Patent 6949340 Issued on September 27, 2005. Estimated Expiration Date: March 28, 2021. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.
435/6, Involving nucleic acid435/91.1, Polynucleotide (e.g., nucleic acid, oligonucleotide, etc.)435/91.2, Acellular exponential or geometric amplification (e.g., PCR, etc.)536/23.1, DNA or RNA fragments or modified forms thereof (e.g., genes, etc.)536/24.3, Probes for detection of specific nucleotide sequences or primers for the synthesis of DNA or RNA536/24.33Primers
Provided are methods for using nucleic acid sequences having two or more degenerately pairing nucleotides, each degenerate nucleotide having a partially overlapping set of complementarity, to reduce the number of hybridizing nucleotide sequences or probes used in biochemical and molecular biological operations having sequence specific hybridization. The method may be employed for various hybridization procedures with sequence specific hybridization, including sequencing methods measuring hybridization directly, and tagging by hybridization methods in which the sequence is determined by analyzing the pattern of tags that hybridize thereto, and hybridization dependent amplification methods. The method involves hybridizing to the nucleic acid sequence of interest a first hybridizing nucleotide sequence and a second hybridizing nucleotide sequence, each comprising a sequence complementary, or complementary except at a position of interest or variable position, to a nucleic acid sequence of interest, and analyzing the whether some, all or none of the probes or tags hybridize.
Other References
Vesnaver et al., The contribution of DNA single-stranded order to the thermodynamics of duplex formation. Proc. Natl. Acad. Sci. USA, 88, 3569-3573, May 1991.
Hill et al., Polymerase recognition of synthetic oligonucleotides incorporating degenerate pyrimidine and purine bases. Proc. Natl. Acad. Sci. USA, 95, 4258-4263, Apr. 1998.
Alper (1994), “Drug Discovery on the Assembly Line,” Science 264:1399-1401.
Bains (1993), “Characterizing and Sequencing cDNAs using Oligonucleotide Hybridization,” J. DNA Sequencing and Mapping 4: 143-150.
Brenner et al. (2000), “Gene Expression Analysis by Massivly Parallel Signature Sequencing (MPSS) on Microbead Arrays,” Nature Biotechnology 18(6):630-634.
Breslauer et al. (1986), “Predicting DNA Duplex Stability from the Base Sequence,” Proc. Natl. Acad. Sci. USA 83:3746-3750.
Church et al. (1998), “Multiplex DNA Sequencing,” Science 240:185-188.
Drmanac et al. (1993), “DNA Sequence Determination by Hybridization: A Strategy for Efficient Large-Scale Sequencing,” Science 260:1649-1652.
Gyllensten et al. (1988), “Generation of Single-Stranded DNA by the Polymerase Chain Reaction and its Application to Direct Sequencing of the HLA-DQA Locus,” Proc. Natl. Acad. Sci. USA. 85:7652-7656.
Liang et al. (1992), “Differential Display of Eukaryotic Messenger RNA by Means of the Polymerase Chain Reaction,” Science 257:967-971.
Maxam et al. (1977), “A New Method for Sequencing DNA,” Proc. Natl. Acad. Sci. USA 74(2):560-564.
Milligan et al. (1993), “Current Concepts in Antisense Drug Design,” Journal of Medicinal Chemistry 36(14):1923-1937.
Moriyama et al. (1998), “Synthesis and RNA Polymerase Incorporation of the Degenerate Ribonucleotide Analogue rPTP,” Nucleic Acids Research26(9):2105-2111.
Needels et al. (1993), “Generation and Screening of an Oligonucleotide-Encoded Synthetic Peptide Library,” Proc. Natl. Acad. Sci. USA 90: 10700-10704.
Pavlov et al. (1994), “DNA Replication Fidelity with 8-Oxodeoxyguanosine Triphosphate,” Biochemistry 33: 4695-4701.
Sanger et al. (1977), “DNA Sequencing with Chain-Terminating Inhibitors,” Proc. Natl. Acad. Sci. USA 74(12):5463-5467.
Schena et al. (1995), “Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray,” Science 270:467-469.
Unrau et al. (1994), “Non-Cloning Amplification of Specific DNA Fragments from Whole Genomic DNA Digest Using DNA ‘Indexers,’” Gene 145:163-169.
Velculescu et al. (1995), “Serial Analysis of Gene Expression,” Science 270:484-486.
Wallace et al. (1979), “Hybridization of Synthetic Oligodeoxyribonucleotides to φ χ 174 DNA: The Effect of Single Base Pair Mismatch,” Nucleic Acids Research 6(11):3543-3557.
Wood et al. (1985), “Base Composition-Independent Hybridization in Tetramethylammonium Chloride: A Method for Oligonucleotide Screening of Highly Complex Gene Libraries,” Proc. Natl. Acad. Sci. USA 82:1585-1588.
Zaccolo et al. (1996), “An Approach to Random Mutagenesis of DNA Using Mixtures of Triphosphate Derivatives of Nucleoside Analogues,” J. Mol. Biol. 255:589-603.
Brenner et al. (1992), “Encoded Combinatorial Chemistry,” Proc. Natl. Acad. Sci. USA 89:5381-5383.
Brown et al. (1997), “Random Mutagenesis of DNA Using Deoxynucleoside 5′-Triphosphate Analogues,” Amersham Life Science News 23: 18-19.
Dollinger (1994), “Nonbiological Applications,” The Polymerase Chain Reaction, pp. 265-274. Mullis et al., Eds. Birkhauser, Boston.
March 28, 2021. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.
