Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads

Journal of Computational Chemistry

Volumn 26, Issue 4, 2005, Pages 352-364

  Meyer, Michael ^a   Hocquet, Alexandre ^b   Sühnel, Jürgen ^c  

^a Revotar Biopharmaceuticals AG   (Germany)

^b LAB DE CHIM PHYS MACROMOLECULAIRE   (France)

^c FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

Density functional theory; Molecular recognition; Sandwiched base tetrads; Solvation; Tetraplex

Indexed keywords

CHEMICAL BONDS; COMPLEXATION; CONFORMATIONS; IONS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POSITIVE IONS; PROBABILITY DENSITY FUNCTION; QUANTUM THEORY; SELF ASSEMBLY; SOLVENTS;

DENSITY FUNCTIONAL THEORY; MOLECULAR RECOGNITION; SANDWICHED BASE TETRADS; SOLVATION; TETRAPLEX;

NUCLEIC ACIDS;

CYTOSINE; GUANINE; POTASSIUM; SODIUM; THYMINE; URACIL;

ALGORITHM; ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; HYDROGEN BOND; THERMODYNAMICS;

ALGORITHMS; BASE PAIRING; CYTOSINE; GUANINE; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR CONFORMATION; POTASSIUM; SODIUM; THERMODYNAMICS; THYMINE; URACIL;

EID: 14744279716     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20176     Document Type: Article

References (61)

1. Arthanari, H.; Bolton, P. H. Chem Biol 2001, 8, 221.
2. Simonsson, T. Biol Chem 2001, 382, 621.
3. Shafer, R. H.; Smirnov, I. Biopolymers 2001, 56, 209.
4. Moine; H.; Mandel, J.-L. Science 2001, 294, 2487.
5. Lane, A. N.; Jenkins, T. C. Curr Org Chem 2001, 5, 845.
6. Sühnel, J. Biopolymers 2001, 61, 32.
7. Keniry, M. A. Biopolymers 2001, 56, 123.
8. Meyer, M.; Sühnel, J. In: Computational Chemistry: Reviews of Current Trends; Leszczynski, J., Ed.; World Scientific Publishing: Singapore, 2003, p. 161, vol. 8.
9. Han, H.; Hurley, L. H. Trends Pharm Sci 2000, 21, 136.
10. Kerwin, S. M. Curr Pharm Des 2000, 6, 441.
11. Neidle, S.; Read, M. A. Biopolymers 2000-2001, 56, 195.
12. Perry, P. J.; Arnold, J. R. P.; Jenkins, T. C. Expert Opin Investig Drugs 2001, 10, 2141.
13. Alberti, P.; Lacroix, L.; Guittat, L.; Hélène, C.; Mergny, J.-L. Min Rev Med Chem 2003, 3, 23.
14. Cuesta, J.; Read, M. A.; Neidle, S. Min Rev Med Chem 2003, 3, 11.
15. Davis, J. T. Angew Chem Int Ed 2004, 43, 668.
16. Shi, X.; Fettinger, J. C.; Cai, M.; Davis, J. T. Angew Chem Int Ed 2000, 39, 3124.
17. Shi, X.; Mullaugh, K. M.; Fettinger, J. C.; Jiang, Y.; Hofstadler, S. A.; Davis, J. T. J Am Chem Soc 2003, 125, 10830.
18. Fojtfk, P.; Kejnovská, I.; Vorlíčková, M. Nucleic Acids Res 2004, 32, 298.
19. Forman, S. L.; Fettinger, J. C.; Pieraccini, S.; Gottarelli, G. Davis, J. T. J Am Chem Soc 2000, 122, 4060.
20. Wong, A.; Fettinger, J. C.; Forman, S. L.; Davis, J. T.; Wu, G. J Am Chem Soc 2002, 124, 742.
21. Phillips, K., Dauter, Z., Murchie, A. I., Lilley, D. M., Luisi, B. J Mol Biol 1997 273, 171.
22. Deng, J.; Xiong, Y.; Sundaralingam, M. Proc Natl Acad Sci USA 2001, 98, 13665.
23. Pan, B.; Xiong, Y.; Shi, K.; Sundaralingam, M. Structure 2003, 11, 1423.
24. Parkinson, G.; Lee, M. P. H.; Neidle, S. Nature 2002, 417, 876.
25. Smirnov, I. V.; Kotch, F. W.; Pickering, I. J.; Davis, J. T.; Shafer, R. H. Biochemistry 2002, 41, 12133.
26. Špačkova, N.; Berger, I.; Šponer, J. J Am Chem Soc1999, 121, 5519.
27. Špačkova, N.; Berger, I.; Koča, J.; Šponer J. J Am Chem Soc 2001, 123, 3295.
28. Meyer, M.; Steinke, T.; Brandi, M.; Sühnel, J. J Comput Chem 2001, 22, 109.
29. Gu, J. D.; Leszczynski, J.; Bansal, M. Chem Phys Lett 1999, 311, 209.
30. Gu, J. D.; Leszczynski, J. J Phys Chem A 2000, 104, 6308.
31. Gu, J. D.; Leszczynski, J. J Phys Chem A 2000, 104, 1898.
32. Gu, J. D.; Leszczynski, J. J Phys Chem A 2000, 104, 7353.
33. Gu, J. D.; Leszczynski, J. Chem Phys Lett 2001, 335, 465.
34. Gu J. D.; Leszczynski, J. J Phys Chem A 2001, 105, 10366.
35. Meyer, M.; Brandl, M; Sühnel, J. J Phys Chem A 2001, 105, 8223.
36. Meyer, M.; Schneider, C.; Brandl, M.; Sühnel, J. J Phys Chem A 2001, 105, 11560.
37. Louit, G.; Hocquet, A; Ghomi, M.; Meyer, M.; Sühnel. J. Phys Chem Commun 2002, 5, 94.
38. Gu, J. D.; Leszczynski, J. Chem Phys Lett 2002, 351, 403.
39. Meyer, M.; Sühnel, J. J Biomol Struct Dyn 2003, 20, 507.
40. Meyer, M.; Sühnel, J. J Phys Chem A 2003, 107, 1025.
41. Louit, G.; Hocquet, A.; Ghomi, M.; Meyer, M.; Sühnel, J. Phys Chem Commun 2003, 6, 1.
42. Gu, J. D.; Leszczynski, J. J Phys Chem B 2003, 107, 6609.
43. Gu, J.; Leszczynski, J. J Phys Chem A 2003, 107, 9447.
44. Gu, J.; Wang, J.; Leszczynski, J. J Phys Chem B 2004, 108, 9277.
45. Gu, J.; Leszczynski, J. J Phys Chem A 2002, 106, 529.
46. Becke, A. D. J Chem Phys 1993, 98, 5648.
47. Lee, C. T.; Yang, W. G.; Parr, R. G. Phys Rev B 1988, 37, 785.
48. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J Phys Chem1994, 98, 11623.
49. Godbout, N.; Salahub, D. R.; Andzelm, J.; Wimmer, E. Can J Chem 1992, 70, 560.
50. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., J.r.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian, Inc.: Pittsburgh, PA, 1988.
51. Meyer, M.; Trowitzsch-Kienast, W., Recent Res Dev Phys Chem 2004, 7, 127.
52. Siegbahn, P. E. M.; Blomberg, M. R. A. Chem Rev 2000, 100, 421.
53. Rulíšek, L.; Šponer, J. J Phys Chem B 2003, 107, 1913.
54. Kuswaha, P. S.; Kumar, A.; Mishra, P. C. Spectrochim Acta A 2004, 60, 719.
55. Feller, D. A. J Phys Chem A 1997, 101, 2723.
56. Glendening, E. D.; Feller, D. A. J Phys Chem 1995, 99, 3060.
57. Hud, N. V.; Smith, F. W.; Anet, F. A. L.; Feigon, J. Biochemistry 1996, 35, 15383.
58. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235.
59. Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S.-H.; Srinivasan, A. R.; Schneider, B. Biophys J 1992, 63, 751.
60. Jing, N.; Xiong, W.; Guan, Y.; Pallansch, L.; Wang, S. Biochemistry 2002, 41, 5397.
61. Fonseca Guerra, C.; Bickelhaupt, F. M.; Snijders, J. G.; Baerends, E. J. J Am Chem Soc 2000, 121, 4117.