Solution measurement of DNA curvature in papillomavirus E2 binding sites

Nucleic Acids Research

Volumn 31, Issue 17, 2003, Pages 5134-5139

  Zimmerman, Jeff M ^a   Maher, L James ^a  

^a MAYO GRADUATE SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DINUCLEOTIDE; VIRUS PROTEIN;

ARTICLE; BASE PAIRING; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA BINDING MOTIF; DNA PROTEIN COMPLEX; ELECTROPHORESIS; HYPOTHESIS; MEASUREMENT; MOLECULAR RECOGNITION; PAPILLOMA VIRUS; PREDICTION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN INTERACTION; X RAY ANALYSIS;

ALGORITHMS; BINDING SITES; BINDING, COMPETITIVE; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; PAPILLOMAVIRIDAE; SOLUTIONS; VIRAL PROTEINS;

DNA VIRUSES; HUMAN PAPILLOMAVIRUS; PAPILLOMAVIRUS;

EID: 0345604432     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg697     Document Type: Article

References (14)

1. Otwinowski, Z., Schevitz, R.W., Zhang, R.G., Lawson, C.L., Joachimiak, A., Marmorstein, R.Q., Luisi, B.F. and Sigler, P.B. (1988) Crystal structure of trp repressor/operator complex at atomic resolution. Nature, 335, 321-329.
2. Jen-Jacobson, L., Engler, L.E. and Jacobson, L.A. (2000) Structural and thermodynamic strategies for site-specific DNA binding proteins. Struct. Fold Des., 8, 1015-1023.
3. Hegde, R.S. (2002) The papillomavirus E2 proteins: structure, function and biology. Annu. Rev. Biophys Biomol. Struct., 31, 343-360.
4. Bedrosian, C.L. and Bastia, D. (1990) The DNA-binding domain of HPV-16 E2 protein interaction with the viral enhancer: protein-induced DNA bending and role of the nonconserved core sequence in binding site affinity. Virology, 174, 557-575.
5. Hines, C.S., Meghoo, C., Shetty, S., Biburger, M., Brenowitz, M. and Hegde, R.S. (1998) DNA structure and flexibility in the sequence- specific binding of papillomavirus E2 proteins. J. Mol. Biol., 276, 809-818.
6. Kim, S.S., Tam, J.K., Wang, A.F. and Hegde, R.S. (2000) The structural basis of DNA target discrimination by papillomavirus E2 proteins. J. Biol. Chem., 275, 31245-31254.
7. Rozenberg, H., Rabinovich, D., Frolow, F., Hegde, R.S. and Shakked, Z. (1998) Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Proc. Natl Acad. Sci. USA, 95, 15194-15199.
8. Hizver, J., Rozenberg, H., Frolow, F., Rabinovich, D. and Shakked, Z. (2001) DNA bending by an adenine-thymine tract and its role in gene regulation. Proc. Natl Acad. Sci. USA, 98, 8490-8495.
9. Hardwidge, P.R., Zimmerman, J.M. and Maher, L.J., III (2000) Design and calibration of a semi-synthetic DNA phasing assay. Nucleic Acids Res., 28, E102.
10. Liu, Y. and Beveridge, D.L. (2001) A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data. J. Biomol. Struct. Dyn., 18, 505-526.
11. Sayle, R.A. and Milner-White, E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
12. Kerppola, T.K. and Curran, T. (1991) DNA bending by Fos and Jun: the flexible hinge model. Science, 254, 1210-1214.
13. Byun, K.S. and Beveridge, D.L. (2003) Molecular dynamics simulations of papillomavirus E2 DNA sequences: dynamical models of oligonucleotide structures in solution. Biopolymers, in press.
14. Hardwidge, P.R. and Maher, L.J. (2001) Experimental evaluation of the Liu-Beveridge dinucleotide step model of DNA structure. Nucleic Acids Res., 29, 2619-2625.