Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Preparing compound containing saccharide radical
Reexamination Certificate
2007-04-17
2007-04-17
Sisson, Bradley L. (Department: 1634)
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Preparing compound containing saccharide radical
C435S006120, C435S183000, C536S023100, C536S024330
Reexamination Certificate
active
09514113
ABSTRACT:
Disclosed are compositions and methods useful for reducing the formation of artifacts during nucleic acid amplification reactions. The method uses special oligonucleotides, referred to herein as template-deficient oligonucleotides, that cannot serve as a template for nucleic acid synthesis over part of their length. This prevents the oligonucleotides from serving as effective templates in the formation of artifacts. The disclosed method involves using a template-deficient oligonucleotide as at least one of the oligonucleotides (preferably a primer) in a nucleic acid amplification reaction, where the template-deficient oligonucleotide comprises one or more template-deficient nucleotides, preferably at or near the 5′ end of the template-deficient oligonucleotide. The disclosed method is useful for reducing artifacts in any nucleic acid amplification reaction involving oligonucleotides. In a preferred form of the method the nucleic acid amplification reaction does not involve thermal cycling. The disclosed method is effective at reducing non-cycle oligonucleotide-based artifacts. Also disclosed are kits useful for reducing artifacts in nucleic acid amplification reactions. The disclosed kits include a template-deficient oligonucleotide, wherein the template-deficient oligonucleotide comprises one or more template-deficient nucleotides, and a nucleic acid polymerase.
REFERENCES:
patent: 5487993 (1996-01-01), Herrnstadt et al.
patent: 5512438 (1996-04-01), Ecker
patent: 5573907 (1996-11-01), Carrino et al.
patent: 5656461 (1997-08-01), Demers
patent: 5792607 (1998-08-01), Backman et al.
patent: 5849544 (1998-12-01), Harris et al.
patent: 5854033 (1998-12-01), Lizardi
patent: 5866336 (1999-02-01), Nazarenko et al.
patent: 5876924 (1999-03-01), Zhang et al.
patent: 5942391 (1999-08-01), Zhang et al.
patent: 6001611 (1999-12-01), Will
patent: 6027923 (2000-02-01), Wallace
patent: 6033881 (2000-03-01), Himmler et al.
patent: 6096880 (2000-08-01), Kool et al.
patent: 6117635 (2000-09-01), Nazarenko et al.
patent: 6124120 (2000-09-01), Lizardi
patent: 6140055 (2000-10-01), Todd et al.
patent: 6143495 (2000-11-01), Lizardi et al.
patent: 6183960 (2001-02-01), Lizardi
patent: 6210884 (2001-04-01), Lizardi
patent: 6221603 (2001-04-01), Mahtani et al.
patent: 6255082 (2001-07-01), Lizardi et al.
patent: 6265559 (2001-07-01), Gildea et al.
patent: 6280949 (2001-08-01), Lizardi
patent: 6291187 (2001-09-01), Kingsmore et al.
patent: 6316230 (2001-11-01), Egholm et al.
patent: 6323009 (2001-11-01), Lasken et al.
patent: 6329150 (2001-12-01), Lizardi et al.
patent: 6344329 (2002-02-01), Lizardi
patent: 6361940 (2002-03-01), Van Ness et al.
patent: 0 745 690 (1996-12-01), None
patent: 0866071 (1998-09-01), None
patent: WO 97/16566 (1997-05-01), None
patent: WO 97/19193 (1997-05-01), None
patent: WO 97/19193 (1997-05-01), None
patent: WO 98/14610 (1998-04-01), None
patent: WO 99/18241 (1999-04-01), None
patent: WO 99/31276 (1999-06-01), None
patent: WO 00/71562 (2000-11-01), None
Sommers and Tautz, “Minimal homology requirements for PCR primrs,” Nucleic Acids Research, 1989, vol. 17, No. 16, p. 6749.
Sommer and Tautz, “Minimal homology requirements for PCR primers,” Nucleic Acids Research, vol. 17, No. 16, 1989, p. 6749.
Asseline, et al., “Solid-phase preparation on 5′, 3′-Heterobifunctional oligonucleotides using modified solid supports,”Tetrahedron48:1233-1254 (1992).
Banér, et al., “Signal amplification of padlock probes by rolling circle replication,”Nucleic Acids Res.26(22):5073-8 (1998).
Beigelman, et al., “Synthesis of 1-Deoxy-D-Ribofuranase phosphoramidite and the incorporation of abasic nucleotides in stem-loop II of a hammerhead ribozyme,”Bioorganic&Medicinal Chemistry Letters4(14):1715-1720 (1994).
Birkenmeyer & Mushahwar, “DNA probe amplification methods,”J. Virological Methods35:117-126 (1991).
Bloch, et al., “Alpha-anomeric DNA: beta-RNA hyrids as new synthetic inhibitors ofEschericha coliRNase H,Drosophilaembryo RNase H and M-MLV reverse transcriptase,”Gene72(1-2):349-60 (1988).
Brownie, et al., “The elimination of primer-dimer accumulation in PCR,”Nucleic Acids Res.25(16):3235-41 (1997).
Cocuzza, “A phosphoramidite reagent for automated solid phase synthesis of 5′-biotinylated oligonucleotides,”Tetrahedron Lett.30:6287-6290 (1989).
Compton, “Nucleic acid sequence-based amplification,”Nature. 350(6313):91-2 (1991).
Connolly & Rider, “Chemical synthesis of oligonucleotides containing a free sulphydryl group and subsequent attachment of thiol specific probes,”Nucleic Acids Res.13(12):4485-502 (1985).
Connolly, “The synthesis of oligonucleotides containing a primary amino group at the 5′-terminus,” Nucleic Acids Res. 15(7):3131-9 (1987).
Craxton, et al., “Linear amplification sequencing, a powerful method for sequencing DNA,”Methods: A Companion in Methods in Enzymology3:20-26 (1991).
Dolinnaya, et al., “Oligonucleotide circularization by template-directed chemical ligation,”Nucleic Acids Res.21(23):5403-7 (1993).
Dreyer & Dervan, “Sequence-specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA X Fe(II),”Proc. Acad. Sci. U. S. A.82(4):968-72 (1985).
Durand, et al., “Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability,”Nucleic Acids Res.18(21):6353-9 (1990).
Egholm, et al., “Peptides Nucleic Acids (PNA). Oligonucleotide Analogues with an Achiral Peptide Backbone,”J. Am. Chem. Soc.114:1895-1897 (1992).
Ferrie, et al., “Development, multiplexing, and application of ARMS tests for common mutations in the CFTR gene,”Am. J. Hum. Genet.51(2):251-62 (1992).
Grzybowski, et al., “Synthesis and antibody-mediated detection of oligonucleotides containing multiple 2,4-dinitrophenyl reporter groups,”Nucleic Acids Res.21(8):1705-12 (1993).
Gupta, et al., “A universal solid support for the synthesis of 3′-thiol group containing oligonucleotides,”Tetrahedron Lett.31:2471-2474 (1990).
Huryn & Okabe, “AIDS-driven nucleoside chemistry,”Chem. Rev.92:1745-1768 (1992).
Jablonski, et al., “Preparation of oligodeoxynucleotide-alkaline phosphatase conjugates and their use as hybridization probes,”Nucleic Acids Res. p, 14(15):6115-28 (1986).
Jones, et al., “Studies on the alkylation of 2′, 3-40 -o-isopropylideneuridine,”J. Carbohydrates Nucleosides, Nucleotides4:301-6 (1977).
Jun-Dong & Li-He, “Application of Wittig reaction to adenosine derivatives,”Synthesis909-911 (1990).
Kalnik, et al., “NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite the cyclic analogue of 2-Deoxyribose,”Biochemistry27:924-931 (1998).
Kumar, et al., “A simple method for introducing a thiol group at the 5′-end of synthetic oligonucleotides,”Nucleic Acids Res.19(16):4561 (1991).
Landegren, “Molecular mechanics of nucleic acid sequence amplification,”Trends Genet.9(6):199-204 (1993).
Landegren, et al., “A ligase-mediated gene detection technique,”Science241:1077-1080 (1988).
Li, et al., “Enzyme-linked synthetic oligonucleotide probes: non-radioactive detection of enterotoxigenicEscherichia coliin faecal specimens,”Nucleic Acids Res.15(13):5275-87 (1987).
Lizardi, et al., “Mutation detection and single-molecule counting using isothermal rolling-circle amplification,”Nat. Genet.19(3):225-32 (1998).
Mackellar, et al., “Synthesis and physical properties of anti-HIV antisense oligonucleotides bearing terminal lipophilic groups,”Nucleic Acids Res.20(13):3411-7 (1992).
Matray & Kool, “A specific partner for abasic damage in DNA,”Nature399(6737):704-8 (1999).
Moran, et
Dean Frank B.
Faruqi A. Fawad
Needle & Rosenberg P.C.
Qiagen GmbH
Sisson Bradley L.
LandOfFree
Method for reducing artifacts in nucleic acid 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 Method for reducing artifacts in nucleic acid amplification, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method for reducing artifacts in nucleic acid amplification will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3755706