Annealing control primer and its uses

Details Annealing control primer and its uses Annealing control primer and its uses

2007-01-10

2009-08-25

Benzion, Gary (Department: 1637)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C435S091200, C536S023100, C536S024330

Reexamination Certificate

active

07579154

ABSTRACT:
The present invention relates to an annealing control primer for improving annealing specificity in nucleic acid amplification and its applications to all fields of nucleic acid amplification-involved technology. The present primer comprises (a) a 3′-end portion having a hybridizing nucleotide sequence substantially complementary to a site on a template nucleic acid to hybridize therewith; (b) a 5′-end portion having a pre-selected arbitrary nucleotide sequence; and (c) a regulator portion positioned between said 3′-end portion and said 5′-end portion comprising at least one universal base or non-discriminatory base analog, whereby said regulator portion is capable of regulating an annealing portion of said primer in association with annealing temperature.

REFERENCES:
patent: 5962228 (1999-10-01), Brenner
patent: WO 00/20630 (2000-04-01), None
GenBank GI:895865 [online] Feb. 17, 1997 [retrieved on Aug. 16, 2008], retrieved from: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?895865:OLD11:1310887 (3 pages).
Abbotts, et al., “Studies on the mechanism ofEscherichia coliDNA polymerase I large fragment. Effect of template sequence and substrate variation on termination of synthesis,”J. Biol ChemOct. 15, 1988;263(29):15094-103.
Amosova, et al., “Effect of the 1-(2′-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole residue on the stability of DNA duplexes and triplexes,”Nucleic Acids Res. May 15, 1997;25(10):1930-4.
Bartl, S. & Weissman, IL. “PCR primers containing an inosine triplet to complement a variable codon within a conserved protein-coding region,”BiotechniquesFeb. 1994;16(2):246-8, 250.
Carter, et al., “The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches,”Nucleic Acids Res.Oct. 15, 1997;25(20):4117-22.
Cornish-Bowden A., “Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations,” 1984.Nucleic Acids Res. 1985; 13(9):3021-3030.
Ehlen T. Dubeau L., “Detection of ras point mutation by polymerase chain reaction using mutation specific, inosine-containing oligonucleotide primers,”Biochem. Biophys. Res. Commun. Apr. 28, 1989;169(2):441-7.
Noma, et al., “Structure and expression of human mitochondrial adenylate kinase targeted to the mitochondrial matrix,”Biochem J. Aug. 15, 2001;358(Pt 1):225-32.
Ryder et al., “Sequence-specific affinity selection of mammalian splicing complexes,”Nucleic Acids Res. Dec. 15, 1990;18(24):7373-9.
Saparbaev, et al., “Interactions of the human, rat,Saccharomyces cerevisiaeandEscherichia coli3- methyladenine-DNA glycosylases with DNA containing Dimp residues,”Nucleic Acids Res. Mar. 15, 2000;28(6):1332-39.
General concepts for PCR Primer Design; Dieffenbach, C.W.; Lowe, TMJ ; Dveksler, G.S. PCR primer: a Laboratory Manual. Cold Spring Harbor Laboratory Press,1995, 133-1 42.
Don, R.H.; Cox, P.T.; Wainwright, B.J.; Baker, K.; Mattick, J.S. Touchdown' PCR to circumvent spurious priming during gene amplification.Nucleic Acids Res., 1991, vol. 19,4008.
Franz, O. ; Bruchhaus, I. ; Roeder, T. Verification of differential gene transcription using virtual northern 'blotting.Nucleic Acids Res., 1999, vol. 27, 1-3.
Frohman, M.A.; Dush, M.K.; Martin, G.R. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer.Proc. Natl. Acad. Sci. USA, 1988, vol. 85, 8998-9002.
Fromont-Racine, M. ; Bertrand, E. ; Pictet, R. ; Grange, T. A highly sensitive method for mapping the 5′ termini of mRNAs.Nucleic Acids Res., 1993, vol. 21, 1683-1684.
Gottschlich, S. ; Goeoegh, T. ; Folz, B.J. ; Lippert, B.M. ; Werner, J.A. Optimized differential display and reamplification parameters for silver staining.Res. Commun. Mol. Path. Pharm., 1997, vol. 97, 237-240.
Gromova, I.; Gromov, P.; Celis, J.E. Identification of true differentially expressed mRNAs in a pair of human bladder transitional cell carcinomas sing an improved differential display procedure.Electrophoresis, 1999, vol. 20, 241-248.
Hogan, B.; Bedding, R.; Costantini, F.; Lacy, E. Manipulating the moue embryo: a laboratory manual. Cold Spring Harbor Laboratory Press, 1994.
Hwang, LT.; Lee, Y.H.; Moon, B.C.; Ahn, K.Y.; Lee, S.W.; Chun, J.Y. Identification and characterization of a new member of the placental prolactin-like protein-C (PLP-C) subfamily, PLP-C˜.Endocrinology, 2000, vol. 141, 3343-3352.
Henegariu, O; Hirschmann, P.; Killian, K.; Kirch, S.; Lengauer, C.; Maiwald, R.; Mielke, K.; Vogt, P. Rapid screening of the Y chromosome in idiopathic sterile men, diagnostic for deletions in AZF, a genetic Y factor expressed during spermatogenesis.Andrologia, 1994, vol. 26, 97-106.
Jefferies, D. ; Botman, M. F. ; Lester, D ; Whitehead, C. C. ; Thorp, B. H. Cloning differentially regulate genes from chondrocyles using agarose gel differential display.Biochim. Biophys. Acta, 1998, vol. 1396,237-241.
Kociok, N.; Unfried, K. ; Eser, P. ; Krott, R. ; Schraermeyer, U. ; Heimann, K. The non-radioisotopic representation of differentially expressed mRNA by a combination of RNA fingerprinting and differential display.Mol. Biotechnol., 1998, vol. 9, 25-33.
Korn, B.; Sedlacek, Z.; Manca, A.; Kioschis, P.; Konecki, D.; Lehrach, H.; Poutska, A. A strategy for the selection of transcribed sequences in the Xq28 region.Hum. Mol. Genet., 1992, vol. 1, 235-242.
Kulp A, D. ; Topping, R. ; Telesnitskt, A. Determination of the site of first strand transfer during Moloney murine leukemia virus reverse transcription and identification of strand transfer-associated reverse transcriptase errors.EMBO J., 1997, vol. 16, 856-865.
Landegren, U.; Nilsson, M.; Kwok, P.-Y. reading bits of genetic information: methods for single-nucleotide polymorphism analysis.Genome Res., 1998, vol. 8, 769-776.
Liang, P. ; Pardee, A.B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction.Science, 1992, vol. 257, 967-971.
Ledbetter, S.A.; Nelson, D.L.; Warren, S.T.; Ledbetter, D.H. Rapid isolation of DNA probes within specific chromosome regions by interspersed repetitive sequence polymerase chain reaction.Genomics, 1990, vol. 6, 475-481.
Loakes, D.; Brown, D.M. 5-Nitroindole as an universal base analog.Nucleic Acids Res, 1994, vol. 22, 4039-4043.
Loakes, D. The applications of universal DNA base analogues.Nucleic Acids Res., vol. 29, 2437-2447.
Matz, M.V. ; Lukyanov, S.A. Different strategies of differential display: areas of application.Nucleic Acids Res., 1998, vol. 26, 5537-5543.
Matz, M.; Shagin, D.; Bogdanova, E.; Britanova, O.; Lukyanov, S.; Diatchenko, L. ; Chenchik., A. Amplification of cDNA ends based on template switching effect and step-out PCR.Nucleic Acids Res., 1999, vol. 27, 1558-1560.
McPherson, M.J.; Moller, S.G. PCR. BIOS Scientific Publishers, Springer-Verlag, 2000 [0392].
Meunier, J.R.; Grimont, PA.D. Factors affecting reproducibility of amplified polymorphic DNA fingerprints.Res. Microbial., 1993, vol. 144, 373-379.
Mullis, K.B. ; Faloona, FA Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction.Methods Enzymol., 1987, vol. 155,335-350.
Mutirangura, A. ; Greenberg, F. ; Butler, M.G. ; Malcolm, S. ; Nicholls, R.D.; Chakravarti, A.; Ledbetter, D.H. Multiplex PCR of three dinucleotide repeats in the Prader-Wi!-li/Angelman critical region (15q11-q13): molecular diagnosis and mechanism of uniparental disomy.Hum. Mol. Genet., 1993, vol. 2, 143-151.
Nichols, R.; Andrews, P.C.; Ahang, P.; Bergstrom, D.E. A universal nucleoside for use at ambiguous sites in DNA primers.Nature, 1994. vol. 369, 492-493.
Ohtsuka, E.; Matsuka, S. ;Ikehara M.; Takahashi, Y.; Matsubara K. An alternative approach to deoxyoligonucleotides as hybridization probes by insertion of deoxyinosine at ambiguous codon positions.J. Biol. Chem., 1985, vol. 260, 2605-2608.
Ralph, D. ; Welsh, J. ; McClelland, M. RNA fingerprinting using arbitrary primed PCR identifies differentially regulated RNAs in Mink lung (Mv1 Lu) cells growth arrested

Affiliated with

Also associated with

Rating

Annealing control primer and its uses does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Annealing control primer and its uses, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Annealing control primer and its uses will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-4053492