Specificity, efficiency, and fidelity of PCR

Genome Research

Volumn 3, Issue 3, 1993, Pages

  Cha, Rita S ^a   Thilly, William G ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED DNA POLYMERASE; PRIMER DNA;

ARTICLE; ARTIFACT; DNA TEMPLATE; METHODOLOGY; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

ARTIFACTS; DNA PRIMERS; DNA-DIRECTED DNA POLYMERASE; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TEMPLATES, GENETIC;

EID: 0027745555     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3.3.S18     Document Type: Article

References (35)

1. Sambrook, J., E.F., Fritsch, and T. Maniatis. 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
2. Keohavong, P., C.C. Wang, R.S. Cha, and W.G. Thilly. 1988. Enzymatic amplification and characterization of large DNA fragments from genomic DNA. Gene 71: 211-216.
3. D.M. Coen. 1991. The polymerase chain reaction. Current protocols in molecular biology. Greene Publishing/Wiley Interscience, New York.
4. Saiki, R.K., S. Scharf, F. Faloona, K. B. Mullis, G.T. Horn, H.A. Erlich, and N. Arnheim. 1985. Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 1350-1354.
5. Mullis, K.B. and F.A. Faloona. 1987. Specific synthesis of DNA in vitro via a polymerase-catalysed chain reaction. Methods Enzymol. 155: 335-350.
6. Scharf, S.J., G.T. Horn, and H.A. Erlich. 1986. Direct cloning and sequence analysis of enzymatically amplified genomic sequences. Science 233: 1076-1078.
7. Keohavong, P., C.C. Wang, R.S. Cha, and W.G. Thilly. 1988. Enzymatic amplification and characterization of large DNA fragments from genomic DNA. Gene 71: 211-216.
8. Keohavong, P., A.G., Kat, N.F. Cariello, and W.G. Thilly. 1988. Laboratory Methods: DNA amplification in vitro using T4 DNA polymerase. DNA 7: 63-70.
9. Vent™ DNA polymerase technical bulletin from New England Biolabs. 1990,1991.
10. Cariello, N.F., W.G. Thilly, J.A. Swenberg, and T.R. Skopek. 1991. Deletion mutagenesis during polymerase chain reaction: Dependence on DNA polymerase. Gene 99: 105-108.
11. Chien, A., D.B. Edgar, and J.M. Trela. 1976. Deoxyribonucleic acid polymerase from the extreme thermophile Thermus acquaticus. J. Bacterol. 127: 1550.
12. Cha, R.S., H. Zarbl, P. Keohavong, and W.G. Thilly. 1992. Mismatch amplification mutation assay (MAMA): Application to the c-H-ras gene. PCR Methods Applic. 2: 14-20.
13. Sarkar, G., S. Kapelner, and S.S. Sommer. 1990. Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res. 18: 7465.
14. Jin, Z., R. Cha, and H. Zarbl. (in prep.).
15. 508 locus. Clin. Chem. 39: 804-809; Witter, C.T. and D.J. Garling. 1991. Rapid cycle DNA amplification: Time and temperature optimization. BioTechniques 10: 76-83.
16. 508 locus. Clin. Chem. 39: 804-809; Witter, C.T. and D.J. Garling. 1991. Rapid cycle DNA amplification: Time and temperature optimization. BioTechniques 10: 76-83.
17. Kowk, S., D.E. Kellogg, N. McKinney, D. Spasic, L. Goda, and J.J. Sninsky. 1990. Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type 1 model studies. Nucleic Acids Res. 17: 2503-2516.
18. Keohavong, P. and W.G. Thilly. 1989. Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acad. Sci. 86: 9253-9257.
19. Ling, L.L., P. Keohavong, C. Dias, and W.G. Thilly. 1991. Optimization of the polymerase chain reaction with regard to fidelity: Modified T7, Taq, and Vent DNA polymerases. PCR Methods Applic. 1: 63-69.
20. Eckert, K.A. and T.A. Kunkel. 1991. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Applic. 1: 17-24.
21. Dunning, A.M., P. Talmud, and S.E. Humphries. 1988. Errors in the polymerase chain reaction. Nucleic Acids Res. 16: 10393.
22. Saiki, R.K., D.H. Gelfand, S. Stoffe., S.J. Scharf, R. Higuchi, G.T. Horn, K.B. Mullis, and H.A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science 239: 487-491.
23. Stratagene Product Catalog, 1992.
24. Wu, D.Y., L. Ugozzoli, B.J. Pal, and R.B. Wallace. 1989. Allele-specific enzymatic amplification of β-globin genomic DNA for diagnosis of sickle cell anemia. Proc. Natl. Acad. Sci. 86: 2757-2760; Newton, C.R., A. Graham, L.E. Heptinstall, S.J. Powell, C. Summers, N. Kalsheker, J. C. Smith, and A.F. Markham. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system. Nucleic Acids. Res. 17: 2503-3516.
25. Wu, D.Y., L. Ugozzoli, B.J. Pal, and R.B. Wallace. 1989. Allele-specific enzymatic amplification of β-globin genomic DNA for diagnosis of sickle cell anemia. Proc. Natl. Acad. Sci. 86: 2757-2760; Newton, C.R., A. Graham, L.E. Heptinstall, S.J. Powell, C. Summers, N. Kalsheker, J. C. Smith, and A.F. Markham. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system. Nucleic Acids. Res. 17: 2503-3516.
26. Bottema, C.D.K. and S.S. Sommer. 1993. PCR amplification of specific alleles: Rapid detection of known mutation and polymorphisms. Mutat. Res. 288: 93-102.
27. Lacy, M.J., L.K. McNeil, M.E. Roth, and D.M. Kranz. 1989. T-cell receptor δ-chain diversity in peripheral lymphocytes. Proc. Natl. Acad. Sci. 86: 1023-1026.
28. Frohman, M.A., M.K. Dush, and G.R. Martin. 1988. Rapid production of full-length cDNAs from rare transcripts: Amplification using a single gene specific oligonucleotide primer. Proc. Natl. Acad. Sci. 85: 8998-9002.
29. Li, H., X. Cui, and N. Arnheim. 1990. Direct electrophoretic detectin of the allelic state of a single DNA molecules in human sperm by using the polymerase chain reaction. Proc. Natl. Acad. Sci. 87: 4580-4584.
30. Jeffreys, A.J., R. Neumann, and V. Wilson. 1990. Repeat unit sequence variation in minisatellites: A novel source of DNA polymorphism for studying variation and mutation by single molecule analysis. Cell 60: 473-485.
31. Ruano, G., K.K. Kidd, and J.C. Stephens. 1990. Haplotype of multiple polymorphisms resolved by enzymatic amplification of single DNA molecules. Proc. Natl. Acad. Sci. 87: 6296-6300.
32. Loeb, L.A. and T.A. Kunkel. 1982. Fidelity of DNA synthesis. Annu. Rev. Biochem. 52: 429-457; Eckert, K.A. and T.A. Kunkel. 1990. High fidelity DNA synthesis by the Thermus acuaticus DNA polymerase. Nucleic Acid Res. 18: 3739-3744.
33. Loeb, L.A. and T.A. Kunkel. 1982. Fidelity of DNA synthesis. Annu. Rev. Biochem. 52: 429-457; Eckert, K.A. and T.A. Kunkel. 1990. High fidelity DNA synthesis by the Thermus acuaticus DNA polymerase. Nucleic Acid Res. 18: 3739-3744.
34. Goodenow, M. T., W. Huet, W. Saurin, S. Kwok, J. Sninsky, and S. Wain-Hobson. 1989. HIV-1 isolates are rapidly evolving quasispecies: Evidence for viral mixtures and preferred nucleitode substitutions. J. AIDS 2: 344-352.
35. Kunkel, T. A. 1985. The mutational specificity of DNA polymerase-β during in vitro DNA synthesis. J. Biol. Chem. 260: 5787-5796.