Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Preparing compound containing saccharide radical
Patent
1997-10-08
2000-09-26
Marschel, Ardin H.
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Preparing compound containing saccharide radical
435 911, 435 9152, 536 2433, 536 221, C12P 1934, C07H 2104
Patent
active
061241202
ABSTRACT:
Disclosed are compositions and a method for amplification of nucleic acid sequences of interest. The method is based on stand displacement replication of the nucleic acid sequences of interest by multiple primers. In one preferred form of the method, referred to as multiple strand displacement amplification, two sets of primers are used, a right set and a left set. The primers in the right set are complementary to one strand of the nucleic acid molecule to be amplified and the primers in the left set are complementary to the opposite strand. The 5' end of primers in both sets are distal to the nucleic acid sequence of interest when the primers have hybridized to the nucleic acid sequence molecule to be amplified. Amplification proceeds by replication initiated at each primer and continuing through the nucleic acid sequence of interest. A key feature of this method is the displacement of intervening primers during replication by the polymerase. In another preferred form of the method, referred to as whole genome strand displacement amplification, a random set of primers is used to randomly prime a sample of genomic nucleic acid (or another sample of nucleic acid of high complexity). By choosing a set of primers which are sufficiently random, the primers in the set will be collectively, and randomly, complementary to nucleic acid sequences distributed throughout nucleic acid in the sample. Amplification proceeds by replication with a highly processive polymerase initiated at each primer and continuing until spontaneous termination. A key feature of this method is the displacement of intervening primers during replication by the polymerase. In this way, multiple overlapping copies of the entire genome to be synthesized in a short time.
REFERENCES:
patent: 4994373 (1991-02-01), Stavrianopoulos et al.
patent: 5001050 (1991-03-01), Blanco et al.
patent: 5043272 (1991-08-01), Hartley
patent: 5198543 (1993-03-01), Blanco et al.
patent: 5328824 (1994-07-01), Ward et al.
patent: 5547843 (1996-08-01), Studier et al.
patent: 5614390 (1997-03-01), McCaslin et al.
patent: 5629179 (1997-05-01), Mierendorf et al.
Aliotta, et al., "Thermostable Bst DNA polymerase I lacks a 3'.fwdarw.5' proofreading exonuclease activity," Genet. Anal. (Netherlands) 12:185-195 (1996).
Arnold, et al., "Assay Formats Involving Acridinium-Ester-Labeled DNA Probes," Clin. Chem. 35(8):1588-1594 (1989).
Birkenmeyer, et al., "Mini-Review: DNA probe amplification methods," J. Virological Methods 35:117-126 (1991).
Boehmer, et al., "Herpes Simplex Virus Type 1 1CP8: Helix-Destabilizing Properties," J. Virology 67(2):711-715 (1993).
Brownstein, et al., "Modulation of Non-Templated Nucleotide Addition by Taq DNA Polymerase: Primer Modifications that Facilitate Genotyping," Biotechniques 20(6):1004-1010 (1996).
Chatterjee, et al., "Cloning and overexpression of the gene encoding bacteriophage T5 DNA polymerse," Gene 97(1):13-19 (1991).
Cheung, et al., "Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed own less than one nanogram of genomic DNA," Proc. Natl. Acad. Sci. USA 93(25):14676-14679 (1996).
Guo, et al., "Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports," Nucleic Acids Res. 22(24):5456-5465 (1994).
Holton, et al., "A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors," Nucl. Acids Res. 19(5):1156 (1991).
Hoy, et al., "Bromodeoxyuridine/DNA analysis of replication in CHO cells after exposure to UV light," Mutation Research 290(2):217-230 (1993).
Itakura, et al., "Synthesis and use of synthetic oligonucleotides," Ann. Rev. Biochem. 53:323-356 (1984).
Jacobsen, et al., "The N-Terminal Amino-Acid Sequences of DNA Polymerase I from Escherichia coli and of the Large and Small Fragments Obtained by a Limited Proteolysis," Eur. J. Biochem. 45(2):623-627 (1974).
Jiang, et al., "An efficient method for generation and subcloning of tandemly repeated DNA sequences with defined length, orientation and spacing," Nuc. Acids Res. 24(16):3278-3279 (1996).
Jung, et al., "Bacteriophage PRD1 DNA polymerase: Evolution of DNA polymerases," Proc. Natl. Acad. Sci. USA 84(23):8287-8291 (1987).
Kaboord, et al., "Accessory proteins function as matchmakers in the assembly of the T4 DNA polymerase holoenzyme," Curr. Biol. 5(2):149-157 (1995).
Kerkhof, "A Comparison of Substrates for Quantifying the Signal from a Nonradiolabeled DNA Probe," Anal. Biochem. 205(2):359-364 (1992).
Khrapko, et al., "Hybridization of DNA with Oligonucleotides Immobilized in Gel: A Convenient Method for Detecting Single Base Substitutions," Mol Biol (Mosk) (USSR) 25(3):718-730 (translation pages 581-591) (1991).
Kong, et al., "Characterization of a DNA Polymerase from the Hyperthermophile Archaea Thermococcus litoralis," J. Biol. Chem. 268(3):1965-1975 (1993).
Kuukasjarvi, et al., "Optimizing DOP-PCR for Universal Amplification of Small DNA Samples in Comparative Genomic Hybridization," Genes, Chromosomes and Cancer 18:94-101 (1997).
Landegren, "Molecular mechanics of nucleic acid sequence amplification," Trends Genetics 9(6):199-202 (1993).
Langer, et al., "Enzymatic synthesis of biotin-labeled polynucleotides: Novel nucleic acid affinity probes," Proc. Natl. Acad. Sci. USA 78(11):6633-6637 (1981).
Lesnick, et al., "Relative Thermodynamic Stability of DNA, RNA, and DNA:RNA Hybrid Duplexes: Relationship with Base Composition and Structure," Biochemistry 34:10807-10815 (1995).
Lockhart, et al., "Expression monitoring by hybridization to high-density oligonucleotide arrays," Nature Biotechnology 14(13):1675-1680 (1996).
Matsumoto, et al., "Primary structure of bacteriophage M2 DNA polymerase: conversed segments within protein-priming DNA polymerases and DNA polymerase I of Escherichia coli (Recombinant DNA; nucleotide sequence; amino acid sequence; protein homology; aphidicolin-resistance mutation; dNTP-bonding site)," Gene 84(2):247-255 (1989).
McGraw, et al., "Sequence-Dependent Oligonucleotide-Target Duplex Stabilities: Rules from Empirical Studies with a Set of Twenty-Mers," Biotechniques 8(6):674-678 (1990).
Narang, et al., "Chemical Synthesis of Deoxyoligonucleotides by the Modified Triester Method," Methods in Enzymology, vol. 65, Chap. 61, pp. 610-620 (Grossman, ed.), (Academic Press, Inc., 1980).
Nielsen, et al., "Peptide Nucleic Acid (PNA). A DNA Mimic with a Peptide Backbone," Bioconjug. Chem. 5(1):3-7 (1994).
Parker, et al., "Targeted Gene Walking Polymerase Chain Reaction," Nucleic Acids Research 19(11): 3055-3060 (1991).
Pease, et al., "Light-generated oligonucleotide arrays for rapid DNA sequence analysis," Proc. Natl. Acad. Sci. USA 91(11):5022-5026 (1994).
Rigler, et al., "Differences in the Mechanism of Stimulation of T7 DNA Polymerase by Two Binding Modes in Escherichia coli Single-stranded DNA-binding Protein," J. Biol. Chem. 270(15):8910-8919 (1995).
Rychlik, et al., "Optimization of the annealing temperature for DNA amplification in vitro," Nucleic Acids Res. 18(21):6409-6412 (1990).
Schena, et al., "Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray," Science 270:467-470 (1995).
Siegel, et al., "A Novel DNA Helicase from Calf Thymus," J. Biol. Chem. 267(19):13629-13635 (1992).
Skaliter, et al., "Rolling circle DNA replication in vitro by a complex of herpes simplex virus type 1-encoded enzymes," Proc. Natl. Acad. Sci. USA 91(22):10665-10669 (1994).
Stimpson, et al., "Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides," Proc. Natl. Acad. Sci. USA 92(14):6379-6383 (1995).
Telenius, et al., "Degenerate Oligonucleotide-Primed PCR: General Amplification of Target DNA by a Single Degenerate Primer," Genomics 13(3):718-725 (1992).
Tsurumi, et al., "Functional Interaction between Epstein-Barr Virus DNA Polymerase Catalytic Subunit and Its Accessory Subunit In Vitro," J. Virology 67(12):7648-7653 (1993).
Tyagi, et al., "Molecular Beacons: Probes that Fluoresce upon Hybridization," Nature Biotechnol.
Marschel Ardin H.
Tung Joyce
Yale University
LandOfFree
Multiple displacement amplification does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Multiple displacement amplification, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Multiple displacement amplification will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2099013