Frame shuffling: A novel method for in vitro protein evolution

Protein Engineering, Design and Selection

Volumn 19, Issue 3, 2006, Pages 135-140

  Kashiwagi, Kenji ^a,b   Isogai, Yasuhiro ^c   Nishiguchi, Kei Ichi ^a   Shiba, Kiyotaka ^a,b  

^a CANCER INSTITUTE   (Japan)

^b RIKEN HARIMA INSTITUTE   (Japan)

^c INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

Author keywords

Artificial protein; Frame shift mutation; in vitro evolution; Microgene; Y family DNA polymerase

Indexed keywords

DNA; GENES; MUTAGENESIS;

ARTIFICIAL PROTEIN; FRAME SHIFT MUTATION; IN VITRO EVOLUTION; MICROGENE; Y-FAMILY DNA POLYMERASE;

ENZYMES;

DNA POLYMERASE; MUTANT PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; FRAMESHIFT MUTATION; METHODOLOGY; MOLECULAR EVOLUTION; MUTAGENESIS; NUCLEOTIDE SEQUENCE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROGENY;

AMINO ACID SEQUENCE; CENTRIFUGATION, DENSITY GRADIENT; CIRCULAR DICHROISM; CODON, TERMINATOR; DIRECTED MOLECULAR EVOLUTION; DNA POLYMERASE BETA; DNA SHUFFLING; ESCHERICHIA COLI; FRAMESHIFT MUTATION; LIGHT; MOLECULAR SEQUENCE DATA; MUTAGENESIS; PEPTIDES; POLYMERASE CHAIN REACTION; PROTEIN ENGINEERING; SCATTERING, RADIATION; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 33644986778     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzj008     Document Type: Article

References (37)

1. Bartel,D.P. and Szostak,J.W. (1993) Science, 261, 1411-1418.
2. Bittker,J.A., Le,B.V., Liu,J.M. and Liu,D.R. (2004) Proc. Natl Acad. Sci. USA, 101, 7011-7016.
3. Boudsocq,F., Iwai,S., Hanaoka,F. and Woodgate,R. (2001) Nucleic Acids Res., 29, 4607-4616.
4. Boudsocq,F., Kokoska,R.J., Plosky,B.S., Vaisman,A., Ling,H., Kunkel,T.A., Yang,W. and Woodgate,R. (2004) J. Biol. Chem., 279, 32932-32940.
5. Brotcorne-Lannoye,A. and Maenhaut-Michel,G. (1986) Proc. Natl Acad. Sci. USA, 83, 3904-3908.
6. Cadwell,R.C. and Joyce,G.F. (1992) PCR Methods Appl., 2, 28-33.
7. Cho,G., Keefe,A.D., Liu,R., Wilson,D.S. and Szostak,J.W. (2000) J. Mol. Biol., 297, 309-319.
8. Cirino,P.C., Mayer,K.M. and Umeno,D. (2003) Methods Mol. Biol., 231, 3-9.
9. Davidson,A.R., Lumb K.J. and Sauer R.T. (1995) Nat. Struct. Biol., 2, 856-864.
10. Friedberg,E.C., Wagner,R. and Radman,M. (2002) Science, 296, 1627-1630.
11. Goodman,M.F. and Tippin,B. (2000) Nat. Rev. Mol. Cell Biol., 1, 101-109.
12. Johnson,R.E., Kondratick,C.M., Prakash,S. and Prakash,L. (1999) Science, 285, 263-265.
13. Kashiwagi,K. and Shiba,K. (2004) J. Mol. Catal. B, 28, 215-221.
14. Kawahara,K. and Tanford,C. (1966) J. Biol. Chem., 241, 3228-3232.
15. Kim,S.R., Maenhaut-Michel,G., Yamada,M., Yamamoto,Y., Matsui,K., Sofuni,T., Nohmi,T. and Ohmori,H. (1997) Proc. Natl Acad. Sci. USA, 94, 13792-13797.
16. Kitamura,K., Kinoshita,Y., Narasaki,S., Nemoto,N., Husimi,Y. and Nishigaki,K. (2002) Protein Eng., 15, 843-853.
17. Kokoska,R.J., Bebenek,K., Boudsocq,F., Woodgate,R. and Kunkel,T.A. (2002) J. Biol. Chem., 277, 19633-19638.
18. Kokoska,R.J., McCulloch,S.D. and Kunkel,T.A. (2003) J. Biol. Chem., 278, 50537-50545.
19. Kolkman,J.A. and Stemmer,W.P. (2001) Nat. Biotechnol., 19, 423-428.
20. Lutz,S., Ostermeier,M., Moore,G.L., Maranas,C.D. and Benkovic,S.J. (2001) Proc. Natl Acad. Sci. USA, 98, 11248-11253.
21. Masutani,C., Kusumoto,R., Yamada,A., Dohmae,N., Yokoi,M., Yuasa,M., Araki,M., Iwai,S., Takio,K. and Hanaoka,F. (1999) Nature, 399, 700-704.
22. Neylon,C. (2004) Nucleic Acids Res., 32, 1448-1459.
23. Ohashi,E., Ogi,T., Kusumoto,R., Iwai,S., Masutani,C., Hanaoka,F. and Ohmori,H. (2000) Genes Dev., 14, 1589-1594.
24. Ohmori,H., et al. (2001) Mol. Cell, 8, 7-8.
25. Prijambada,I.D., Yomo,T., Tanaka,F., Kawama,T., Yamamoto,K., Hasegawa,A., Shima,Y., Negoro,S. and Urabe,I. (1996) FEBS Lett., 382, 21-25.
26. Rost,B. and Sander,C. (1993) J. Mol. Biol., 232, 584-599.
27. Saito,H., Honma,T., Minamisawa,T., Yamazaki,K., Noda,T., Yamori,T. and Shiba,K. (2004) Chem. Biol., 11, 765-773.
28. Sambrook,J. and Russel,D.W. (eds) (2001) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
29. Shiba,K., Takahashi,Y. and Noda,T. (1997) Proc. Natl Acad. Sci. USA, 94, 3805-3810.
30. Shiba,K., Hatada,T., Takahashi,Y. and Noda,T. (2002a) J. Biochem. (Tokyo), 132, 689-696.
31. Shiba,K., Takahashi,Y. and Noda,T. (2002b) J. Mol. Biol., 320, 833-840.
32. Shiba,K. (2004) J. Mol. Catal. B, 28, 145-153.
33. Strauss,B.S., Roberts,R., Francis,L. and Pouryazdanparast,P. (2000) J. Bacteriol., 182, 6742-6750.
34. Tsuji,T., Onimaru,M., Kitagawa,M., Kojoh,K., Tabata,N. and Yanagawa,H. (2004) Methods Enzymol., 388, 61-75.
35. Wagner,J., Gruz,P., Kim,S.R., Yamada,M., Matsui,K., Fuchs,R.P. and Nohmi,T. (1999) Mol. Cell, 4, 281-286.
36. Wagner,J. and Nohmi,T. (2000) J. Bacteriol., 182, 4587-4595.
37. Zhang,Y., Yuan,F., Wu,X., Wang,M., Rechkoblit,O., Taylor,J.S., Geacintov,N.E. and Wang,Z. (2000) Nucleic Acids Res., 28, 4138-4146.