Recognition of DNA by single-chain derivatives of the phage 434 repressor: High affinity binding depends on both the contacted and non-contacted base pairs

Nucleic Acids Research

Volumn 25, Issue 11, 1997, Pages 2047-2054

  Chen, Jinqiu ^a   Pongor, Sándor ^a   Simoncsits, Andrés ^a  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

REPRESSOR PROTEIN; SPACER DNA; VIRUS DNA;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIOPHAGE; BASE PAIRING; BINDING AFFINITY; BINDING SITE; CONSENSUS SEQUENCE; CONTROLLED STUDY; COVALENT BOND; DNA SEQUENCE; MUTAGENESIS; NONHUMAN; OPERATOR GENE; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN;

BACTERIOPHAGE LAMBDA; BINDING SITES; CONSENSUS SEQUENCE; DIMERIZATION; DNA; DNA MUTATIONAL ANALYSIS; DNA-BINDING PROTEINS; OPERON; PROTEIN BINDING; REPRESSOR PROTEINS; SEQUENCE ANALYSIS, DNA; VIRAL PROTEINS;

BACTERIOPHAGE 434; DNA VIRUSES;

EID: 0030844255     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/25.11.2047     Document Type: Article

References (50)

1. Pabo,C.O. and Sauer,R.T. (1992) Annu. Rev. Biochem., 61, 1053-1095.
2. Klug,A. (1993) Gene, 135, 83-92.
3. Rhodes,D., Schwabe,J.W.R., Chapman,L. and Fairall,L. (1996) Phil. Trans. R. Soc. Lond. B 351, 501-509.
4. Harrison,S.C. (1991) Nature, 353, 715-719.
5. Wilson,D.S. and Desplan,C. (1995) Curr. Biol., 5, 32-34.
6. Schwabe,J.W.R. and Klug,A. (1994) Nature Struct. Biol., 1, 345-349.
7. Herr,W. and Cleary,M.A. (1995) Genes Dev., 9, 1679-1693.
8. Ogata,K., Morikawa,S., Nakamura,H., Sekikawa,A., Inoue,T., Kanai,H., Sarai,A., Ishii,S. and Nishimura,Y. (1994) Cell, 79, 639-648.
9. Berg,J.M. and Shi,Y. (1996) Science, 271, 1081-1085.
10. Desjarlais,J.R. and Berg,J.M. (1993) Proc. Natl. Acad. Sci. USA, 90, 2256-2260.
11. Choo,Y., Sánchez-Garcia,I. and Klug,A. (1994) Nature, 372, 642-645.
12. Pomerantz,J.L., Sharp,P.A. and Pabo,C.O. (1995) Science, 267, 93-96.
13. Percipalle,P., Simoncsits,A., Zakhariev,S., Guamaccia,C., Sanchez,R. and Pongor,S. (1995) EMBO J., 14, 3200-3205.
14. Robinson,C.R. and Sauer,R.T. (1996) Biochemistry, 35, 109-116.
15. Simoncsits,A., Chen,J., Percipalle,P., Wang,S., TöröI. and Pongor,S. (1991) J. Mol. Biol., 261, 118-131.
16. Ptashne,M. (1992) A Genetic Switch. Cell Press and Blackwell Scientific Publications, Cambridge, MA, USA.
17. Sevilla-Sierra,P., Otting,G. and Wütrich,K. (1994) J. Mol. Biol., 235, 1003-1020.
18. Wharton,R.P. and Ptashne,M. (1985) Nature, 316, 601-605.
19. Hollis,M., Valenzula,D., Pioli,D., Wharton,R. and Ptashne,M. (1988) Proc. Natl. Acad. Sci. USA, 85, 5834-5838.
20. Choo,Y. and Klug,A. (1994) Proc. Natl. Acad. Sci. USA, 91, 11168-11172.
21. Desjarlais,J.R. and Berg,J.M. (1994) Proc. Natl. Acad. Sci. USA, 91, 11099-11103.
22. Wharton,R.P., Brown,E.L. and Ptashne,M. (1984) Cell, 38, 361-369.
23. Poteete,A.R., Ptashne,M., Ballivet,M. and Eisen,H. (1982) J. Mol. Biol., 157, 21-48.
24. Aggarwal,A.K., Rodgers,D.W., Drottar,M., Ptashne,M. and Harrison,S.C. (1988) Science, 242, 899-907.
25. Shimon,L.J.W. and Harrison,S.C. (1993) J. Mol. Biol., 232, 826-838.
26. Rodgers,D.W. and Harrison,S.C. (1993) Structure, 1, 227-240.
27. Koudelka,G.B., Bell,A.C. and Hilchey,S.P (1996) In Sharma,R.H. and Sharma,M.H. (eds), Biological Structure and Dynamics, Adenine Press, Inc., NY., Vol. I, pp. 135-153.
28. Koudelka,G.B., Harrison,S.C. and Ptashne,M. (1987) Nature, 326, 886-888.
29. Koudelka,G.B., Harbury,P., Harrison,S.C. and Ptashne,M. (1988) Proc. Natl. Acad. Sci. USA, 85, 4633-4637.
30. Koudelka,G.B. and Carlson,P. (1992) Nature, 355, 89-91.
31. Bell,A.C. and Koudelka,G.B. (1993) J. Mol. Biol., 234, 542-553.
32. Bell,A.C. and Koudelka,G.B. (1995) J.Biol. Chem., 270, 1205-1212.
33. Wu,L., Vertina,A. and Koudelka,G.B. (1992) J.Biol. Chem., 267, 9134-9139.
34. Wu,L. and Koudelka,G.B. (1993) J.Biol. Chem., 268, 18975-18981.
35. Blackwell,T.K.and Weintraub,H. (1990) Science, 250, 1104-1110.
36. Thiesen,H.-J. and Bach,C. (1990) Nucleic Acids Res., 18, 3203-3209.
37. McCabe,P.C. (1990) In Innis,M.A., Gelfand,D.H., Sninsky,J.J. and White,T.J. (eds), PCR Protocols. Academic Press, Inc., San Diego, CA, pp.76-83.
38. Kunkel,T.A., Bebenek,K. and McClary,J. (1991) Methods Enzymol., 204, 125-139.
39. Anderson,J.E., Ptashne,M. and Harrison,S.C. (1987) Nature, 326, 846-852.
40. Koudelka,G.B. and Lam,C.-Y. (1993) J. Biol. Chem., 268, 23812-23817.
41. Travers,A.A. and Klug,A. (1990) In Cozzarelli,N.R. and Wang,J.C. (eds.), DNA Topology and its Biological Effects, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. pp. 57-106.
42. Drew,H.R., McCall,M.J. and Calladine,C.R.(1990) In Cozzarelli,N.R. and Wang,J.C. (eds), DNA Topology and its Biological Effects, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. pp. 1-56.
43. Lehming,N., Sartorius,J., Oehler,S., Wilcken-Bergman,B.v. and Müller-Hill,B. (1988) Proc. Natl. Acad. Sci. USA, 85, 7947-7951.
44. Suzuki,M., Yagi,N. and Gerstein,M. (1995) Protein Eng., 8, 329-338.
45. Hilchey,S.P., Wu,L. and Koudelka,G.B. (1995) J. Biomol. Struct. Dyn., 12, a092.
46. Choo,Y. and Klug,A. (1994) Proc. Natl. Acad. Sci. USA, 91, 11163-11167.
47. Jamieson,A.C., Kim,S.H. and Wells,J.A. (1994) Biochemistry, 33, 5689-5695.
48. Rebar,E.J. and Pabo,C.O. (1994) Science, 263, 671-673.
49. Wu,H., Yang,W.-P. and Barbas,C.F., III. (1995) Proc. Natl. Acad. Sci. USA, 92, 344-348.
50. Gogos,J.A., Jin,J., Wan,H., Kokkinidis,M. and Kafatos,F.C. (1996) Proc. Natl. Acad. Sci. USA, 93, 2159-2164.