DNA bending: The prevalence of kinkiness and the virtues of normality

Nucleic Acids Research

Volumn 26, Issue 8, 1998, Pages 1906-1926

  Dickerson, Richard E ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA;

AMINO ACID SEQUENCE; ARTICLE; DNA STRUCTURE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

BACTERIAL PROTEINS; BASE COMPOSITION; BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; DNA; DNA RESTRICTION ENZYMES; DNA-BINDING PROTEINS; HOMEODOMAIN PROTEINS; HUMANS; INTEGRATION HOST FACTORS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; REPRESSOR PROTEINS; RNA CAP-BINDING PROTEINS; RNA-BINDING PROTEINS; SOFTWARE; TATA BOX; TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTORS; VIRAL PROTEINS;

EID: 0032522139     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/26.8.1906     Document Type: Article

References (52)

1. Schultz, S. C. Shields G. C. and Steitz T. A. (1991) Science, 253, 1001-1007.
2. Parkinson, G., Gunasekera, A., Vojtechovsky, J., Zhang, X., Kunkel, T. A., Berman H. and Ebrighl R. H. (1996) Nat. Struct. Biol., 3, 837-841.
3. Lewis, M., Chang, G., Horton, N. C., Kercherl, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G. and Lu, P. (1996) Science, 271, 1247-1254.
4. Schumacher, M. A., Choi, K. Y. Zalkin H. and Brennan R. G. (1994) Science. 266, 763-770.
5. Yang, W. and Steitz, T. A. (1995) Cell, 82, 193-207.
6. Rice, P. A., Yang, S.-W., Mizuuchi, K. and Nash, H. A. (1996) Cell, 87, 1295-1306.
7. Kim, Y., Geiger, J. H., Hahn, S. and Sigler, P. B. (1993) Nature, 365, 512-520.
8. Kim J. L., Nikolov, D. B. and Burley, S. K. (1993) Nature, 365, 520-527.
9. Nikolov, D. B., Chen, H., Malay, E. D., Hoffman, A., Roeder R. G. and Burley S. K. (1996) Proc. Natl. Acad. Sci. USA, 93, 4862-4867.
10. Juo, Z. S., Chiu, T. K., Leiberman, P. M., Baikalov, I., Berk, A. J. and Dickerson, R. E. (1996) J. Mol. Biol., 261, 239-254.
11. Beamer, L. J. and Pabo, C. O. (1992) J. Mol. Biol., 227, 177-196.
12. Lim, W. A., Hodel, A., Sauer, R. T. and Richards, F. M. (1994) Proc. Natl. Acad. Sci. USA, 91, 423-427.
13. Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne M. and Harrison S. C. (1988) Science, 242, 899-907.
14. Shimon, L. J. W. and Harrison, S. C. (1993) J. Mol. Biol., 232, 826-838.
15. Rodgers, D. W. and Harrison, S. C. (1993) Structure, 1, 227-240.
16. Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos K. and Wilson K. S. (1993) EMBO J., 12, 1781-1795.
17. Kostrewa, D. and Winkler, F. K. (1995) Biochemistry, 34, 683-696.
18. Dickerson, R. E. (1998) In Neidle, S. (ed.), Oxford Handbook of Nucleic Acid Structure. Oxford University Press, Chapter 7.
19. Dickerson, R. E. (1998) In Sarma, R. H. and Sarma, M. H. (eds). Structure, Motion, Interaction and Expression of Biological Macromolecules. Proceedings of Tenth Conversation in Biomolecular Stereodynamics, Academic Press, Schenectady, NY, USA.
20. Lavery, R. and Sklenar, H. (1988) J. Biomol. Struct. Dynam., 6, 63-91.
21. Babcock, M. S., Pednault, E. P. D. and Olson, W. K. (1993) J. Biomol. Struct. Dynam., 11, 597-628.
22. Dickerson, R. E. and Drew, H. R. (1981) J. Mol. Biol., 149, 761-786.
23. Privé, G. G., Yanagi, K. and Dickerson, R. E. (1991) J. Mol. Biol., 217, 177-199.
24. Yanagi, K., Privé, G. G. and Dickerson, R. E. (1991) J. Mol. Biol., 217, 201-214.
25. Calladine, C. R. and Drew, H. R. (1992, 1997) Understanding DNA: The Molecule and How it Works. Academic Press, San Diego, etc., pp. 49-53.
26. Travers, A. (1993) DNA-Protein Interactions. Chapman and Hall, London, pp. 8-12.
27. Dickerson, R. E., Goodsell, D. S. and Kopka, M. L. (1996) J. Mol. Biol., 256, 108-125.
28. Zhurkin, V. B., Lysov, Y. P. and Ivanov, V. I. (1979) Nucleic Acids Res., 6, 1081-1096.
29. Zhurkin, V. B., Lysov, Y. P., Floremiev, V. L. and Ivanov, V. I. (1982) Nucleic Acids Res., 10, 1811-1830.
30. Zhurkin, V. B. (1983) FEBS Lett., 158, 293-297.
31. Ulyanov, N. B. and Zhurkin, V. B. (1984) J. Biomol. Struct. Dyn., 2, 361-385.
32. Zhurkin, V. B. (1985) J. Biomol. Struct. Dyn., 2, 785-804.
33. Sarai, A., Mazur, J., Nussinov, R. and Jernigan, R. L. (1989) Biochemistry, 28, 7842-7849.
34. Calladine, C. R. and Drew, H. R. (1986) J. Mol. Biol., 192, 907-918.
35. Calladine, C. R., Drew, H. R. and McCall, M. J. (1988) J. Mol. Biol., 201, 127-137.
36. Li, T., Stark, M. R., Johnson, A. D. and Wolberger C. (1995) Science, 270, 262-269.
37. Hirsch, J. A. and Aggarwal, A. K. (1995) EMBO J., 14, 6280-6291.
38. Wolberger, C., Vershon, A. K., Liu, B., Johnson, A. D. and Pabo C. O. (1991) Cell, 67, 517-528.
39. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery, R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C. -S., Wang, A. H. -J. and Zhurkin, V. B. (1989) EMBO J., 8, 1-4.
40. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery, R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C. -S., Wang, A. H. -J. and Zhurkin, V. B. (1989) J. Biomol. Struct. Dynam. 6, 627-634.
41. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery, R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C. -S., Wang, A. H. -J. and Zhurkin, V. B. (1989) Nucleic Acids Res. 17, 1797-1803.
42. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Lavery, R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C. -S., Wang, A. H. -J. and Zhurkin, V. B. (1989) J. Mol. Biol. 206, 787-791.
43. Guzikevich-Guerstein, G. and Shakked, Z. (1996) Nature Struct. Biol., 3, 32-37.
44. Young, M. A., Ravishanker, G., Beveridge, D. L. and Herman, H. M. (1995) Biophys. J., 68, 2454-2468.
45. Zhurkin, V. B., Gorin, A. A., Charakhchyan, A. A. and Ulyanov, N. B. (1990) In Beveridge, D. L. and Lavery, R. (eds), Theoretical Biochemistry and Molecular Biophysics. Adenine Press, Schenectady NY, pp. 411-432.
46. Maroun, R. C. and Olson, W. I. (1988) Biopolymers, 27, 585-603.
47. El Hassan, M. A. and Calladine, C. R. (1997) Phil. Trans. Roy. Sol. Lond., A355, 43-100.
48. Dickerson, R. E., Goodsell, D. S. and Neidle, S. A. (1994) Proc. Natl. Acad. Sci. USA, 91, 3579-3583.
49. Goodsell, D. S. and Dickerson, R. E. (1994) Nucleic Acids Res., 22, 5497-5503.
50. Goodsell, D. S., Kaczor-Grzeskowiak, M. and Dickerson, R. E. (1994) J. Mol. Biol., 239, 79-96.
51. Otwinowski, Z., Schevitz, R. W., Zhang, R. -G., Lawson, C. L., Joachimiak, A. J., Marmorstein, R., Luisi, B. F. and Sigler, P. B. (1988) Nature, 335, 321-329.
52. Mondragon, A. and Harrison, S. C. (1991) J. Mol. Biol., 219, 321-334.