) Craig, Alister G.; Nizetic, Dean; Lehrach, Hans Nucleic Acids Research, Vol. 17, Issue 12 https://doi.org/10.1093/nar/17.12.4605	journal	January 1989
Dissociation of Duplexes Formed by Hybridization of DNA with Gel-Immobilized Oligonucleotides Livshits, M. A.; Florentiev, V. L.; Mirzabekov, A. D. Journal of Biomolecular Structure and Dynamics, Vol. 11, Issue 4 https://doi.org/10.1080/07391102.1994.10508032	journal	February 1994
Quantitative measurements on the duplex stability of 2,6‐diaminopurine and 5‐chloro‐uracil nucleotides using enzymatically synthesized oligomers Hoheisel, Jorg D.; Lehrach, Hans FEBS Letters, Vol. 274, Issue 1-2, p. 103-106 https://doi.org/10.1016/0014-5793(90)81340-T	journal	November 1990
Sensitive detection of genes by sandwich hybridization and time-resolved fluorometry Dahlén, Patrik; Syvänen, Ann-Christine; Hurskainen, Pertti Molecular and Cellular Probes, Vol. 1, Issue 2 https://doi.org/10.1016/0890-8508(87)90024-7	journal	June 1987
DNA sequencing by primer walking with strings of contiguous hexamers Kieleczawa, J.; Dunn, J.; Studier, F. Science, Vol. 258, Issue 5089 https://doi.org/10.1126/science.1465615	journal	December 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
Multiplex DNA sequencing Church, G.; Kieffer-Higgins, S. Science, Vol. 240, Issue 4849 https://doi.org/10.1126/science.3353714	journal	April 1988
Rapid shotgeun cloning utillizing the two base recongition endonuclease Cvi JI Fitzgerald, Michael C.; Skowron, Peter; Van Etten, James L. Nucleic Acids Research, Vol. 20, Issue 14 https://doi.org/10.1093/nar/20.14.3753	journal	January 1992
DNA Sequence Confidence Estimation Lipshutz, Robert J.; Taverner, Fred; Hennessy, Kevin Genomics, Vol. 19, Issue 3 https://doi.org/10.1006/geno.1994.1089	journal	February 1994
A new method for sequencing DNA. Maxam, A. M.; Gilbert, W. Proceedings of the National Academy of Sciences, Vol. 74, Issue 2 https://doi.org/10.1073/pnas.74.2.560	journal	February 1977
One-step labelling of oligonucleotides with fluoresceine during automated synthesis Suhubert, F.; Ahlert, K.; Cech, D. Nucleic Acids Research, Vol. 18, Issue 11 https://doi.org/10.1093/nar/18.11.3427	journal	January 1990
Light-directed, spatially addressable parallel chemical synthesis Fodor, S.; Read, J.; Pirrung, M. Science, Vol. 251, Issue 4995 https://doi.org/10.1126/science.1990438	journal	February 1991
Genomic Southern analysis with alkaline-phosphatase-conjugated oligonucleotide probes and the chemiluminescent substrate AMPPD Cate, Richard L.; Ehrenfels, Christian W.; Wysk, Mark Genetic Analysis: Biomolecular Engineering, Vol. 8, Issue 3 https://doi.org/10.1016/1050-3862(91)90044-R	journal	May 1991
Low pressure DNA shearing: a method for random DNA sequence analysis Schriefer, Lawrence A.; Gebauer, Beth K.; Qiu, Lisa Q. Q. Nucleic Acids Research, Vol. 18, Issue 24 https://doi.org/10.1093/nar/18.24.7455	journal	January 1990
A versatile solid support system for oligodeoxynucleotide probe-based hybridization assays Ness, Jeffrey Van; Kalbfleisch, Sonja; Petne, Charles R. Nucleic Acids Research, Vol. 19, Issue 12 https://doi.org/10.1093/nar/19.12.3345	journal	January 1991
Nucleic acid hybridization assays employing dA-tailed capture probes. Single capture methods Morrissey, David V.; Collins, Mark L. Molecular and Cellular Probes, Vol. 3, Issue 2 https://doi.org/10.1016/0890-8508(89)90029-7	journal	June 1989
Selecting varieties using a series of trials and a combinatorial ordering method Guénoche, A.; Vandeputte-Riboud, B.; Denis, Jb Agronomie, Vol. 14, Issue 6 https://doi.org/10.1051/agro:19940602	journal	January 1994
Chemical ligation of DNA: the first non-enzymatic assembly of a biologically active gene Shabarova, Zoe A.; Merenkova, Irena N.; Oretskaya, Tatyana S. Nucleic Acids Research, Vol. 19, Issue 15 https://doi.org/10.1093/nar/19.15.4247	journal	January 1991
Specificity of the nick-closing activity of bacteriophage T4 DNA ligase Wu, Dan Y.; Wallace, R. Bruce Gene, Vol. 76, Issue 2, p. 245-254 https://doi.org/10.1016/0378-1119(89)90165-0	journal	March 1989
Distribution of high mobility group proteins 1/2,E and 14/17 and linker histones H1 and H5 on transcribed and non-transcribed regions of chicken erythrocyte chromatin Postnikov, Yuri V.; Shick, Valentin V.; Belyavsky, Alexander V. Nucleic Acids Research, Vol. 19, Issue 4 https://doi.org/10.1093/nar/19.4.717	journal	January 1991
Enhanced DNA sequencing by hybridization. Broude, N. E.; Sano, T.; Smith, C. L. Proceedings of the National Academy of Sciences, Vol. 91, Issue 8 https://doi.org/10.1073/pnas.91.8.3072	journal	April 1994
Inhibitory Effects of Human and Bovine Milk Constituents on Rotavirus Infections Kvistgaard, A. S.; Pallesen, L. T.; Arias, C. F. Journal of Dairy Science, Vol. 87, Issue 12 https://doi.org/10.3168/jds.S0022-0302(04)73551-1	journal	December 2004
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
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
Rapid renaturation of complementary DNA strands mediated by cationic detergents: a role for high-probability binding domains in enhancing the kinetics of molecular assembly processes. Pontius, B. W.; Berg, P. Proceedings of the National Academy of Sciences, Vol. 88, Issue 18 https://doi.org/10.1073/pnas.88.18.8237	journal	September 1991
Sequencing by hybridization: Towards an automated sequencing of one million M13 clones arrayed on membranes Drmanac, Radoje; Drmanac, Snezana; Labat, Ivan Electrophoresis, Vol. 13, Issue 1 https://doi.org/10.1002/elps.11501301115	journal	January 1992
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
DNA sequencing by hybridization — a megasequencing method and a diagnostic tool? Mirzabekov, Andrei D. Trends in Biotechnology, Vol. 12, Issue 1 https://doi.org/10.1016/0167-7799(94)90008-6	journal	January 1994
Derivatization of unprotected polynucleotides Chu, Barbara C. F.; Wahl, Geoffrey M.; Orgel, Leslie E. Nucleic Acids Research, Vol. 11, Issue 18 https://doi.org/10.1093/nar/11.18.6513	journal	January 1983
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
Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Pease, A. C.; Solas, D.; Sullivan, E. J. Proceedings of the National Academy of Sciences, Vol. 91, Issue 11 https://doi.org/10.1073/pnas.91.11.5022	journal	May 1994
Convergent Evolution of Alternative Splices at Domain Boundaries of the BK Channel Fodor, Anthony A.; Aldrich, Richard W. Annual Review of Physiology, Vol. 71, Issue 1 https://doi.org/10.1146/annurev.physiol.010908.163124	journal	March 2009
Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores. Brumbaugh, J. A.; Middendorf, L. R.; Grone, D. L. Proceedings of the National Academy of Sciences, Vol. 85, Issue 15 https://doi.org/10.1073/pnas.85.15.5610	journal	August 1988
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
Proposal for sequencing DNA using ligation of hexamers to generate sequential elongation primers (SPEL-6) Szybalski, W. Gene, Vol. 90, Issue 1 https://doi.org/10.1016/0378-1119(90)90458-4	journal	May 1990
A universal nucleoside for use at ambiguous sites in DNA primers Nichols, R.; Andrews, P. C.; Zhang, P. Nature, Vol. 369, Issue 6480 https://doi.org/10.1038/369492a0	journal	June 1994
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
Likelihood DNA Sequencing By Hybridization Lipshutz, Robert J. Journal of Biomolecular Structure and Dynamics, Vol. 11, Issue 3 https://doi.org/10.1080/07391102.1993.10508020	journal	December 1993
DNA sequencing with chain-terminating inhibitors Sanger, F.; Nicklen, S.; Coulson, A. R. Proceedings of the National Academy of Sciences, Vol. 74, Issue 12 https://doi.org/10.1073/pnas.74.12.5463	journal	December 1977
Genomic sequencing. Church, G. M.; Gilbert, W. Proceedings of the National Academy of Sciences, Vol. 81, Issue 7 https://doi.org/10.1073/pnas.81.7.1991	journal	April 1984
A ligase-mediated gene detection technique Landegren, U.; Kaiser, R.; Sanders, J. Science, Vol. 241, Issue 4869 https://doi.org/10.1126/science.3413476	journal	August 1988
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
Microplate hybridization of amplified viral DNA segment. Inouye, S.; Hondo, R. Journal of Clinical Microbiology, Vol. 28, Issue 6 https://doi.org/10.1128/JCM.28.6.1469-1472.1990	journal	January 1990
Constant denaturant capillary electrophoresis (CDCE): a high resolution approach to mutational anaylsis Khrapko, K.; Hanekamp, J. S.; Thilly, W. G. Nucleic Acids Research, Vol. 22, Issue 3 https://doi.org/10.1093/nar/22.3.364	journal	January 1994
Affinity chromatography of a sequence-specific DNA binding protein using teflon-linked oligonucleotides Duncan, Craig H.; Cavalier, Sharon L. Analytical Biochemistry, Vol. 169, Issue 1 https://doi.org/10.1016/0003-2697(88)90260-6	journal	February 1988
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
Site-directed modification of DNA duplexes by chemical ligation Dolinnaya, N. G.; Sokolova, N. I.; Gryaznova, O. I. Nucleic Acids Research, Vol. 16, Issue 9 https://doi.org/10.1093/nar/16.9.3721	journal	January 1988
Technique for maintaining and screening many microbial cultures Sharpe, A. N.; Diotte, M. P.; Dudas, I. Food Microbiology, Vol. 6, Issue 4 https://doi.org/10.1016/S0740-0020(89)80007-3	journal	December 1989
Microarrays: their origins and applications Ekins, Roger; Chu, Frederick W. Trends in Biotechnology, Vol. 17, Issue 6 https://doi.org/10.1016/S0167-7799(99)01329-3	journal	June 1999

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