Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Patent
1998-06-03
2000-10-24
Brusca, John S.
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
702 27, 435 6, 536 231, 536 242, 536 243, 536 254, G06N 312, C12Q 168, C12N 1511, C07H 2104
Patent
active
061380776
ABSTRACT:
The invention provides a computerized method, associated apparatus, and computer program product for determining a set of non-hybridizing oligonucleotides. The invention represents a first oligonucleotide in the computer's memory, generates a set of oligonucleotides, including the first oligonucleotide, that meet a specified condition that determines whether the generated oligonucleotides will not hybridize with the first oligonucleotide. The invention also examines each of the generated oligonucleotides in the set to remove oligonucleotides from the set that hybridize with other nucleotides in the set. Thus, the invention develops a minimally cross-hybridizing set of oligonucleotides that can be used for tracking, identifying, and/or sorting classes or subpopulations of molecules by the user of oligonucleotide tags.
REFERENCES:
patent: 4942124 (1990-07-01), Church
patent: 5149625 (1992-09-01), Church
patent: 5302509 (1994-04-01), Cheeseman
patent: 5482836 (1996-01-01), Cantor et al.
patent: 5514543 (1996-05-01), Grossman
patent: 5552278 (1996-09-01), Brenner
patent: 5599675 (1997-02-01), Brenner
patent: 5604097 (1997-02-01), Brenner
patent: 5635400 (1997-06-01), Brenner
patent: 5654413 (1997-08-01), Brenner
patent: 5658736 (1997-08-01), Wong
patent: 5695934 (1997-12-01), Brenner
patent: 5846719 (1998-12-01), Brenner et al.
patent: 5863722 (1999-01-01), Brenner
Search Report from International Patent Application PCT/US95/12791 (published as WO 96/12014).
Search Report from International patent Application PCT/US96/09513 (published as WO 96/41011).
Aslanidis, et al., "Ligation-independent Cloning of PCR Products (LIC-PCR)," Nucleic Acids Research 18:6069-6074 (1990).
Beck, et al., "A Strategy for the Amplification, Purification, and Selection of M13 Templates for Large-Scale DNA Sequencing," Analytical Biochem. 212:498-505 (1993).
Brenner, et al., "Encoded Combinatorial Chemistry," Proc. Natl. Acad. Sci. U.S.A. 89:5381-5383 (1992).
Broude, et al., "Enhanced DNA Sequencing by Hybridization," Proc. Natl. Acad. Sci. 91:3072-3076 (1994).
Brown, et al., "A New Base-Stable Linker for Solid-Phase Oligonucleotide Synthesis," J. Chem. Soc. Commun. 891-893 (1989).
Chetverin, et al., "Oligonucleotide Arrays: New Concepts and Possibilities," Biotechnology 12:1093-1099 (1994).
Church, et al., "Multiple DNA Sequencing," Science 240:185-188 (1988).
Coche, et al., "Reducing Bias in cDNA Sequence Representation by Molecular Selection," Nucleic Acids Research 22:4545-4546 (1994).
Crick, et al., "Codes without Commas," Proc. Natl. Acad. Sci. 43:416-421 (1957).
Egholm, et al., "PNA Hybridizes to Complementary Oligonucleotides Obeying the Watson-Crick Hydrogen-Bonding Rules," Nature 365:566-568 (1993).
Gronostajski, "Site-Specific DNA Binding of Nuclear Factor I: Effect of the Spacer Region," Nucleic Acids Research 15:5545-5559 (1987).
Gryaznov, et al., "Modulation of Oligonucleotide Duplex and Triplex Stability via Hydrophobic Interactions," Nucleic Acids Research 21:5909-5915 (1993).
Hensel, et al., "Simultaneous Identification of Bacterial Virulence Genes by Negative Selection," Science 269:400-403 (1995).
Hunkapiller, et al., "Large-Scale and Automated DNA Sequence Determination," Science 254:59-67 (1991).
Ji and Smith, "Rapid Purification of Double-Stranded DNA by Triple-Helix-Mediated Affinity Capture," Anal. Chem. 65:1323-1328 (1993).
Kuijper, et al., "Functional Cloning Vectors for Use in Directional cDNA Cloning Using Cohesive Ends Produced with T4 DNA Polymerase," Gene 112:147-155 (1992).
Maskos and Southern, "Oligonucleotide Hybridization on Glass Supports: a Novel Linker for Oligonucleotide Synthesis and Hybridization Properties of Oligonucleotides Synthesized in situ," Nucleic Acids Research 20:1679-1684 (1992).
Matteucci, et al., "Targeted Random Mutagenesis: the Use of Ambiguously Synthesized Oligonucleotides to Mutagenize Sequences Immediately 5' of an ATG Initiation Codon," Nucleic Acids Research 11:3113-3121 (1983).
Matthews and Kricka, "Analytical Strategies for the Use of DNA Probes," Anal. Biochem. 169:1-25 (1988).
Needels, et al., "Generation and Screening of an Oligonucleotide-Encoded Synthetic Peptide Library," Proc. Natl. Acad. Sci. 90:10700-10704 (1993).
Nielsen, et al., "Synthesis Methods for the Implementation of Encoded Combinatorial Chemistry," J. Am. Chem. Soc. 115:9812-9813 (1993).
Ohlmeyer, et al., "Complex Synthetic Chemical Libraries Indexed with Molecular Tags," Proc. Natl. Acad. Sci. 90:10922-10926 (1993).
Oliphant, et al., "Cloning of Random-Sequence Oligodeoxynucleotides," Gene 44:177-183 (1986).
Oliphant and Struhl, "Defining the Consensus Sequences of E. Coli Promoter Elements by Random Selection," Nucleic Acids Research 16:7673-7683 (1988).
Rychlik, W., and Rhoads, R.E., "A Computer Program for Choosing Optimal Oligonucleotides for Filter Hybridization, Sequencing, and in vitro Amplification of DNA," Nucleic Acids Research 17(21):8543-8551 (1989).
Shoemaker, et al., "Quantitative Phenotypic Analysis of Yeast Deletion Mutants Using a Highly Parallel Molecular Bar-Coding Strategy," Nature Genetics 14:450-456 (1996).
Wetmur, "DNA Probes: Applications of the Principles of Nucleic Acid Hybridization," Critical Reviews in Biochemistry and Molecular Biology 26:227-259 (1991).
Yang and Youvan, "A Prospectus for Multispectral-Multiplex DNA Sequencing," Biotechnology 7:576-580 (1989).
Brusca John S.
Lynx Therapeutics, Inc.
Macevicz Stephen C.
Shibuya Mark L.
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