Error-prone rolling circle amplification: The simplest random mutagenesis protocol

Nature Protocols

Volumn 1, Issue 5, 2006, Pages 2493-2497

  Fujii, Ryota ^a,b   Kitaoka, Motomitsu ^a   Hayashi, Kiyoshi ^a  

^a NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORIDE; MANGANESE CHLORIDE; MANGANESE DERIVATIVE;

ARTICLE; GENE LIBRARY; GENE TRANSFER; METHODOLOGY; MUTAGENESIS; MUTATION; NUCLEIC ACID AMPLIFICATION; PLASMID;

CHLORIDES; GENE LIBRARY; GENE TRANSFER TECHNIQUES; MANGANESE COMPOUNDS; MUTAGENESIS; MUTATION; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PLASMIDS;

EID: 34548860346     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.403     Document Type: Article

References (28)

1. Bloom, J.D. et al. Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol. 15, 447-452 (2005).
2. Jaeger, K.E. & Eggert, T. Enantioselective biocatalysis optimized by directed evolution. Curr. Opin. Biotechnol. 15, 305-313 (2004).
3. Arnold, F.H., Wintrode, P.L., Miyazaki, K. & Gershenson, A. How enzymes adapt: Lessons from directed evolution. Trends Biochem. Sci. 26 100-106 (2001).
4. Johannes, T.W. & Zhao, H. Directed evolution of enzymes and biosynthetic pathways. Curr. Opin. Microbiol. 9, 261-267 (2006).
5. Reetz, M.T. Directed evolution of enantioselective enzymes as catalysts for organic synthesis. Adv. Catal. 49, 1-69 (2006).
6. Aharoni, A., Griffiths, A.D. & Tawfik, D.S. High-throughput screens and selections of enzyme-encoding genes. Curr. Opin. Chem. Biol. 9 210-216 (2005).
7. Goddard, J.P. & Reymond, J.L. Enzyme assays for high-throughput screening. Curr. Opin. Biotechnol. 15, 314-322 (2004).
8. Taylor, S.V., Kast, P. & Hilvert, D. Investigating and engineering enzymes by genetic selection. Angew. Chem. Int. Ed. Engl. 40 3310-3335 (2001).
9. Lin, H. & Cornish, V.W. Screening and selection methods for large-scale analysis of protein function. Angew. Chem. Int. Ed. Engl. 41 4402-4425 (2002).
10. Reetz, M.T. & Jaeger, K.E. Superior biocatalysts by directed evolution. In Biocatalysis - From Discovery to Application 31-57 (Springer-Verlag, Berlin, 1999).
11. Leung, D.W., Chen, E. & Goeddel, D.W. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Techniques 1, 11-15 (1989).
12. Greener, A., Callahan, M. & Jerpseth, B. In in vitro Mutagenesis Protocols (ed. Trower, M.K.) (Humana press, New Jersey, 1996).
13. Kornberg, A. & Baker, T. In DNA Replication (W.H. Freeman & Company, NY, 1992).
14. Fire, A. & Xu, S.Q. Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. USA 92, 4641-4645 (1995).
15. Liu, D.Y., Daubendiek, S.L., Zillman, M.A., Ryan, K. & Kool, E.T. Rolling circle DNA synthesis: Small circular oligonucleotides as efficient templates for DNA polymerases. J. Am. Chem. Soc. 118 1587-1594 (1996).
16. Lizardi, P.M. et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19, 225-232 (1998).
17. Dean, F.B., Nelson, J.R., Giesler, T.L. & Lasken, R.S. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11 1095-1099 (2001).
18. Fujii, R., Kitaoka, M. & Hayashi, K. One-step random mutagenesis by error-prone rolling circle amplification. Nucleic Acids Res. 32 e145 (2004).
19. Ding, X., Snyder, A.K., Shaw, R., Farmerie, W.G. & Song, W.Y. Direct retransformation of yeast with plasmid DNA isolated from single yeast colonies using rolling circle amplification. BioTechniques 35 774-779 (2003).
20. Camps, M., Naukkarinen, J., Johnson, B.P. & Loeb, L.A. Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I. Proc. Natl. Acad. Sci. USA 100, 9727-9732 (2003).
21. Henke, E. & Bornscheuer, U.T. Directed evolution of an esterase from Psueudomonas fluorescens. Random mutagenesis by error-prone PCR or a mutator strain and identification of mutants showing enhanced enantioselectivity by a resorufin-based fluorescence assay. Biol. Chem. 380, 1029-1033 (1999).
22. Bornscheuer, U.T., Altenbuchner, J. & Meyer, H.H. Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones. Biotechnol. Bioeng. 58, 554-559 (1998).
23. Reetz, M.T., Zonta, A., Schimossek, K., Liebeton, K. & Jaeger, K.E. Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution. Angew. Chem. Int. Ed. Engl. 36, 2830-2832 (1997).
24. de Vega, M., Lazaro, J.M. & Salas, M. Phage φ29 DNA polymerase residues involved in the proper stabilisation of the primer-terminus at the 3′-5′ exonuclease active site. J. Mol. Biol. 304, 1-9 (2000).
25. Voss, C., Schmidt, T., Schleef, M., Friehs, K. & Flaschel, E. Production of supercoiled multimeric plasmid DNA for biopharmaceutical application. J. Biotechnol. 105, 205-213 (2003).
26. pUC19 β-lactamase from Escherichia coli. J. Biol. Chem. 274, 23052-23060 (1999).
27. pUC19 β-lactamase on susceptibility to β-lactams. Antimicrob. Agents Chemother. 39 1878-1880 (1995).
28. Blanco, L. et al. Highly efficient DNA-synthesis by the phage φ29 DNA polymerase. J. Biol. Chem. 264, 8935-8940 (1989).