A synthetic miniprotein that binds specific DNA sequences by contacting both the major and the minor groove

Chemistry and Biology

Volumn 10, Issue 8, 2003, Pages 713-722

  Blanco, Juan B ^a   Vázquez, M Eugenio ^a   Martinez Costas, José ^a   Castedo, Luis ^a   Mascareñas, José L ^a  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

INSERTION SEQUENCES;

EID: 0041412710     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(03)00172-8     Document Type: Article

References (44)

1. Latchman, D.S. (1998). Eukaryotic Transcription Factors (San Diego, CA: Academic Press).
2. White R.J. Gene Transcription, Mechanism and Control. 2001;Blackwell Science, Oxford.
3. Pabo C.O., Sauer R.T. Transcriptional factors. Structural families and principles of DNA recognition Annu. Rev. Biochem. 61:1992;1053-1095.
4. Burley S.K. DNA-binding motifs from eukaryotic transcription factors. Curr. Opin. Struct. Biol. 4:1994;3-11.
5. Alberts B., Bray D., Lewis J., Raff M., Roberts K., Watson J.D. Control of gene expresion. Third Edition Molecular Biology of the Cell. 1994;Garland Publishing, New York. 401-474.pp.
6. Suzuki M., Suckow J., Kisters-Woike B., Aramaki H., Makino K. Multi-helical DNA-binding domains. their structures and modes of DNA-binding Adv. Biophys. 32:1996;31-52.
7. Branden, C., and Tooze, J. (1999). In Introduction to Protein Structure. (New York: Garland Publishing), pp. 129-203.
8. Latchman, D.S. (1998). In Eukaryotic Transcription Factors. (London: Academic Press), pp. 233-270.
9. Luscombe, N.M., Austin, S.E., Berman, H.M., and Thornton, J.M. (2000). An overview of the structures of protein-DNA complexes. Genome Biol. 1, reviews001.1-001.37.
10. Jones N. Transcriptional regulation by dimerization. two sides to an incestuous relationship Cell. 61:1990;9-11.
11. Tjian R., Maniatis T. Transcriptional activation. a complex puzzle with few easy pieces Cell. 77:1994;5-8.
12. Wolberger C. Combinatorial transcription factors. Curr. Opin. Genet. Dev. 8:1998;552-559.
13. Khorasanizadeh S., Rastinejad F. Nuclear-receptor interactions on DNA-response elements. Trends Biochem. Sci. 26:2001;384-390.
14. Pedone P.V., Ghirlando R., Clore G.M., Gronnenborn A.M., Felsenfeld G., Omichinski J.G. The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding. Proc. Natl. Acad. Sci. USA. 93:1996;2822-2826.
15. Feng J.A., Johnson R.C., Dickerson R.E. Hin recombinase bound to DNA. the origin of specificity in major and minor groove interactions Science. 263:1994;348-355.
16. Ghosh I., Yao S., Chmielewski J. DNA-binding peptides. Barton D., Nakanishi K. Comprehensive Natural Products Chemistry. 1999;Elsevier, New York. 477-490.pp.
17. Hu J.C., Sauer R.T. The basic-region leucine-zipper family of DNA binding proteins. Nucleic Acids Mol. Biol. 6:1992;82-101.
18. Hurst H.C. Transcription factors 1. bZIP proteins Protein Profile. 2:1995;101-168.
19. Weiss M.A. Thermal unfolding studies of a leucine zipper domain and its specific DNA complex. implications for scissor's grip recognition Biochemistry. 29:1990;8020-8024.
20. O'Neil K.T., Hoess R.H., Degrado W.F. Design of DNA-binding peptides based on the leucine zipper motif. Science. 249:1990;774-778.
21. Landschulz W.H., Johnson P.F., McKnight S.L. The DNA binding domain of the rat liver nuclear protein C/EBP is bipartite. Science. 243:1989;1681-1688.
22. Turner R., Tjian R. Leucine repeats and an adjacent DNA binding domain mediate the formation of functional cFos-cJun heterodimers. Science. 243:1989;1689-1694.
23. Talanian R.V., McKnight C.J., Kim P.S. Sequence-specific DNA binding by a short peptide dimer. Science. 249:1990;769-771.
24. Cuenoud B., Shepartz A. Altered specificity of DNA-binding proteins with transition metal dimerization domains. Science. 259:1993;510-513.
25. Morii T., Shimomura M., Morimoto M., Saito I. Sequence-specific DNA binding by a geometrically constrained peptide dimer. J. Am. Chem. Soc. 115:1993;1150-1151.
26. Morii T., Saimei Y., Okagami M., Makino K., Sugiura Y. Factors governing the sequence-selective DNA binding of geometrically constrained peptide dimers. J. Am. Chem. Soc. 119:1997;3649-3655.
27. Aizawa Y., Sugiura Y., Morii T. Comparison of the sequence-selective DNA binding by peptide dimers with covalent and noncovalent dimerization domains. Biochemistry. 38:1999;1626-1632.
28. Caamaño A.M., Vázquez M.E., Martínez-Costas J., Castedo L., Mascareñas J.L. A light-modulated sequence-specific DNA-binding peptide. Angew. Chem. Int. Ed. Engl. 39:2000;3104-3107.
29. Sato S., Hagihara M., Sugimoto K., Morii T. Chemical approaches untangling sequence-specific DNA binding by proteins. Eur. J. Chem. 8:2002;5067-5071.
30. Zondlo N.J., Schepartz A. Highly specific DNA recognition by a designed miniature protein. J. Am. Chem. Soc. 121:1999;6938-6939.
31. Chin J.W., Schepartz A. Concerted evolution of structure and function in a miniature protein. J. Am. Chem. Soc. 123:2001;2929-2930.
32. Stanojevic D., Verdine G.L. Deconstruction of GCN4/GCRE into a monomeric peptide-DNA complex. Nat. Struct. Biol. 2:1995;450-457.
33. Vázquez M.E., Caamaño A.M., Martínez-Costas J., Castedo L., Mascareñas J.L. Design and synthesis of a peptide that binds specific DNA sequences through simultaneous interaction in the major and in the minor groove. Angew. Chem. Int. Ed. Engl. 40:2001;4723-4725.
34. Ellenberger T.E., Brandl C.J., Struhl K., Harrison S.C. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α-helices. crystal structure of the protein-DNA complex Cell. 71:1992;1223-1237.
35. Coll M., Frederick C.A., Wang A.H.J., Rich A. A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl. Acad. Sci. USA. 84:1987;8385-8389.
36. Vázquez M.E., Caamaño A.M., Castedo L., Mascareñas J.L. An Fmoc solid-phase approach to linear polypyrrole-peptide conjugates. Tetrahedron Lett. 40:1999;3621-3624.
37. He G.-X., Browne K.A., Groppe J.C., Blaskó A., Mei H.-Y., Bruice T.C. Chemistry of phosphodiesters, DNA and models. 3. Microgonotropens and their interactions with DNA. 1. Synthesis of the tripyrrole peptides dien-microgonotropen-a, -b, and -c and characterization of their interactions with dsDNA. J. Am. Chem. Soc. 115:1993;7061-7071.
38. Rentzeperis D., Marky L.A., Dwyer T.J., Geierstanger B.H., Pelton J.G., Wemmer D.A. Interaction of minor groove ligands to an AAATT/AATTT site. correlation of thermodynamic characterization and solution structure Biochemistry. 34:1995;2937-2945.
39. Chen F.-M., Sha F. Circular dichroic and kinetic differentiation of DNA binding modes of distamycin. Biochemistry. 37:1998;11143-11151.
40. Satz A.L., Bruice T.C. Recognition in the minor groove of double-stranded DNA by microgonotropens. Acc. Chem. Res. 35:2002;86-95.
41. Dervan P. Molecular recognition of DNA by small molecules. Bioorg. Med. Chem. 9:2001;2215-2235.
42. Hollenbeck J.J., Oakley M.G. GCN4 binds with high affinity to DNA sequences containing a single consensus half-site. Biochemistry. 39:2000;6380-6389.
43. Mammen M., Choi S.-K., Whitesides G.M. Polyvalent interactions in biological systems. implications for design and use of multivalent ligands and inhibitors Angew. Chem. Int. Ed. Engl. 37:1998;2755-2794.
44. Mammen M., Shakhnovich E.I., Whitesides G.M. Using a convenient, quantitative model for torsional entropy to establish qualitative trends for molecular processes that restrict conformational freedom. J. Org. Chem. 63:1998;3168-3175.