A structural snapshot of base-pair opening in DNA

Proceedings of the National Academy of Sciences of the United States of America

Volumn 96, Issue 21, 1999, Pages 11809-11814

  Van Aalten, Daan M F ^a   Erlanson, Daniel A ^b,c   Verdine, Gregory L ^b   Joshua Tor, Leemor ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b HARVARD UNIVERSITY   (United States)

^c Sunesis Pharmaceuticals Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; CYTOSINE; DOUBLE STRANDED DNA; GUANINE; OLIGONUCLEOTIDE;

ARTICLE; BASE PAIRING; CALCIUM BINDING; CRYSTAL STRUCTURE; DNA CROSS LINKING; DNA HELIX; MOLECULAR DYNAMICS; PRIORITY JOURNAL; STRESS; TORSION;

BASE PAIRING; BASE SEQUENCE; CALCIUM; CRYSTALLOGRAPHY, X-RAY; DNA; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES;

EID: 0032739283     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.96.21.11809     Document Type: Article

References (42)

1. Joshua-Tor, L., Frolow, F., Appella, E., Hope, H., Rabinovich, D. & Sussman, J. L. (1992) J. Mol. Biol. 225, 397-431.
2. Morden, K. M., Chu, Y. G., Martin, F. H. & Tinoco, I., Jr. (1983) Biochemistry 22, 5557-5563.
3. Kalnik, M. W., Norman, D. G., Zagorski, M. G., Swann, P. F. & Patel, D. J. (1989) Biochemistry 28, 294-303.
4. Kalnik, M. W., Norman, D. G., Li, B. F., Swann, P. F. & Patel, D. J. (1990) J. Biol. Chem. 265, 636-647.
5. Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. D. (1994) Cell 76, 357-369.
6. Reinisch, K. M., Chen, L., Verdine, G. L. & Lipscomb, W. N. (1995) Cell 82, 143-153.
7. Lau, A. Y., Schärer, O. D., Samson, L., Verdine, G. L. & Ellenberger, T. (1998) Cell 95, 249-258.
8. Vassylyev, D. G., Kashiwagi, T., Mikami, Y., Ariyoshi, M., Iwai, S., Ohtsuka, E. & Morikawa, K. (1995) Cell 83, 773-782.
9. Sawa, R., Mcauley-Hecht, K., Brown, T. & Pearl, L. (1995) Nature (London) 373, 487-493.
10. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E. & Tainer, J. A. (1996) Nature (London) 384, 87-92.
11. Barrett, T. E., Savva, R., Panayotou, G., Barlow, T., Brown, T., Jiricny, J. & Pearl, L. H. (1998) Cell 92, 117-129.
12. Roberts, R. J. & Cheng, X. (1998) Annu. Rev. Biochem. 67, 181-198.
13. Wolfe, S. A., Ferentz, A. E., Grantcharova, V., Churchill, M. E. A. & Verdine, G. L. (1995) Chem. Biol. 2, 213-221.
14. Erlanson, D. A. & Verdine, G. L. (1993) J. Am. Chem. Soc. 115, 12583-12584.
15. Erlanson, D. A., Wolfe, S. A., Chen, L. & Verdine, G. L. (1997) Tetrahedron 33, 12041-12056.
16. Wolfe, S. A. & Verdine, G. L. (1993) J. Am. Chem. Soc. 115, 12585-12586.
17. Lipanov, A., Kopka, M. L., Kaczor-Grzeskowiak, M., Quintana, J. & Dickerson, R. E. (1993) Biochemistry 32, 1373-1389.
18. Otwinowski, Z. & Minor, W. (1997) Methods Enzymol. 276, 307-326.
19. Navaza, J. & Saludjian, P. (1997) Methods Enzymol. 276, 581-594.
20. Heinemann, U. & Alings, C. (1989) J. Mol. Biol. 210, 369-381.
21. Brünger, A. T. (1988) J. Mol. Biol. 203, 803-816.
22. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Gross-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) Acta Crystallogr. D 54, 905-921.
23. Pannu, N. S. & Read, R. J. (1996) Acta Crystallogr. A 52, 659-668.
24. Brünger, A. T. (1992) Nature (London) 355, 472-474.
25. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991) Acta Crystallogr. A 47, 110-119.
26. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992) Biophys. J. 63, 751-759.
27. Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999) Acta Crystallogr. D 55, 191-205.
28. Gunsteren, W. F. v. & Berendsen, H. J. C. (1987) Biomolecular Software (University of Groningen, The Netherlands).
29. Berendsen, H. J. C., Postma, J. P. M., Gunsteren, W. F. v. & Hermans, J. (1981) in Intermolecular Forces, ed. Pullmann, B. (Reidel, Dordrecht).
30. Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. (1977) J. Comp. Phys. 23, 327-341.
31. Berendsen, H. J. C., Postma, J. P. M., DiNola, A. & Haak, J. R. (1984) J. Chem. Phys. 81, 3684-3690.
32. Amadei, A., Linssen, A. B. M. & Berendsen, H. J. C. (1993) Proteins 17, 412-425.
33. Yuan, H., Quintana, J. & Dickerson, R. E. (1992) Biochemistry 31, 8009-8021.
34. Grzeskowiak, K., Goodsell, D. S., Kaczor-Grzeskowiak, M., Cascio, D. & Dickerson, R. E. (1993) Biochemistry 32, 8923-8931.
35. Goodsell, D. S., Grzeskowiak, K. & Dickerson, R. E. (1995) Biochemistry 34, 1022-1029.
36. Lide, D. R. (1958) J. Chem. Phys. 29, 1426-1427.
37. Weiss, S. & Leroi, G. E. (1968) J. Chem. Phys. 48, 962-967.
38. Esnouf, R. M. (1997) J. Mol. Graphics 15, 132-134.
39. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.
40. Bacon, D. J. & Anderson, W. F. (1988) J. Mol. Graphics 6, 219-220.
41. Merritt, E. A. & Murphy, M. E. P. (1994) Acta Crystallogr. D 50, 869-873.
42. Lu, X. J., Hassan, M. A. E. & Hunter, C. A. (1997) J. Mol. Biol. 273, 668-680.