Towards the design of rare cutting restriction endonucleases: Using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude

Journal of Molecular Biology

Volumn 283, Issue 1, 1998, Pages 59-69

  Lanio, Thomas ^a   Jeltsch, Albert ^a   Pingoud, Alfred ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

DNA recognition; In vitro evolution; Protein engineering; Restriction modification system; Specificity change

Indexed keywords

DNA FRAGMENT; RESTRICTION ENDONUCLEASE;

ARTICLE; CONTROLLED STUDY; DNA CLEAVAGE; DNA FLANKING REGION; ENZYME ACTIVITY; ENZYME SPECIFICITY; EVOLUTION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL;

EID: 0032538280     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2088     Document Type: Article

References (26)

1. Alves, J., Selent, U. & Wolfes, H. (1995). Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences. Biochemistry, 34, 11191-11197.
2. Chen, K. & Arnold, F. H. (1993). Turning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl Acad. Sci. USA, 90, 5618-5622.
3. Crameri, A., Whitehorn, E., Tate, E. & Stemmer, W. P. C. (1996). Improved green fluorescent protein by molecular evolution using DNA shuffling. Nature Biotechnol. 14, 315-319.
4. Crameri, A., Dawes, G., Rodriguez, E., Silver, S. & Stemmer, W. P. C. (1997). Molecular evolution of an arsenate detoxification pathway by DNA shuffling. Nature Biotechnol. 15, 436-438.
5. Eun, H.-M. (1996). Enzymology Primer for Recombinant DNA Technology, Academic Press, London.
6. Ito, W., Ishiguro, H. & Kurosawa, Y. (1991). A general method for introducing a series of mutations into cloned DNA using the polymerase chain reaction. Gene, 102, 67-70.
7. Jeltsch, A., Fritz, A., Alves, J., Wolfes, H. & Pingoud, A. (1993). A fast and accurate enzyme-linked immunosorbent assay for the determination of the DNA cleavage activity of restriction endonucleases. Anal. Biochem. 213, 234-240.
8. Jeltsch, A., Wenz, C., Stahl, F. & Pingoud, A. (1996a). Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme. EMBO J. 15, 5104-5111.
9. Jeltsch, A., Wenz, C., Wende, W., Selent, U. & Pingoud, A. (1996b). Engineering novel restriction endonucleases: principles and applications. Trends Biotechnol. 14, 235-238.
10. 2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry, 34, 683-696.
11. Kucher, O. & Arnold, F. H. (1997). Directed evolution of enzyme catalysis. Trends Biotechnol. 15, 523-530.
12. Lanio, T., Selent, U., Wenz, C., Wende, W., Schulz, A., Adiraj, M., Katti, S. B. & Pingoud, A. (1996). EcoRV- T94V: a mutant restriction endonucleaase with an altered substrate specificity towards modified oligodeoxynucleotides. Protein Eng. 9, 1005-1010.
13. Moore, J. C. & Arnold, F. H. (1996). Directed evolution to improve enzyme fitness. Nature Biotechnol. 14, 458-467.
14. Perona, J. J. & Martin, A. M. (1997). Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis. J. Mol. Biol. 273, 207-225.
15. Pingoud, A. & Jeltsch, A. (1997). Recognition and cleavage of DNA by type-II restriction endonucleases. Eur. J. Biochem. 246, 1-22.
16. Pingoud, A., Alves, J. & Geiger, R. (1993). Restriction enzymes. Methods Mol. Biol. 16, 107-200.
17. Roberts, R. J. & Halford, S. E. (1993). Type II restriction enzymes. In Nucleases (Linn, S. M., Lloyd, R. S. & Roberts, R. J., eds), pp. 35-88, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
18. Roberts, R. J. & Macelis, D. (1998). REBASE-restriction enzymes and methylases. Nucl. Acids Res. 26, 338-350.
19. 6-methyltransferase. J. Biol. Chem. 273, 17333-17347.
20. Stemmer, W. P. C. (1994). Rapid evolution of a protein in vitro by DNA shuffling. Nature, 370, 389-391.
21. Taylor, J. D. & Halford, S. E. (1989). Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry, 28, 6198-6207.
22. Van Cleve, M. D. & Gumport, R. I. (1992). Influence of enzyme-substrate contacts located outside the EcoRI recognition site on cleavage of duplex oligodeoxyribonucleotide substrates by EcoRI endonuclease. Biochemistry, 31, 334-339.
23. Wenz, C., Selent, U., Wende, W., Jeltsch, A., Wolfes, H. & Pingoud, A. (1994). Protein engineering of the restriction endonuclease EcoRV: replacement of an amino acid residue in the DNA binding site leads to an altered selectivity towards unmodified and modified substrates. Biochim. Biophys. Acta, 1219, 73-80.
24. Wenz, C., Jeltsch, A. & Pingoud, A. (1996). Probing the indirect readout of the restriction enzyme EcoRV. J. Biol. Chem. 271, 5565-5573.
25. Windolph, S., Fritz, A., Oelgeschlager, T., Wolfes, H. & Alves, J. (1997). Sequence context influencing cleavage activity of the K130E mutant of the restriction endonuclease EcoRI identified by a site selection assay. Biochemistry, 36, 9478-9485.
26. Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K. & Wilson, K. S. (1993). The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12, 1781-1795.