Single-chain 434 repressors with altered DNA-binding specificities: Isolation of mutant single-chain repressors by phenotypic screening of combinatorial mutant libraries

Genetica

Volumn 106, Issue 1-2, 1999, Pages 85-92

  Simoncsits, A ^a   Tjornhammar M L ^a   Wang, S ^a   Pongor, S ^a  

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

Author keywords

Combinatorial library; Helix turn helix proteins; Protein DNA interaction; Selection; Single chain proteins

Indexed keywords

COMBINATORIAL LIBRARY; MUTANT PROTEIN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROTEIN DNA BINDING; PROTEIN ISOLATION; SINGLE CHAIN 434 REPRESSOR;

EID: 0343852153     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1003728911906     Document Type: Article

References (28)

1. Greisman H.A. and Pabo C.O.: A general strategy for selecting high-affinity zinc finger proteins for diverse DNA sites, Science 275 (1997): 657-661.
2. Kim J.-S. and Pabo C.O.: Getting a handhold on DNA: Design of poly-zinc finger proteins with femtomolar dissociation constants, Proc. Natl. Acad. Sci. USA 95 (1998): 2812-2817.
3. Liu Q., Segal D.J., Ghiara J.B. and Barbas C.F. III: Design of polydactyl zinc-finger proteins for unique addressing within complex genomes, Proc. Natl. Acad. Sci. USA 94 (1997): 5525-5530.
4. Choo Y., Castellanos A., Garcia-Hernandez B., Sanchez-Garcia I. and Klug A.: Promoter-specific activation of gene expression directed by bacteriophage-selected zinc fingers, J. Mol. Biol. 273 (1997): 525-532.
5. Kim J.-S. and Pabo C.O.: Transcriptional repression by zinc finger peptides. Exploring the potential for applications in gene therapy, J. Biol Chem. 272 (1997): 29795-29800.
6. Berg J.M.: Letting your fingers do the walking, Nature Biotech. 15 (1997): 323.
7. Choo Y. and Klug A.: Designing DNA-binding proteins on the surface of filamentous phage, Curr. Opin. Biotechnol. 6 (1995): 431-436.
8. Rebar E.J., Greisman, H.A. and Pabo C.O.: Phage display methods for selecting zinc finger proteins with novel DNA-binding specificities, Methods Enzymol. 267 (1996): 129-149.
9. Berg J.M. and Shi Y.: Galvanization of biology: A growing appreciation for theroles of zinc, Science 271 (1996): 1081-1085.
10. Rhodes D., Schwabe J.W.R., Chapman L. and Fairall L.: Towards understanding of protein-DNA recognition, Phil. Trans. R. Soc. Lond. B. 351 (1996): 501-509.
11. Harrison S.C. and Aggarwal A.K.: DNA recognition by proteins with the helix-turn-helix motif, Annu. Rev. Biochem. 59 (1990): 933-969.
12. Simoncsits A., Chen J., Percipalle P., Wang S., Törö I. and Pongor S.: Single-chain repressors containing engineered DNA-binding domains of the phage 434 repressor recognize symmetric or asymmetric DNA operators, J. Mol. Biol. 267 (1997): 118-131.
13. Percipalle P., Simoncsits A., Zakhariev S., Guarnaccia C., Sanchez, R. and Pongor, S.: Rationally designed helix-turn-helix proteins and their conformational changes upon DNA binding, EMBO J. 14 (1995): 3200-3205.
14. Chen J., Pongor S. and Simoncsits A.: 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 Res. 25 (1997): 2047-2054.
15. Wharton R.P. and Ptashne M.: Changing the binding specificity of a repressor by redesigning an α-helix, Nature 316 (1985): 601-605.
16. Wharton R. P. and Ptashne M.: A new specificity mutant of 434 repressor that defines an amino acid-base pair contact, Nature 326 (1987): 888-891.
17. Huang L., Sera T. and Schultz P.G.: A permutational approach toward protein-DNA recognition, Proc. Natl. Acad. Sci. USA, 91 (1994): 3969-3973.
18. Aggarwal A.K., Rodger D.W., Drottar M., Ptashne M. and Harrison S.C.: Recognition of DNA operator by the repressor of phage 434: A view at high resolution, Science 242 (1988): 899-907.
19. Choo Y. and Klug A.: Toward a code for interaction of zinc fingers with DNA: Selection of randomized fingers displayed on phage, Proc. Natl. Acad. Sci. USA 91 (1994): 11163-11167.
20. Choo Y. and Klug A.: Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions, Proc. Natl. Acad. Sci. USA 91 (1994): 11168-11172.
21. Seeman N.C., Rosenberg M.J. and Rich A.: Sequence-specific recognition of double helical nucleic acids by proteins, Proc. Natl. Acad. Sci. USA 73 (1976): 804-808.
22. Pabo C.O. and Sauer R.T.: Transcription factors: Structural families and principles of DNA recognition, Annu. Rev. Biochem. 61 (1992): 1053-1095.
23. Suzuki M.: A framework for the DNA-protein recognition code of the probe helix in transcription factors: The chemical and stereochemical rules, Structure 2 (1994): 317-326.
24. Mandel-Gutfreund Y., Schueler O. and Margalit H.: Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles, J. Mol. Biol. 253 (1995): 370-382.
25. Shimon L.J. and Harrison S.C.: The phage 434 OR2/R1-69 complex at 2.5 A resolution, J. Mol. Biol. 232 (1993): 826-838.
26. Rodgers D.W. and Harrison S.C.: The complex between phage 434 repressor DNA-binding domain and operator site OR3: Structural differences between consensus and non-consensus half-sites, Structure 1 (1993): 227-240.
27. Miller J.H.: Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1972.
28. Gill S.C. and von Hippel P.H.: Calculation of protein extinction coefficients from amino acid sequence data, Anal. Biochem. 182 (1989): 319-326.