Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues

Chemistry - A European Journal

Volumn 15, Issue 31, 2009, Pages 7601-7610

  Zendlová, Lucie ^a   Řeha, David ^b   Hocek, Michal ^a   Hobza, Pavel ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Ab initio calculations; Density functional calculations; DNA structures solvent effects stacking interactions

Indexed keywords

AB INITIO CALCULATIONS; AROMATICITY; BASE PAIRS; CONTINUUM SOLVENTS; DENSITY FUNCTIONAL; DENSITY FUNCTIONAL CALCULATIONS; DESOLVATION; DESOLVATION ENERGY; DNA DOUBLE HELICES; DNA DUPLEXES; DNA STRUCTURES SOLVENT EFFECTS STACKING INTERACTIONS; EMPIRICAL FORCE; INTERACTION ENERGIES; MOLECULAR DYNAMICS SIMULATIONS; NUCLEIC ACID BASIS; SELF-CONSISTENT CHARGES; STRUCTURAL CHANGE; SUGAR PHOSPHATE; THEORETICAL STUDY; TIGHT BINDING;

COMPUTATIONAL GEOMETRY; DENSITY FUNCTIONAL THEORY; DNA; GENES; HYDROPHOBICITY; MOLECULAR DYNAMICS; NUCLEIC ACIDS; PHOSPHATES; SOLVENTS; SUGAR (SUCROSE); SUGARS; SYSTEM STABILITY;

SIMULATORS;

DNA; SOLVENT;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; NUCLEOTIDE SEQUENCE; THEORETICAL MODEL; THERMODYNAMICS;

BASE PAIRING; BASE SEQUENCE; DNA; MODELS, THEORETICAL; MOLECULAR STRUCTURE; SOLVENTS; THERMODYNAMICS;

EID: 67949095707     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.200802170     Document Type: Article

References (59)

1. For reviews, see: a) L. Wang. P. G. Schultz, Chem. Commun. 2002, 1-11:
2. b)A. A. Henry, F. E. Romesberg, Curr. Opin. Chem. Biol. 2003, 7. 727-733:
3. c)E.T. Kool. J.C. Morales. K.M. Guckian. Angew. Chem. 2000, 112, 1046-1068;
4. Angew. Chem. Int. Ed. 2000, 39, 990-1009;
5. d) E. T. Kool, Acc. Chem. Res. 2002, 35, 936-943.
6. a) A. K. Ogawa, O. K. Abou-Zied, V. Tsui, R. Jimenez. D. A. Case, F. E. Romesberg, J. Am. Chem. Soc. 2000, 122, 9917-9920:
7. b) K. M. Guckian. T. R. Krugh, E. T. Kool, J. Am. Chem. Soc. 2000, 122, 6841-6847:
8. c)J.S. Lai, J. Qu. E. T. Kool, Angew. Chem. 2003, 115. 6155-6159:
9. Angew. Chem. Int. Ed. 2003, 42, 5973-5977;
10. d) J. S. Lai. E. T. Kool, J. Am. Chem. Soc. 2004, 126, 3040-3041.
11. a) A. A. Henry, A. G. Olsen. S. Malsuda, C. Yu. B. H. Geierstanger, F. E. Romesberg, J. Am. Chem. Soc. 2004, 126, 6923-6931:
12. b) A. A. Henry, C. Z. Yu. F. E. Romesberg, J. Am. Chem. Soc. 2003, 125, 9638-9646:
13. c) G.T. Hwang, RE. Romesberg, Nucleic Acids Res. 2006, 34, 2037-2045:
14. d) S. Matsuda. A. A. Henry. F. E. Romesberg, J. Am. Chem. Soc. 2006, 128, 6369-6375:
15. e) Y. Kim. A. M. Leconte. Y. Hari, F.E. Romesberg, Angew. Chem. 2006, 118, 7973-7976;
16. Angew. Chem. Int. Ed. 2006, 45, 7809-7812;
17. f) S. Matsuda, J. D. Filio, A. A. Henry, P. Rai, S. J. Wilkens, T. J. Dwyer, B. H. Geierstanger, D. E. Wemmer, P. G. Schultz, G. Spraggon. F. E. Romesberg, J. Am. Chem. Soc. 2007, 129, 10466-10473;
18. g) S. Matsuda. A. M. Leconte, F. E. Romesberg, J. Am. Chem. Soc. 2007, 129, 5551-5557.
19. A. M. Leconte, G. T. Hwang, S. Malsuda, P. Capek, Y. Hari, F. E. Romesberg. J. Am. Chem. Soc. 2009. DOI: 10.1021/ja078223d.
20. a) C Brotschi. A. Häberli, C.J. Leumann, Angew. Chem. 2001, 113, 3101-3103:
21. Angew. Chem. Int. Ed. 2001, 40, 3012-3014:
22. b) C. Brotschi, G. Mathis. C.J. Leumann. Chem. Eur. J. 2005. 11, 1911-1923:
23. c) A. Zahn. C. Brotschi, C.J. Leumann, Chem. Eur. J. 2005. 11, 2125-2129.
24. a) D. Reha. M. Hocek, P. Hobza. Chem. Eur. J. 2006, 12, 35873595;
25. b) C. Fonseca Guerra. F. M. Bickelhaupl, Angew. Chem. 2002, 114, 2194-2197;
26. Angew. Chem. Int. Ed. 2002, 41, 2092-2095:
27. c) C. Fonseca Guerra. F. M. Bickelhaupt, J. Chem. Phys. 2003, 119, 4262-4273:
28. d) C. Fonseca Guerra, F. M. Bickelhaupt, E. J. Baerends. ChemPhysChem 2004, 5, 481-487;
29. e) C. Fonseca Guerra, E.J. Baerends, F. M. Bickelhaupt, Int. J. Quantum Chem. 2006, 106, 2428-2443.
30. Z. Johar, A. Zahn, C. J. Leumann, B. Jaun. Chem. Eur. J. 2008, 14, 1080-1086.
31. a) I. Singh. W. Hecker. A. K. Prasad, V. S. Parmar, O. Seitz. Chem. Commun. 2002, 500-501;
32. b) C. Beuck. I. Singh, A. Bhattacharya. W. Hecker. V. S. Parmar. O. Seitz, E. Weinhold. Angew. Chem. 2003, 115,4088-4091;
33. Angew. Chem. Int. Ed. 2003, 42, 3958-3960.
34. A. Zahn. C. J. Leumann. Chem. Eur. J. 2008, 14, 1087-1094.
35. a) J. Gao, C. Slrässler, D. Tahmassebi, E. T. Kool. J. Am. Chem. Soc. 2002, 124, 11590-11591;
36. b) J. Gao, S. Watanabe. E. T. Kool, J. Am. Chem. Soc. 2004, 126, 12748-12749;
37. c) J. N. Wilson, Y. N. Teo, E. T. Kool, J. Am. Chem. Soc. 2007, 129, 15426-15427.
38. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K.M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 5179-5197.
39. C. I. Bayly. P. Cieplak. W. D. Cornell. P. A. Kollman. J. Phys. Chem. 1993, 97, 10269-10280.
40. J. M. Wang. R. M. Wolf. J. W. Caldwell, P. A. Kollman. D. A. Case. J. Comput. Chem. 2005, 26, 114-114.
41. G. C. Shields. C. A. Laughton, M. Orozco, J. Am. Chem. Soc. 1997, 119, 7463-7469.
42. a) M. Elstner, D. Porezag, G. Jungnickel. J. Eisner, M. Haugk, T. Frauenheim, S. Suhai, G. Seifert, Phys. Rev. B 1998, 58, 7260-7268:
43. b) M. Elstner, P. Hobza, T. Frauenheim. S. Suhai. E. Kaxiras, J. Chem. Phys. 2001, 114, 5149-5155.
44. T. Kubaf, M. Hanus. F. Ryjáček, P. Hobza. Chem. Eur. J. 2006, 12, 280-290.
45. D. Reha, M. Kabelá̌. F. Ryjáček. J. Šponer, J. E. Šponer. M. Elstner. S. Suhai, P. Hobza, J. Am. Chem. Soc. 2002, 124, 3366-3376.
46. P. Jurečka. J. Černý. P. Hobza, D. R. Salahub, J. Comput. Chem. 2007, 28, 555-569.
47. J. M. Tao, J. P. Perdew, V. N. Slaroverov, G. E. Scuseria, Phys. Rev. Lett. 2003, 91, 146401.
48. R. Krishnan, J. S. Binkley, R. Seeger. J. A. Pople, J. Chem. Phys. 1980, 72, 650-654.
49. P. M. W. Gill, B. G. Johnson. J. A. Pople, M. J. Frisch, Chem. Phys. Lett. 1992, 197, 499-505.
50. M. J. Frisch, J. A. Pople, J. S. Binkley, J. Chem. Phys. 1984, 80, 32653269.
51. T. Clark. J. Chandrasekhar. G. W. Spitznagel. P. v. R. Schleyer, J. Comput. Chem. 1983, 4, 294-301.
52. P. Jurečka, J. Šponer, J. Černý. P. Hobza. Phys. Chem. Chem. Phys. 2006, 8, 1985-1993.
53. A. Klamt, G. Schuurmann, J. Chem. Soc. Perkin Trans. 2 1993, 799805.
54. R. Alrichs, M. Bär. M. Häser, H. Horn, C. Kölmel, Chem. Phys. Lett. 1989, 162, 165-169.
55. P. K. Weiner. P. A. Kollman, J. Comput. Chem. 1981, 2, 287-303.
56. Gaussian 03. Revision A.1, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria. M. A. Robb, J. R. Cheeseman. J. A. Montgomery, Jr., T. Vreven. K. N. Kudin. J. C. Burant, J. M. Millam. S. S. Iyengar, J. Tomasi. V. Barone, B. Mennucci, M. Cossi. G. Scalmani. N. Rega, G. A. Petersson. H. Nakatsuji. M. Hada, M. Ehara, K. Toyota, R. Fukuda. J. Hasegawa, M. lshida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo. J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman. J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe. P. M. W. Gill. B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J. A. Pople, Gaussian. Inc. Wallingford CT. 2003.
57. C. Brotschi, C.J. Leumann, Angew. Chem. 2003, 115, 1694-1697:
58. Angew. Chem. Int. Ed. 2003, 42,1655-1658.
59. C. Brotschi, C.J. Leumann, Chem. Commun. 2005, 2023-2025.