Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2007-09-04
2007-09-04
Horlick, Kenneth R. (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S023100
Reexamination Certificate
active
10302362
ABSTRACT:
This invention provides novel processes for amplifying nucleic acid sequences of interest, including linear and non-linear amplification. In linear amplification, a single initial primer or nucleic acid construct is utilized to carry out the amplification process. In non-linear amplification, a first initial primer or nucleic acid construct is employed with a subsequent initial primer or nucleic acid construct. In other non-linear amplification processes provided by this invention, a first initial primer or nucleic acid construct is deployed with a second initial primer or nucleic acid construct to amplify the specific nucleic acid sequence of interest and its complement that are provided. A singular primer or a singular nucleic acid construct capable of non-linear amplification can also be used to carry out non-linear amplification in accordance with this invention. Post-termination labeling process for nucleic acid sequencing is also disclosed in this invention that is based upon the detection of tagged molecules that are covalently bound to chemically reactive groups provided for chain terminators. A process for producing nucleic acid sequences having decreased thermodynamic stability to complementary sequences is also provided and achieved by this invention. Unique nucleic acid polymers are also disclosed and provided in addition to other novel compositions, kits and the like.
REFERENCES:
patent: 4707440 (1987-11-01), Stavrianopoulos
patent: 4729947 (1988-03-01), Middendorf et al.
patent: 4749647 (1988-06-01), Thomas et al.
patent: 5027880 (1991-07-01), Morii et al.
patent: 5047519 (1991-09-01), Hobbs et al.
patent: 5093232 (1992-03-01), Urdea et al.
patent: 5171534 (1992-12-01), Smith et al.
patent: 5230781 (1993-07-01), Middendorf et al.
patent: 5241060 (1993-08-01), Engelhardt et al.
patent: 5260433 (1993-11-01), Engelhardt et al.
patent: 5270184 (1993-12-01), Walker et al.
patent: 5332666 (1994-07-01), Prober et al.
patent: 5346603 (1994-09-01), Middendorf et al.
patent: 5360523 (1994-11-01), Middendorf et al.
patent: 5439793 (1995-08-01), Rose et al.
patent: 5462584 (1995-10-01), Gavlin et al.
patent: 5462854 (1995-10-01), Coassin et al.
patent: 5470723 (1995-11-01), Walker et al.
patent: 5476928 (1995-12-01), Ward et al.
patent: 5508178 (1996-04-01), Rose et al.
patent: 5563050 (1996-10-01), Peyman et al.
patent: 5569582 (1996-10-01), Tavernarakis et al.
patent: 5595891 (1997-01-01), Rose et al.
patent: 5612199 (1997-03-01), Western et al.
patent: 5639873 (1997-06-01), Barascut et al.
patent: 5665545 (1997-09-01), Malek et al.
patent: 5683872 (1997-11-01), Rudert et al.
patent: 5714323 (1998-02-01), Ohshima et al.
patent: 5798276 (1998-08-01), Haugland et al.
patent: 6270967 (2001-08-01), Whitcombe et al.
patent: 6326145 (2001-12-01), Whitcombe et al.
patent: 6764821 (2004-07-01), Rabbani et al.
patent: 7001721 (2006-02-01), Whitcombe et al.
patent: 265429 (1987-09-01), None
patent: 0302308 (1993-11-01), None
patent: 0231495 (1999-06-01), None
patent: 2338301 (1999-12-01), None
patent: 2338302 (2000-08-01), None
patent: WO9200989 (1992-01-01), None
patent: WO 9200989 (1992-01-01), None
patent: WO9502690 (1995-01-01), None
patent: WO9704131 (1997-02-01), None
patent: WO 9806732 (1998-02-01), None
patent: WO9806732 (1998-02-01), None
patent: WO9843991 (1998-10-01), None
patent: WO 9843991 (1998-10-01), None
Saiki, R.K. et al.,Science 230:1350-1354 (1985).
Meyers, T.W. and Gelfand, D.H.,Biochemistry 30(31):7661-7666 (1991).
Landegren U. et al.,Science 241;1077 (1988).
Wu D. and Wallace, R.B.,Genomics 4:560-569 (1989).
Barany F.,Proc. Natl. Acad. Sci.(USA)88:189-193 (1991).
Kwoh D.Y. et al.,Proc. Natl. Acad. Sci.(USA)86:1173-1177 (1989).
Kievits, T. et al.,Journal of Virological Methods 35:273-286 (1991).
Walker, G.T. et al.,Proc. Natl. Acad. Sci.(USA)89:392-396 (1992).
Saiki R.K. et al.,Science 239:487-491 (1988).
Auer, T. et al.,Nucleic Acids Research 24(24):5021-5025 (1996).
Maxam A. M. and Gilbert, W.,Proc. Natl. Acad. Sci.(USA)74(2):560-564 (1977).
Sanger F., et al.,Proc. Natl. Acad. Sci.(USA)74(12):5463-5467 (1977).
Beck S., et al.,Nucleic Acids Research 17(13):5115-5123 (1989).
Ansorge W., et al.,Journal of Biochemical and Biophysical Methods 13:315-323 (1986).
Sequenase Images™ Protocol Book, United States Biochemical Corporation, Cleveland, Ohio, pp. 106-107 (1993).
Wetmur J.G.,Critical Reviews in Biochemistry and Molecular Biology 26(¾):227-259 (1991).
Kornberg A. and Baker T.A.,DNA Replication, 2ndEdition, W.H. Freeman and Co., New York, New York, pp. 44-46 (1992).
Adams, R.L.P. et al.,The Biochemistry of the Nucleic Acids, Chapman & Hall, London, U.K., p. 31 (1992).
Prober J.M., et al.,Science238:336-341 (1987).
Kornberg A. and Baker T.A.,DNA Replication, 2ndEdition, W.H. Freeman and Co., New York, New York, pp. 447-449 (1992).
Wilton, S.D. et al., “Snapback SSCP Analysis: Engineered Conformation Changes for the Rapid Typing of Known Mutations,” Human Mutation 11:252-258 (1998).
Patel, R. et al., “Formation of chimeric DNA primer extension products by template switching onto an annealed downstream oligonucleotide,”Proc. Natl. Acad. Sci.(USA)93:2969-2974 (1996).
Walker, G.T et al., “Strand displacement amplification—an isothermal, in vitro DNA amplification technique,”Nucleic Acids Research 20(7):1691-1696 (1992).
Kurfurst, R. et al., “Oligo-alpha-Deoxyribonucleotides with a Modified Nucleic Base and Covalently Linked to Reactive Agents,”Tetrahedron 49(32):6975-6990 (1993).
Honeyman K. et al., “Development of a snapback method of single-stand conformation polymorphism analysis for genotyping Golden Retrievers for the X-linked muscular dystrophy allele,”AJVR 60(6):734-737 (1999).
Grein, T., et al., “3 Deaza and 7 Deazapurines: duplex stability of oligonucleotides containing modified adenine or guanine bases,”Bioorganic&Medicinal Chemistry Letters 4:971-976 (1994).
Sagi, J., et al., “Base-modified oligodeoxynucleotides. I. effect of 5-alkyl, 5-(1-alkenyl) and 5-(1-alkynyl) substitution of the pyrmidines on duplex stability and hydrophobicity,”Tetrahedron Letters 34:2191-2194 (1993).
Sanghvi, Y.S., “Heterocyclic Base Modifications in Nucleic Acids and their Applications in Antisense Oligonucleotides,” Chapter 15 (pp. 273-288) ofAntisense Research and Applications, CRC Press, UK (1993).
Sowers, L.C., et al., “Equilibrium between a Wobble and Ionized Base Pair Formed between Fluorouracil and Guanine in DNA as Studied by Proton and Fluorine NMR,”J. Bio. Chem. 263:14794-14801 (1988).
Nielson, et al., 1993 “Peptide Nucleic Acids (PNA): Oligonucleotide Analogs with a Polyamide Backbone” in Peptide Nucleic Acids, CRC Press, Inc. pp. 363-373.
Gen Bank Gl: 310749 (4 pages).
Output from http://www.bioinfo.rpi.edu/applications/mfold/dna/ (7 pages).
Zuker 2003 “Mfold web server for nucleic acid folding and hybridization predicition” Nucleic Acids Res. 31:3406-3415.
Lodmell et al. 1995 “Genetic and Comparative Analyses Reveal an Alternative Secondary Structure in the Region of nt 912 inEscherichia coli16S RNA” Proc. Nat'l. Acad. Sci. US 92:10555-10559.
Pollack et al. 1993 “An RNA Stem-Loop Structure Directs Hepatitis B Virus Genomic RNA Encapsidation” J. Virol. 67:3254-3263.
Blanco et al. 1989 “Highly Efficient DNA Synthesis by the phage ø29 DNA Polymerase: Symmetrical Mode of DNA Replication” J. Biol. chem. 264:8935-8940.
Kremsky et al. 1987 “Immobilization of DNA via oligonucleotides containing an aldehyde or carboxylic acid group at the 5′ terminus” Nucleic Acids Res. 15:2891-2909.
Whitcombe, D. et al.,Nature Biotechnology 17:804-807 (1999).
Grein, T., et al., “3 Deaze and 7 Deazapurines: duplex stability of oligonucleotides containing modified adenine or guanine bases,”Bioorganic & Medicinal Chemistry Letters4:971-976 (1994).
Sagi, J., et al., “Base-modified oligodeoxynucleotides. I. effect of 5-alk
Coleman Jack
Donegan James J.
Rabbani Elazar
Stavrianopoulos Jannis G.
Walner Marleen
Bogdanos, Esq. Natalie
Enzo Biochem, Inc.
Horlick Kenneth R.
Tung Joyce
LandOfFree
Processes for non-linearly amplifying nucleic acids does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Processes for non-linearly amplifying nucleic acids, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Processes for non-linearly amplifying nucleic acids will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3785822