Sequence-dependent dynamics in duplex DNA

Biophysical Journal

Volumn 78, Issue 5, 2000, Pages 2560-2571

  Okonogi, T M ^a   Alley, S C ^a,b   Reese, A W ^a   Hopkins, P B ^a   Robinson, B H ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA;

ARTICLE; CHROMATIN; ELECTRON SPIN RESONANCE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DNA BINDING;

EID: 0034106191     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76800-7     Document Type: Article

References (37)

1. Allison, S. A., J. H. Shibata, J. Wilcoxon, and J. M. Schurr. 1982. NMR relaxation in DNA. I. The contribution of torsional deformation modes of the elastic filament. Biopolymers. 21:729-762.
2. Aloyo, M. C., D. Campbell, N. J. Combates, J. Gonzales, Y. Kwok, R. D. Sheardy, and S. A. Winkle. 1993. Restriction enzymes have altered cleavage rates at sites near certain sequences. Biophys. J. 64:A280.
3. Chedin, F., E. Dervyn, R. Dervyn, S. D. Ehrlich, and P. Noirot. 1994. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol. Microbiol. 12:561-569.
4. Dlakic, M., and R. E. Harrington. 1995. Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays. J. Biol. Chem. 270:29945-29952.
5. Drew, H. R., and A. A. Travers. 1985. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186:773-790.
6. Fujimoto, B. S., and J. M. Schurr. 1990. Dependence of the torsional rigidity of DNA on base composition. Nature. 344:175-177.
7. Grove, A., A. Galeone, L. Mayol, and E. P. Geiduschek. 1996a. Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J. Mol. Biol. 260:120-125.
8. Grove, A., A. Galeone, L. Mayol, and E. P. Geiduschek. 1996b. On the connection between inherent DNA flexure and preferred binding of hydroxymethyluracil-containing DNA by the type II DNA-binding protein TF1. J. Mol. Biol. 260:196-206.
9. Hagerman, P. J. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-286.
10. Hagerman, P. J. 1990. Sequence directed curvature of DNA. In Annual Review of Biochemistry. D. M. Engelman, C. R. Cantor, and T. D. Pollard, editors. Annual Reviews, Palo Alto, CA. 755-781.
11. Harrington, R. E., and I. Winicov. 1994. New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility. Prog. Nucleic Acid Res. Mol. Biol. 47:195-270.
12. Hogan, M. E., and R. H. Austin. 1987. Importance of DNA stiffness in protein-DNA binding specificity. Nature. 329:263-266.
13. Hustedt, E. J., A. Spaltenstein, J. J. Kirchner, P. B. Hopkins, and B. H. Robinson. 1993. Motions of short DNA duplexes: an analysis of DNA dynamics using an EPR-active probe. Biochemistry. 32:1774-1787.
14. Kahn, J. D., E. Yun, and D. M. Crothers. 1994. Detection of localized DNA flexibility. Nature. 368:163-166.
15. Kim, U. S., B. S. Fujimoto, C. E. Furlong, J. A. Sundstrom, R. Humbert, D. C. Teller, and J. M. Schurr. 1993. Dynamics and structures of DNA: long-range effects of a 16 base-pair (CG)8 sequence on secondary structure. Biopolymers. 33:1725-1745.
16. Lundin, M., J. O. Niehlin, and H. Ronne. 1994. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1. Mol. Cell. Biol. 14:1979-1985.
17. Mailer, C., D. A. Haas, E. J. Hustedt, J. G. Gladden, and B. H. Robinson. 1991. Low-power electron paramagnetic resonance spin-echo spectroscopy. J. Magn. Res. 91:475-496.
18. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
19. Miller, T. R., S. C. Alley, A. W. Reese, M. S. Solomon, W. V. McCallister, C. Mailer, B. H. Robinson, and P. B. Hopkins. 1995. A probe for sequence-dependent nucleic acid dynamics. J. Am. Chem. Soc. 117:9377-9378.
20. Naimushin, A., B. S. Fujimoto, and J. M. Schurr. 2000. Dynamic bending rigidity of a 200 bp DNA in 4 mM ionic strength: a transient polarization grating study. Biophys. J. 78:1498-1518.
21. Nardulli, A. M., L. E. Romine, C. Carpo, G. L. Greene, and B. Rainish. 1996. Estrogen receptor affinity and location of consensus and imperfect estrogen response elements influence transcription activation of simplified promoters. Mol. Endocrinol. 10:694-704.
22. Okonogi, T. M., A. W. Reese, S. C. Alley, P. B. Hopkins, and B. H. Robinson. 1997. Sequence dependent dynamics of duplex DNA. In 20th International EPR Conference, 39th Rocky Mountain Conference, Denver, CO (poster).
23. Okonogi, T. M., A. W. Reese, S. C. Alley, P. B. Hopkins, and B. H. Robinson. 1998. How far does bending flexibility transmit in duplex DNA? Biophys. J. 72:A287 (poster).
24. Okonogi, T. M., A. W. Reese, S. C. Alley, P. B. Hopkins, and B. H. Robinson. 1999. Flexibility of duplex DNA on the sub-microsecond timescale. Biophys. J. 77:3256-3276.
25. Patikoglou, G., and S. K. Burley. 1997. Eukaryotic transcription factor-DNA complexes. In Annual Review of Biophysics and Biomolecular Structure. W. L. H. R. M. Stroud, W. K. Olson, M. P. Sheetz, editors. Annual Reviews, Palo Alto, CA. 289-325.
26. Ramsauer, V., L. Aguilar, M. Ballester, R. D. Sheardy, and S. A. Winkle. 1997. The conformation of (CG) DNA segments regulates RNA polymerase activity. Biophys. J. 72:A98.
27. Reese, A. W. 1996. Analysis of CW-EPR spectra and the internal dynamics of DNA. Ph.D. thesis. University of Washington, Seattle, WA.
28. Richmond, T. J., J. T. Finch, B. Rushton, D. Rhodes, and A. Klug. 1984. Structure of the nucleosome core particle at 7 A resolution. Nature. 311:532-537.
29. Satchwell, S. C., H. R. Drew, and A. A. Travers. 1986. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:659-675.
30. Schellman, J. A., and S. C. Harvey. 1995. Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys. Chem. 55:95-114.
31. Schurr, J. M., J. J. Delrow, B: S. Fujimoto, and A. S. Benight. 1997a. The question of long-range allosteric transitions in DNA. Biopolymers. 44:283-308.
32. Schurr, J. M., B. S. Fujimoto, and B. H. Robinson. 1997b. Diffusional spinning as a probe of DNA fragment's conformation (comment). J. Chem. Phys. 106:815-816.
33. Schurr, J. M., U. S. Kim, L. Song, and B. S. Fujimoto. 1991. Dynamics and structures of DNA. Biochem. Soc. Trans. 19:497.
34. Song, L., and J. M. Schurr. 1990. Dynamic bending rigidity of DNA. Biopolymers. 30:229-237.
35. Thompson, B. J., M. N. Camien, and R. C. Warner. 1976. Kinetics of branch migration in double-stranded DNA. Proc. Natl. Acad. Sci. USA. 73:2299-2303.
36. Wolffe, A. P. 1994. Architectural transcription factors (comment). Science. 264:1100-1101.
37. Wu, P., B. S. Fujimoto, and J. M. Schurr. 1987. Time-resolved fluorescence polarization anisotropy of short restriction fragments: the friction factor for rotation of DNA about its symmetry axis. Biopolymers. 26:1463-1488.