Molecular dynamics simulations in aqueous solution of triple helices containing d(G·C·C) trios

Journal of the American Chemical Society

Volumn 120, Issue 44, 1998, Pages 11226-11233

  Soliva, Robert ^a   Laughton, Charles A ^b   Luque, F Javier ^a   Orozco, Modesto ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA;

AQUEOUS SOLUTION; ARTICLE; DNA BINDING; DNA STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; TRIPLE HELIX;

EID: 0032508869     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja981121q     Document Type: Article

References (58)

1. Cooney, M.; Czernuszewicz, G.; Postel, E. H.; Flint, S. J.; Hogan, M. E. Science 1988, 241, 456.
2. Hélène, C.; Toulme, J. J. Biochem. Biophys. Acta 1990, 1049, 99.
3. Strobel, S.A.; Dervan, P. Methods Enzymol. 1992, 216, 309.
4. Grigoriev, M.; Praseuth, D.; Guieysee, A. L.; Robin, P.; Thuong, N. T.; Hélène, C.; Harel-Bellan, A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 3501.
5. Sun, J. S.; Garestier, T.; Hélène, C. Curr. Opin. Struct. Biol. 1996, 6, 327.
6. Arnott, S.; Bond, P. J.; Selsing, E.; Smith, P. J. C. Nucleic Acids Res. 1976, 11, 4141.
7. Raghunathan, G.; Miles, H. T.; Sasisekharan, V. Biochemistry 1993, 32, 455.
8. Betts, L.; Josey, J. A.; Veal, J. M.; Jordan, S. R. Science 1995, 270, 1838.
9. Shields, G.; Laughton, C. A.; Orozco, M. J. Am. Chem. Soc. 1997, 119, 7463-7469.
10. Macaya, R. F.; Schultze, P.; Feigon, J. J. Am. Chem. Soc 1992, 114, 781.
11. Howard, F. B.; Miles, H. T.; Liu, K.; Frazier, J.; Raghunathan, G.; Sasisekharan, V. Biochemistry 1993, 31, 10671.
12. Radhakrishnan, I.; Patel, D. J. Biochemistry 1994, 33, 1405.
13. Radhakrishnan, I.; Patel, D. J. Structure 1994, 2, 395.
14. Bornet, O.; Lancelot, G. J. Biomol. Struct. Dyn. 1995, 12, 803.
15. Wang, E.; Koshlap, K. M.; Gillespie, P.; Dervan, P. B.; Feigon, J. J. Mol. Biol. 1996, 257, 1052.
16. Koshlap, K. M.; Schultze, P.; Brunar, H.; Dervan, P. B.; Feigon. J. Biochemistry 1997, 36, 2659.
17. Lee, J. S.; Johnson, D. A.; Moogan, A. R. Nucleic Acids Res. 1979, 6, 3073.
18. Völker, J.; Klump, H. H. Biochemistry 1994, 33, 13502.
19. Wittung, P.; Nielsen, P.; Nordén, B. Biochemistry 1997, 36, 7973.
20. Rajagopal, P.; Feigon, J. Biochemistry 1989, 28, 7859.
21. Rajagopal, P.; Feigon, J. Nature 1989, 339, 637.
22. Plum, G. E.; Breslauer, K. J. J. Mol. Biol. 1995, 248, 679.
23. Colominas, C.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1996, 188, 6811.
24. (a) Sponer, J.; Leszczynski, J.; Vetter, V.; Hobza, P. J. Biomol. Struct. Dyn. 1998, 13, 695.
25. (b) Spackova, N.; Berger, I.; Egli, M.; Sponer, J. J. Am. Chem. Soc. 1998, 120, 6147.
26. Laaksonen, A.; Nilsson, L. G.; Johnsson, B.; Teleman, O. Biochemistry 1989, 129, 175.
27. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K.; Fergurson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. J. Am. Chem. Soc. 1995, 117, 5179.
28. Van Vlijmen, H.; Rmae, G. L.; Pettitt, M. Biopolymers 1990, 30, 517.
29. Mohan, V.; Smith, P. E.; Pettit, M. J. Am. Chem. Soc. 1993, 115, 9297.
30. Mohan, V.; Smith, P. E.; Pettit, M. J. Phys. Chem. 1993, 97, 12984.
31. Weerasinghe, S.; Smith, P. E.; Mohan, V.; Cheng, Y.-K.; Pettit, M. J. Am. Chem. Soc. 1995, 117, 2147.
32. Weerasinghe, S.; Smith, P. E.; Pettit, M. Biochemistry 1995, 34, 16269.
33. Shields, C.; Laughton, C. A.; Orozco, M. J. Am. Chem. Soc. 1998, In Press.
34. York, D. M.; Yang, W.; Lee, H.; Darden, T.; Pedersen, L. G. J. Am. Chem. Soc. 1995, 117, 5001.
35. Cheetham, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4193.
36. Cheetham, T. E.; Kollman, P. A. J. Mol. Biol. 1996, 259, 434.
37. Yang, L.; Pettit, M. J. Phys. Chem. 1996, 100, 2564.
38. Cheatham, T. E.; Kollman, P. A. J. Am. Chem. Soc. 1997, 119, 4805.
39. Cieplak, P.; Cheatham, T. E.; Kollman, P. A. J. Am. Chem. Soc. 1997, 119, 6722.
40. Spector, T. I.; Cheatham, T. E.; Kollman, P. A. J. Am. Chem. Soc. 1997, 119, 7095.
41. Darden, T. E.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.
42. Essmann, V.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
43. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
44. Jorgensen, W. L.; Chandresekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
45. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269.
46. Gilson, M. K.; Honig, P. H. Nature 1987, 330, 84.
47. Gilson, M. K.; Honig, P. H. Proteins 1988, 4, 7.
48. Honig, B.; Sharp, K.; Yang, A. J. Phys. Chem. 1993, 97, 1101.
49. Delphi Computer Program; BIOSYM: San Diego, CA, 1994.
50. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 100, 1657.
51. Roberts, R. W.; Crothers, D. M. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 4320.
52. Lyamichev, V. I.; Frank-Kamenetskii, M. D.; Soyfer, V. N. Nature 1990, 344, 568.
53. Mirkin, S. M.; Frank-Camenetskii, M. D. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 541.
54. Dreyfus, M.; Beusande, O.; Dodin, G.; Dubois, J. E. J. Am. Chem. Soc. 1976, 93, 6338.
55. Another nonexplored possibility of neutral d(G·C·C) is the formation of a wobble Hoogsteen-like pairing between G and C. This interaction can be stabilized by a single H-bond, and accordingly it cannot be expected to contribute significantly to the stability of the triplex. Whether or not this type of interaction might exist at neutral pH will be investigated in future works.
56. Umemoto, U.; Sarma, M. H.; Gupta, G.; Luo, J.; Sarma, R. H. J. Am. Chem. Soc. 1990, 112, 4539.
57. (a) Guieysse, A. L.; Praseuth, D.; Hélène, C. J. Mol. Biol. 1997, 267, 289.
58. (b) Jiménez-García, E.; Vaquero, A.; Espinás, M. L.; Soliva, R.; Orozco, M.; Bernués, I.; Azorín, F. J. Biol. Chem. In press, 1998.