Alcohol-mediated error-prone PCR

DNA and Cell Biology

Volumn 23, Issue 11, 2004, Pages 789-795

  Claveau, S ^a   Sasseville, M ^a,b   Beauregard, M ^a  

^a UNIVERSITÉ DU QUÉBEC À TROIS RIVIÈRES   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

2 PROPANOL; ALCOHOL; BUTANOL; DNA POLYMERASE; PROPANOL; UREA;

ANALYTICAL ERROR; ARTICLE; ENZYME STABILITY; GENE FREQUENCY; GENE MUTATION; HEAT SENSITIVITY; HYDROPHOBICITY; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; MOLECULAR MECHANICS; MUTAGENICITY; MUTATIONAL ANALYSIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STANDARD;

EID: 9644266716     PISSN: 10445498     EISSN: None     Source Type: Journal    
DOI: 10.1089/dna.2004.23.789     Document Type: Article

References (31)

1. ABABNEH, A.M., LARGE, C.C., and GEORGHIOU, S. (2003). Solvation of nucleosides in aqueous mixtures of organic solvents: Relevance to DNA open basepairs. Biophys. J. 2, 1111-1127.
2. AYED, A., and DUCKWORTH, H.A. (1999). A stable intermediate in the equilibrium unfolding of Escherichia coli citrate synthase. Protein Sci. 8, 1116-1126.
3. BEAUREGARD, M., DUPONT, C., TEATHER, R.M., and HEFFORD, M.A. (1995). Design, expression and initial characterization of MB1, a de novo protein enriched in essential amino acids. Bio/Technology 13, 974-981.
4. BORNSCHEUER, U.T., BESSLER, C., SRINIVAS, R., and KRISHNA, S.H. (2002). Optimizing lipases and related enzymes for efficient application. Trends Biotechnol. 10, 433-437.
5. CADWELL, R.C., and JOYCE, G.F. (1992). Randomization of genes by in vitro mutagenesis. PCR Methods Applic. 2, 28-33.
6. CHAO, K.M., PEARSON, W.R., and MILLER, W. (1992). Aligning two sequences within a specified diagonal band. Comput. Appl. Biosci. 8, 481-487.
7. CHIANG, L., KOVARI, I., and HOWE, M. (1993). Mutagenic oligonucleotide-directed PCR amplification (Mod-PCR): An efficient method for generating random base substitution mutations in a DNA sequence element. PCR Methods Applic. 2, 210-217.
8. CHU, C.T., PARRIS, D.S., DIXON, R.A., FARBER, F.E., and SCHAFFER, P.A. (1979). Hydroxylamine mutagenesis of HSV DNA and DNA fragments: Introduction of mutations into selected regions of the viral genome. Virology 98, 169-181.
9. COX, E.C. (1976). Bacterial mutator genes and the control of spontaneous mutation. Annu. Rev. Genet. 10, 135-156.
10. DILL, K.A. (1990). Dominant forces in protein folding. Biochemistry 31, 7133-7155.
11. FROMANT, M., BLANQUET, S., and PLATEAU, P. (1995). Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction. Anal. Biochem. 1, 347-353.
12. HUANG, H., and KEOHAVONG, P. (1996). Fidelity and predominant mutations by Deep Vent wild-type and exonuclease-deficient DNA polymerases during in vitro DNA amplification. DNA Cell Biol. 15, 589-594.
13. KAMATARI, Y.O., KONNO, T., KATAOKA, M., and AKASAKA, K. (1996). The methanol-induced globular and expanded denatured states of cytochrome c: A study by CD fluorescence, NMR and small-angle X-ray scattering. J. Mol. Biol. 3, 512-523.
14. KAUFMAN, D.L., and EVANS, G.A. (1990). Restriction endonuclease cleavage at the termini of PCR products. Biotechniques 3, 304-306.
15. KEOHAVONG, P., LING, L., DIAS, C., and THILLY, W.G. (1993). Predominant mutations induced by the Thermococcus litoralis, Vent DNA polymerase during DNA amplification in vitro. PCR Methods Applic. 2, 288-292.
16. KHAN, F., KHAN, R.H., and MUZAMMIL, S. (2000). Alcohol-induced versus anion-induced states of alpha-chymotrypsinogen A at low pH. Biochim. Biophys. Acta. 2, 229-236.
17. KLESS, H., and VERMAAS, W. (1996). Combinatorial mutagenesis and structural simulations in the environment of the redox-active tyrosine YZ of photosystem II. Biochemistry 51, 16458-16464.
18. KONG, H., KUCERA, B., and JACK, W.E. (1993). Characterization of a DNA polymerase from hyperthermophile archaea Thermococcus litoralis. J. Biol. Chem. 268, 1965-1975.
19. LEUNG, D.W., ELLSON, C., and GOEDDEL, D.V. (1989). A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique 1, 11-15.
20. MATTILA, P., KORPELA, J., TENKANEN, T., and PITKANEN, K. (1991). Fidelity of DNA synthesis by the Thermococcus litoralis DNA polymerase - An extremely heat stable enzyme with proof-reading activity. Nucleic Acids Res. 19, 4967-4973.
21. MOTT, J., VAN ARSDELL, J., and PLATT, T., (1984). Targeted mutagenesis in vitro: lac repressor mutations generated using AMV reverse transcriptase and dBrUTP. Nucleic Acids Res. 12, 4139-4152.
22. SHORTLE, D., and BOBSTEIN, D. (1983). Directed mutagenesis with sodium bisulfite. Methods Enzymol. 100, 457-468.
23. SMITH, M. (1989). In vitro mutagenesis. Annu. Rev. Genet. 19, 423-462.
24. STEMMER, W.P.C. (1994). DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91, 10747-10751.
25. SUNDD, M., KUNDU, S., and JAGANNADHAM, M.V. (2000). Alcohol-induced conformational transitions in ervatamin C. An alpha-helix to beta-sheet switchover. J. Protein Chem. 3,169-176.
26. TANFORD, C. (1973). The hydrophobic effect (Wiley-Interscience, New York).
27. TINDALL, K.R., and KUNKEL, T.A. (1988). Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27, 6008-6013.
28. VARTANIAN, J.P., HENRY, M., and WAIN-HOBSON, S. (1996). Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res. 14, 2627-2631.
29. VELICEBELI, G., and STURTEVANT, J.M. (1979). Thermodynamics of the denaturation of lysozyme in alcohol-water mixtures. Biochemistry 7, 1180-1186.
30. WICK, M.J., MIHIC, S.J., UENO, S., MASCIA, M.P., TRUDELL, J.R., BROZOWSKI, S.J., YE, Q., HARRISON, N.L., and HARRIS, R.A. (1998). Mutations of gamma-aminobutyric acid and glycine receptors change alcohol cutoff: Evidence for an alcohol receptor? Proc. Natl. Acad. Sci. USA 11, 6504-6509.
31. ZHAO, H., GIVER, L.,SHAO, Z., AFFHOLTER, A., and ARNOLD, F.H. (1998). Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol. 16, 258-261.