Theoretical investigation of DNA oligomer systems. Modification of the hydrogen atoms transfer in a base pair due to time-dependent interaction with stacked base pairs

Chemical Physics

Volumn 325, Issue 2-3, 2006, Pages 389-396

  Villani, Giovanni ^a  

^a AREA DELLA RICERCA   (Italy)

Author keywords

Base pair; Base stacking; DNA oligomers; Time dependent coupling

Indexed keywords

EID: 33744989479     PISSN: 03010104     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemphys.2006.01.015     Document Type: Article

References (51)

1. Zoete V., and Meuwly M. J. Chem. Phys. 121 (2004) 4377
2. Ivanov V., Zeng Y., and Zocchi G. Phys. Rev. E 70 (2004) 51907
3. Hanlon S. Biochem. Biophys. Res. Commun. 23 (1966) 861
4. Herskovits T.T., Singer S.S., and Geiduschek E.P. Arch. Biochem. Biophys. 94 (1961) 99
5. Newcomb L.F., and Gellman S.H. J. Am. Chem. Soc. 116 (1994) 4993
6. Kratochvil M., Sponer J., and Hobza P. J. Am. Chem. Soc. 122 (2000) 3495
7. Kratochvil M., Engkvist O., Sponer J., Jungwirth P., and Hobza P. J. Phys. Chem. A 102 (1998) 6921
8. Sponer J., Leszczynski J., and Hobza P. J. Mol. Struct. (Theochem) 573 (2001) 43
9. Ts'o P.O.P., Melvin I.S., and Olson A.C. J. Am. Chem. Soc. 85 (1962) 1289
10. Sollie T.N., and Schellman J.A. J. Mol. Biol. 33 (1968) 61
11. Nakano N.I., and Igarashi S.J. Biochemistry 9 (1970) 577
12. Mitchell P.R., and Sigel H. Eur. J. Biochem. 88 (1978) 149
13. Saenger W. Principles of Nucleic Acid Structure (1984), Springer, New York
14. Morcillo J., Gallego E., and Peral F. J. Mol. Struct. 157 (1987) 353
15. Sartorius J., and Schneider H.-J. J. Chem. Soc. Park. Tr. 2 (1997) 2319
16. Mizutani M., Kubo I., Jitsukawa H., and Masuda H. Inorg. Chem. 38 (1999) 420
17. Allawi H.T., and Santalucia J. Nucl. Acids Res. 26 (1998) 2694
18. Nakano S., Fujimoto M., Hara H., and Sugimoto N. Nucl. Acids Res. 27 (1999) 2957
19. Bommarito S., Peyret N., and Santalucia J. Nucl. Acids Res. 28 (2000) 1929
20. Aida M. J. Theor. Biol. 130 (1988) 327
21. Sponer J., Leszczynski J., and Hobza P. J. Phys. Chem. 100 (1996) 5590
22. Sugiyama H., and Saito I. J. Am. Chem. Soc. 118 (1996) 7063
23. Shinoda T., Shima N., and Tsukada M. Int. J. Quantum Chem. 49 (1994) 849
24. Kurita N., and Kobayashi K. Comput. Chem. 24 (2000) 351
25. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz Jr. K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. J. Am. Chem. Soc. 117 (1995) 5179
26. Hobza P., Kabelac M., Sponer J., Mejzlik P., and Vondrasek J. J. Comput. Chem. 18 (1997) 1136
27. Sponer J., Gabb H.A., Leszczynski J., and Hobza P. Biophys. J. 73 (1997) 76
28. Sponer J., Florian J., Ng H.-L., Sponer J.E., and Spackova N. Nucl. Acids Res. 28 (2000) 4893
29. Fogolari F., Elcock A.H., Esposito G., Viglino P., Briggs J.M., and McCammon J.A. J. Mol. Biol. 267 (1997) 368
30. Schneider B., and Berman H.M. Biophys. J. 69 (1995) 2661
31. Norberg J., and Nilsson L. Biophys. J. 74 (1998) 394
32. Warshel A., and Russell S.T. Q. Rev. Biophys. 17 (1984) 283
33. Florian J., Sponer J., and Warshel A. J. Phys. Chem. B 103 (1999) 884
34. Friedman R.A., and Honig B. Biophys. J. 69 (1995) 1528
35. Drew H.R., Wing R.M., Takano T., Broka C., Tanaka S., Itakura K., and Dickerson R.E. Proc. Natl. Acad. Sci. USA 78 (1981) 2179
36. Wing R.M., Drew H.P., Takano T., Broka C., Tanaka S., Itakura K., and Dickerson R.E. Nature 287 (1980) 755
37. Dickerson R.E. Helix structure and molecular recognition by B-DNA. In: Neidle S. (Ed). Oxford Handbook of Nucleic Acid Structure (1999), Oxford University Press, Oxford
38. Lankas F., Cheatham III T.E., Spacková N., Hobza P., Langowski J., and Sponer J. Biophys. J. 82 (2002) 2592
39. Dornberger U., Leijon M., and Fritzsche H. J. Biol. Chem. 274 (1999) 6957
40. Ng H.-L., Kopka M.L., and Dickerson R.E. Proc. Natl. Acad. Sci. USA 97 (2000) 2035
41. Trantirek L., Stefl R., Vorlickova M., Koca J., Sklenar V., and Kypr J. J. Mol. Biol. 297 (2000) 907
42. Lankas F., Sponer J., Hobza P., and Langowski J. J. Mol. Biol. 299 (2000) 695
43. Villani G. Chem. Phys. 316 (2005) 1
44. G. Villani, Chem. Phys., submitted for publication.
45. Poltev V.I., and Shulyupina N.V. J. Biomol. Struct. Dyn. 3 (1986) 739
46. Ferretti A., Lami A., and Villani G. J. Chem. Phys. 106 (1997) 834
47. Villani G. Chem. Phys. 302 (2004) 309
48. Watson J.D., and Crick F.H.C. Nature 171 (1953) 737 964
49. Löwdin P.O. Rev. Mod. Phys. 35 (1963) 724
50. Löwdin P.O. Adv. Quantum Chem. 2 (1965) 213
51. Leroy J.L., Charretier E., Kochoyan M., and Guéron M. Biochemistry 27 (1988) 8894