Surprising roles of electrostatic interactions in DNA-ligand complexes

Biopolymers

Volumn 69, Issue 1, 2003, Pages 87-99

  Howerton, Shelley B ^a   Nagpal, Akankasha ^a   Williams, Loren Dean ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Adriamycin; Alkaline metal; Anomalous scattering; Daunomycin; Intercalation; Major groove; Minor groove; Thallium; X ray diffraction

Indexed keywords

CONFORMATIONS; ELECTROSTATICS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; POSITIVE IONS; SUBSTITUTION REACTIONS; THERMOANALYSIS; X RAY DIFFRACTION ANALYSIS; X RAY SCATTERING;

LIGAND COMPLEXES; MOLECULAR INTERACTIONS;

DNA SEQUENCES;

AMMONIA; ANTHRACYCLINE DERIVATIVE; DNA; DOXORUBICIN; LIGAND; POTASSIUM; SODIUM; THALLIUM; WATER;

ARTICLE; BASE MISPAIRING; COMPLEX FORMATION; DNA BINDING; DNA DRUG COMPLEX; ELECTRICITY; GEOMETRY; LIGAND BINDING; RADIATION SCATTERING; STRUCTURE ANALYSIS; X RAY DIFFRACTION;

ANTIBIOTICS, ANTINEOPLASTIC; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DATABASES, NUCLEIC ACID; DNA; DOXORUBICIN; ELECTROSTATICS; KINETICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES;

EID: 0038036707     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/bip.10319     Document Type: Article

References (54)

1. Wang, A. H.; Ughetto, G.; Quigley, G. J.; Rich, A. Biochemistry 1987, 26, 1152-1163.
2. Frederick, C. A.; Williams, L. D.; Ughetto, G.; van der Marel, G. A.; van Boom, J. H.; Rich, A.; Wang, A. H.-J. Biochemistry 1990, 29, 2538-2549.
3. Williams, L. D.; Egli, M.; Ughetto, G.; van der Marel, G. A.; van Boom, J. H.;, Quigley, G. J.; Wang, A. H.-J.; Rich, A.; Frederick, C. A. J Mol Biol 1990, 215, 313-320.
4. Lipscomb, L. A.; Peek, M. E.; Zhou, F. X.; Bertrand, J. A.; VanDerveer, D.; Williams, L. D. Biochemistry 1994, 33, 3649-3659.
5. Chaires, J. B.; Fox, K. R.; Herrara, J. E.; Britt, M.; Waring, M. J. Biochemistry 1987, 26, 8227-8236.
6. Capranico, G.; Kohn, K. W.; Pommier, Y. Nucleic Acids Res 1990, 18, 6611-6619.
7. Chaires, J. B.; Satyanarayana, S.; Suh, D.; Fokt, I.; Przewloka, T.; Priebe, W. Biochemistry 1996, 35, 2047-2053.
8. Qu, X.; Chaires, J. B. J Am Chem Soc 2001, 123, 1-7.
9. Leonard, G. A.; Brown, T.; Hunter, W. N. Eur J Biochem 1992, 204, 69-74.
10. Hu, G. G.; Shui, X.; Leng, F.; Priebe, W.; Chaires, J. B.; Williams, L. D. Biochemistry 1997, 36, 5940-5946.
11. Shui, X.; McFail-Isom, L.; Hu, G. G.; Williams, L. D. Biochemistry 1998, 37, 8341-8355.
12. McFail-Isom, L.; Sines, C.; Williams, L. D. Curr Opin Struct Biol 1999, 9, 298-304.
13. Howerton, S. B.; Sines, C. C.; VanDerveer, D.; Williams, L. D. Biochemistry 2001, 40, 10023-10031.
14. Brown, I. D. Acta Crystallogr 1988, B44, 545-553.
15. Wulfsberg, G. Principles of Descriptive Inorganic Chemistry; University Science Books: Sausalito, CA, 1991.
16. Pedersen, P. A.; Nielsen, J. M.; Rasmussen, J. H.; Jorgensen, P. L. Biochemistry 1998, 37, 17818-17827.
17. Villeret, V.; Huang, S.; Fromm, H. J.; Lipscomb, W. N. Proc Natl Acad Sci USA 1995, 92, 8916-8920.
18. Loria, J. P.; Nowak, T. Biochemistry 1998, 37, 6967-6974.
19. Basu, S.; Szewczak, A. A.; Cocco, M.; Strobel, S. A. J Am Chem Soc 2000, 122, 3240-3241.
20. Basu, S.; Rambo, R. P.; Strauss-Soukup, J.; Cate, J. H.; Ferre-D'Amare, A. R.; Strobel, S. A.; Doudna, J. A. Nat Struct Biol 1998, 5, 986-992.
21. Badger, J.; Kapulsky, A.; Gursky, O.; Bhyravbhatla, B.; Caspar, D. L. Biophys J 1994, 66, 286-892.
22. Badger, J.; Li, Y.; Caspar, D. L. Proc Natl Acad Sci USA 1994, 91, 1224-1228.
23. Gill, H. S.; Eisenberg, D. Biochemistry 2001, 40, 1903-1912.
24. Clowney, L.; Jain, S. C.; Srinivasan, A. R.; Westbrook, J.; Olson, W. K.; Berman, H. M. J Am Chem Soc 1996, 118, 509-518.
25. Gelbin, A.; Schneider, B.; Clowney, L.; Hsieh, S.-H.; Olson, W. K.; Berman, H. M. J Am Chem Soc 1996, 118, 519-529.
26. Parkinson, G.; Vojtechovsky, J.; Clowney, L.; Brunger, A. T.; Berman, H. M. Acta Crystallogr, Sect D: Biol Crystallogr 52, 57-64.
27. Neidle, S.; Taylor, G. Biochim Biophys Acta 1977, 479, 450-459.
28. Kleywegt, G. J.; Jones, T. A. Acta Crystallogr, Sect D: Biol Crystallogr 1999, 55, 941-944.
29. Dauter, Z.; Adamiak, D. A. Acta Crystallogr D, Biol Crystallogr 2001, 57, 990-995.
30. Martin, A. C. R. www.rubic.rdg.ac.uk/~andrew/bioinf.org/software/profit/index.html.
31. Schuerman, G. S.; Van Meervelt, L. J Am Chem Soc 122, 232-240.
32. Williams, L. D.; Frederick, C. A.; Ughetto, G.; Rich, A. Nucleic Acids Res 1990, 18, 5533-5541.
33. Wang, A. H.-J.; Gao, Y.-G.; Liaw, Y.-C.; Li, Y.-K. Biochemistry 1991, 30, 3812-3815.
34. Gao, Y. G.; Liaw, Y. C.; Li, Y. K.; van der Marel, G. A.; van Boom, J. H.; Wang, A. H. Proc Natl Acad Sci USA 88, 4845-4849.
35. Cirilli, M.; Bachechi, F.; Ughetto, G.; Colonna, F. P.; Capobianco, M. L. J Mol Biol 1993, 230, 878-889.
36. Berger, I.; Su, L.; Spitzner, J. R.; Kang, C.; Burke, T. G.; Rich, A. Nucleic Acids Res 1995, 23, 4488-4494.
37. Gao, Y. G.; Robinson, H.; Wijsman, E. R.; vander-Marel, G. A.; vanBoom, J. H.; Wang, A. H. J. J Am Chem Soc 1997, 119, 1496-1497.
38. Berman, H. M.; Zardecki, C.; Westbrook, J. Acta Crystallogr, Sect D: Biol Crystallogr 1998, 54, 1095-1104.
39. Shui, X.; Sines, C.; McFail-Isom, L.; VanDerveer, D.; Williams, L. D. Biochemistry 1998, 37, 16877-16887.
40. Hud, N. V.; Polak, M. Curr Opin Struct Biol 2001, 11, 293-301.
41. Minasov, G.; Tereshko, V.; Egli, M. J Mol Biol 1999, 291, 83-99.
42. Sines, C. C.; McFail-Isom, L.; Howerton, S. B.; VanDerveer, D.; Williams, L. D. J Am Chem Soc 2000, 122, 11048-11056.
43. Pjura, P. E.; Grzeskowiak, K.; Dickerson, R. E. J Mol Biol 1987, 197, 257-271.
44. Teng, M.; Usman, N.; Frederick, C. A.; Wang, A. H.-J. Nucleic Acids Res 1988, 16, 2671-2690.
45. Gao, Q.; Williams, L. D.; Egli, M.; Rabinovich, D.; Chen, S.-H.; Quigley, G. J.; Rich, A. Proc Natl Acad Sci USA 88, 2422-2426.
46. Williams, L. D.; Gao, Q. Biochemistry 1992, 31, 4315-4324.
47. Peek, M. E.; Lipscomb, L. A.; Bertrand, J. A.; Gao, Q.; Roques, B. P.; Garbay-Jaureguiberry, C.; Williams, L. D. Biochemistry 1994, 33, 3794-3800.
48. Peek, M. E.; Lipscomb, L. A.; Haseltine, J. Gao, Q.; Roques, B. P.; Garbay-Jaureguiberry, C.; Williams, L. D. J Bioorg Med Chem 1995, 3, 693-699.
49. Yang, X.; Gerczei, T.; Glover, L. T.; Correll, C. C. Nat Struct Biol 2001, 8, 968-973.
50. Batey, R. T.; Rambo, R. P.; Lucast, L.; Rha, B.; Doudna, J. A. Science 2000, 287, 1232-1239.
51. Batey, R. T.; Sagar, M. B.; Doudna, J. A. J Mol Biol 2001, 307, 229-246.
52. Tereshko, V.; Wilds, C. J.; Minasov, G.; Prakash, T. P.; Maier, M. A.; Howard, A.; Wawrzak, Z.; Manoharan, M.; Egli, M. Nucleic Acids Res 2001, 29, 1208-1215.
53. Coll, M.; Solans, X.; Font-Altaba, M.; Subirana, J. A. J Biomol Struct Dynam 1987, 4, 797-811.
54. Malinina, L.; Urpi, L.; Salas, X.; Huynh-Dinh, T.; Subirana, J. A. J Mol Biol 1994, 243, 484-493.