Differential solvation and tautomer stability of a model base pair within the minor and major grooves of DNA

Journal of the American Chemical Society

Volumn 127, Issue 44, 2005, Pages 15612-15617

  Dupradeau, François Yves ^a,b   Case, David A ^b   Yu, Chengzhi ^b   Jimenez, Ralph ^b   Romesberg, Floyd E ^b  

^a UNIVERSITÉ DE PICARDIE JULES VERNE   (France)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC HYDROCARBONS; COMPUTER SIMULATION; GROUND STATE; HYDROGEN BONDS; MOLECULAR DYNAMICS;

DNA DUPLEXES; ENOL MOIETY; MINOR GROOVES; SYN-ENOL;

DNA;

2 (2' HYDROXYPHENYL)BENZOXAZOLE; BENZOXAZOLE DERIVATIVE; DOUBLE STRANDED DNA; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; DNA REPLICATION; HYDROGEN BOND; ISOMER; ISOMERIZATION; LIGHT; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; SIMULATION; SOLVATION; TAUTOMER; TAUTOMERIC SHIFT;

BASE PAIRING; BENZOXAZOLES; DNA; ISOMERISM; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTONS; SOLUBILITY;

EID: 27644456343     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja054607x     Document Type: Article

References (59)

1. Tamm, C.; Strazewski, P. Angew. Chem. Int. Ed. Engl. 1990, 29 (1), 36-57.
2. Topal, M. D.; Fresco, J. R. Nature 1976, 163, 289-293.
3. Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737-738.
4. Broo, A.; Holmen, A. J. Phys. Chem. A 1997, 101 (19), 3589-3600.
5. Colominas, C.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1996, 118 (29), 6811-6821.
6. Gorb, L.; Leszczynski, J. J. Am. Chem. Soc. 1998, 120 (20), 5024-5032.
7. Gould, I. R.; Burton, N. A.; Hall, R. J.; Hillier, I. H. J. Mol. Struct. (THEOCHEM) 1995, 331, 147-154.
8. Guallar, V.; Douhal, A.; Moreno, M.; Lluch, J. M. J. Phys. Chem. A 1999, 103 (31), 6251-6256.
9. Hobza, P.; Sponer, J. Chem. Rev. 1999, 99 (11), 3247-3276.
10. Kwiatkowski, J. S.; Zeilinski, T. J.; Rein, R. Adv. Quantum Chem. 1986, 18, 85-130.
11. Sabio, M.; Topiol, S.; Lumma, W. C., Jr. J. Phys. Chem. 1990, 94 (4), 1366-1372.
12. Taylor, C. A.; El-Bayoumi, M. A.; Kasha, M. Proc. Natl. Acad. Sci. U.S.A. 1969, 63, 253-260.
13. Chen, Y.; Gai, F.; Petrich, J. W. J. Am. Chem. Soc. 1993, 115 (22), 10158-10166.
14. Chou, P.-T.; Wei, C-Y.; Wu, G.-R.; Chen, W.-S. J. Am. Chem. Soc. 1999, 121 (51), 12186-12187.
15. Douhal, A.; Guallar, V.; Moreno, M.; Lluch, J. M. Chem. Phys. Lett. 1996, 256, 370-376.
16. Takeuchi, S.; Tahara, T. J. Phys. Chem. A 1998, 102 (40), 7740-7753.
17. Chachisvilis, M.; Fiebig, T.; Douhal, A.; Zewail, A. H. J. Phys. Chem. A 1998, 102 (4), 669-673.
18. Chen, Y.; Gai, F.; Petrich, J. W. Chem. Phys. Lett. 1994, 222, 329-334.
19. Egli, M.; Gessner, R. V. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 180-184.
20. Lippert, B. J. Chem. Soc., Dalton Trans. 1997, 21, 3971-3976.
21. Dickerson, R. E.; Kopka, M. L.; Pjura, P. E. In DNA-Ligand Interactions; Guschlbauer, W., Sawnger, W., Eds.; Plenum Publishing Corporation: New York, 1987; pp 45-62.
22. Gago, F.; Reynolds, C. A.; Graham, W. Mol. Pharm. 1989, 35, 232-241.
23. Geierstanger, B. H.; Wemmer, D. E. Annu. Rev. Biophys. Biomol. Struct. 1995, 24, 463-493.
24. Neidle, S.; Pearl, L. H.; Skelley, J. V. Biochem. J. 1987, 243, 1-13.
25. Wang, A. H.-J. In Nucleic Acids and Molecular Biology; Eckstein, F., Lilley, D. M. J., Eds.; Springer-Verlag: Berlin, Heidelberg, 1987; Vol. 1, pp 54-69.
26. Lane, A. N.; Jenkins, T. C.; Frenkiel, T. A. Biochim. Biophys. Acta 1997, 1350, 205-220.
27. Morávek, Z.; Neidle, S.; Schneider, B. Nucleic Acids Res. 2002, 30, 1182-1191.
28. Young, M. A.; Jayaram, B.; Beveridge, D. L. J. Am. Chem. Soc. 1997, 119, 59-69.
29. Hud, N. V.; Feignon, J. J. Am. Chem. Soc. 1997, 119, 5756-5757.
30. Shui, X.; McFail-Isom, L.; Hu, G. G.; Williams, L. D. Biochemistry 1998, 37, 8341-8355.
31. Shui, X.; Sines, C. C.; McFail-Isom, L.; VanDerveer, D.; Williams, L. D. Biochemistry 1998, 37, 16877-16887.
32. Young, M. A.; Ravishanker, G.; Beveridge, D. L. Biophys. J. 1997, 73, 2313-2336.
33. Li, Y.; Korolev, S.; Waksman, G. EMBO J. 1998, 17, 7514-7525.
34. Abou-Zied, O. K.; Jimenez, R.; Romesberg, F. E. J. Am. Chem. Soc. 2001, 123 (19), 4613-4614.
35. Abou-Zied, O. K.; Jimenez, R.; Thompson, E. H. Z.; Millar, D. P.; Romesberg, F. E. J. Phys. Chem. A 2002, 106 (15), 3665-3672.
36. Ogawa, A. K.; Abou-Zied, O. K.; Tsui, V.; Jimenez, R.; Case, D. A.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122 (41), 9917-9920.
37. Arthen-Engeland, T.; Bultmann, T.; Ernsting, N. P.; Rodriguez, M. A.; Thiel, W. Chem. Phys. 1992, 163, 43-53.
38. Barbara, P. F.; Walsh, P. K.; Brus, L. E. J. Phys. Chem. 1989, 93 (1), 29-34.
39. Krishnamurthy, M.; Dogra, S. K. J. Photochem. 1986, 32, 235-242.
40. Kyrychenko, A.; Herbich, J.; Wu, F.; Thummel, R. P.; Waluk, J. J. Am. Chem. Soc. 2000, 122 (12), 2818-2827.
41. Mosquera, M.; Penedo, J. C.; Rios Rodriguez, M. C.; Rodríguez- Prieto, F. J. Phys. Chem. 1996, 100 (13), 5398-5407.
42. Smith, T. P.; Zaklika, K. A.; Thakur, K.; Walker, G. C.; Tominaga, K.; Barbara, P. F. J. Phys. Chem. 1991, 95 (25), 10465-10475.
43. Woolfe, G. J.; Melzig, M.; Schneider, S.; Dörr, F. Chem. Phys. 1983, 77, 213-221.
44. Wang, H.; Zhang, H.; Abou-Zied, O. K.; Yu, C.; Romesberg, F. E.; Glasbeek, M. Chem. Phys. Lett. 2003, 367, 599-608.
45. Schweitzer, B. A.; Kool, E. T. J. Am. Chem. Soc. 1995, 117 (7), 1863-1872.
46. Imahori, K.; Watanabe. K. J. Polym. Sci., Part C: Polym. Symp. 1970, 30, 633-656.
47. Case, D. A.; et al. AMBER 8; University of California: San Francisco, CA, 2004.
48. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. J.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
49. Cheatham, T. E. I.; Cieplak, P.; Kollman, P. A. J. Biomol. Struct. Dyn. 1999, 16, 845-862.
50. Cieplak, P.; Cornell, W. D.; Bayly, C. I.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1357-1377.
51. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
52. Frisch, M. J.; et al. Gaussian 98. revision A. 10: Gaussian Inc.: Pittsburgh, PA, 2001.
53. Pigache, A.; Cieplak, P.; Dupradeau, F.-Y. In Automatic and Highly Reproducible RESP and ESP Charge Derivation: Application to the Development of Programs RED and X RED, 227th National Meeting of the American Chemical Society, Anaheim, CA, March 27-April 1, 2004; American Chemical Society: Washington. DC, 2004.
54. Dai, J.; Punchihewa, C.; Mistry, P.; Ooi, A. T.; Yang, D. J. Biol. Chem. 2004, 279, 46096-46103.
55. Dickerson, R. E.; Goodsell, D. S.; Neidle, S. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 3579-3583.
56. Kopka, M. L.; Fratini, A. V.; Drew, H. R.; Dickerson, R. E. J. Mol. Biol. 1983, 163, 129-146.
57. Drew, H. R.; Dickerson, R. E. J. Mol. Biol. 1981, 151, 535-556.
58. Feig, M.; Pettitt, B. M. Biophys. J. 1999, 77, 1769-1781.
59. Zimmer, C.; Wahnert, U. Prog. Biophys. Mol. Biol. 1986, 47, 31-112.