Interaction of cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine-cytosine base tetrads with k+, Na+ and Li+ Ions—A Density Functional Study

Journal of Biomolecular Structure and Dynamics

Volumn 20, Issue 4, 2003, Pages 507-517

  Meyer, Michael ^a   Sühnel, Jürgen ^b  

^a Revotar Biopharmaceuticals AG   (Germany)

^b FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

Density functional theory; Molecular recognition; Quantum chemistry; Tetrad; Tetraplex

Indexed keywords

CYTOSINE; GUANINE; LITHIUM ION; POTASSIUM ION; SODIUM ION; THYMINE; URACIL;

ARTICLE; CALCULATION; DENSITY FUNCTIONAL THEORY; ENERGY; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; QUANTUM CHEMISTRY; QUANTUM THEORY;

ALGORITHMS; BASE PAIRING; CATIONS, MONOVALENT; CYTOSINE; ELECTROSTATICS; GUANINE; HYDROGEN BONDING; LITHIUM; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; POTASSIUM; SODIUM; THERMODYNAMICS; THYMINE; URACIL;

EID: 0037320773     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2003.10506868     Document Type: Article

References (49)

1. Arthanari, H., and Bolton, P. H., 2001. Chem. & Biol., 8:221–230.
2. Simonsson, T., 2001. Biol. Chem., 382:621–628.
3. Shafer, R. H., and Smirnov, I., 2001. Biopolymers, 56:209–227.
4. Moine, H., and Mandel, J.-L., 2001. Science, 294:2487–2488.
5. Han, H., and Hurley, L. H., 2000. Trends. Pharm. Sci., 21:136–142.
6. Kerwin, S. M., 2000. Curr. Pharm. Des., 6:441–471.
7. Neidle, S., and Read, M. A., 2001. Biopolymers, 56:195–208.
8. Perry, P. J., Arnold, J. R. P., and Jenkins, T. C., 2001. Expert. Opin. Investig. Drugs, 10:2141–2156.
9. Gilbert, D. E., and Feigon, J., 1999. Curr. Opin. Struct. Biol., 9:305–314.
10. Lane, A. N., and Jenkins, T. C., 2001. Curr. Org. Chem., 5:845–869.
11. Sühnel, J., 2002. Biopolymers, 61:31–51.
12. Patel, D. J., Bouaziz, S., Kettani, A., and Wang, Y., 1999. Oxford Handbook of Nucleic Acid Structure Edited by:Neidle, S., 389–453. Oxford:Oxford University Press. In
13. Keniry, M. A., 2001. Biopolymers, 56:123–146.
14. Deng, J., Xiong, Y., and Sundaralingam, M., 2001. Proc. Natl. Acad. Sci., 98:13665–13670.
15. Cheong, C., and Moore, P. B., 1992. Biochemistry, 31:8406–8414.
16. Patel, P. K., Koti, A. S. R., and Hosur, R. V., 1999. Nucleic Acids Res., 27:3836–3843.
17. Patel, P. K., Bhavesh, N. S., and Hosur, R. V., 2000. Biochem. Biophys. Res. Comm., 270:967–971.
18. Patel, P. K., and Hosur, R. V., 1999. Nucleic Acids Res., 27:2457–2464.
19. Bouaziz, S., Kettani, A., and Patel, D. J., 1998. J. Mol. Biol., 282:637–652.
20. Escaja, N., Pedroso, E., Rio, M., and Gonzalez, C., 2000. J. Am. Chem. Soc., 122:12732–12742.
21. Gallego, J., Chou, S.-H., and Reid, B. R., 1997. J. Mol. Biol., 273:840–856.
22. Parkinson, G. N., Lee, M. P. H., and Neidle, S., 2002. Nature, 417:876–880.
23. Wang, Y., and Patel, D. J., 1993. Structure, 1:263–282.
24. Phillips, K., Dauter, Z., Murchie, A. I., Lilley, D. M., and Luisi, B., 1997. J. Mol. Biol., 273:171–182.
25. Guschlbauer, W., Chantot, J. F., and Thiele, D., 1990. J. Biomol. Struct. Dyn., 8:491–511.
26. Spackova, N., Berger, I., and Sponer, J., 1999. J. Am. Chem. Soc., 121:5519
27. Jing, N., Xiong, W., Guan, Y., Pallansch, L., and Wang, S., 2002. Biochemistry, 41:5397–5403.
28. Kotch, F. W., Fettinger, J. C., and Davis, J. T., 2000. Org. Lett., 2:3277–3280.
29. Meyer, M., Steinke, T., Brandl, M., and Sühnel, J., 2001. J. Comput. Chem., 22:109–124.
30. Gu, J., and Leszczynski, J., 2002. J. Phys. Chem. A, 106:529–532.
31. Hud, N. V., Smith, F. W., Anet, F. A. L., and Feigon, J., 1996. Biochemistry, 35:15838–15390.
32. Gu, J., and Leszczynski, J., 2000. J. Phys. Chem. A, 104:6308–6313.
33. Gu, J., and Leszczynski, J., 2001. J. Phys. Chem. A, 105:10366–10371.
34. Becke, A. D., 1993. J. Chem. Phys., 98:5648–5652.
35. Lee, C., Yang, G., and Parr, R. G., 1988. Phys. Rev. B, 37:785–789.
36. Stephens, P. J., Delvin, F. J., Chabolowski, C. F., and Frisch, M. J., 1994. J. Phys. Chem., 98:11623–11627.
37. Godbout, N., Salahub, D. R., Andzelm, J., and Wimmer, E., 1992. Can. J. Chem., 70:560–571.
38. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Jr., 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. G., Chen, W., Wong, M. W., Andres, J. L., Head-Gordon, M., Replogle, E. S., and Pople, J. A., 1998. GAUSSIAN, 98 Gaussian, Inc., Pittsburgh PA
39. Boys, S. F., and Bernardi, F., 1970. Mol. Phys., 19:553–577.
40. Gu, J., Leszczynski, J., and Bansal, M., 1999. Chem. Phys. Lett., 311:209–214.
41. Meyer, M., Brandl, M., and Sühnel, J., 2001. J. Phys. Chem., A 105:8223–8225.
42. Meyer, M., Schneider, C., Brandl, M., and Sühnel, J., 2001. J. Phys. Chem. A, 105:11560–11573.
43. Loit, G., Hocquet, A., Ghomi, M., Meyer, M., and Sühnel, J., 2002. Phys. Chem. Comm., 5:94–98.
44. Gu, J., and Leszczynski, J., 2000. J. Phys. Chem. A, 104:7353–7358.
45. Meyer, M., and Sühnel, J., 2003. J. Phys. Chem. A, 107 in press
46. Burgess, J., Ions in Solution:Basic Principles of Chemical Interactions 1998Chichester:Ellis Horwood Limited.
47. Kettani, A., Bouaziz, S., Gorin, A., Zhao, H., Jones, R. A., and Patel, D. J., 1998. J. Mol. Biol., 282:619–636.
48. Hardin, C. C., Watson, T., Corregan, M., and Bailey, C., 1992. Biochemistry, 31:833–841.
49. Chaput, J. C., and Switzer, C., 1999. Proc. Natl. Acad. Sci., 96:10614–10619.