Methods and compositions for efficient nucleic acid sequencing

Drmanac, Radoje

Title: Methods and compositions for efficient nucleic acid sequencing

Patent · Tue Jul 04 00:00:00 EDT 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.

View Patent

Cite

Export

Save

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-31-109-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)

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
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
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
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
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
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
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
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
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
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
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
Multiplex DNA sequencing Church, G.; Kieffer-Higgins, S. Science, Vol. 240, Issue 4849 https://doi.org/10.1126/science.3353714	journal	April 1988
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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

Similar Records

Methods and compositions for efficient nucleic acid sequencing

Patent · Tue Jan 01 00:00:00 EST 2002 · OSTI ID:1175815

Drmanac, Radoje

Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

Patent · Tue Jun 27 00:00:00 EDT 1995 · OSTI ID:1175815

Weier, H U.G.; Gray, J W

Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

Patent · Sun Jan 01 00:00:00 EST 1995 · OSTI ID:1175815

Weier, Heinz-Ulrich G; Gray, Joe W

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Methods and compositions for efficient nucleic acid sequencing

Citation Formats

References (55)

Similar Records

Related Subjects