Are the hydrogen bonds of RNA (A·U) stronger than those of DNA (A·T)? A quantum mechanics study

Chemistry - A European Journal

Volumn 11, Issue 17, 2005, Pages 5062-5066

  Pérez, Alberto ^a   Sponer, Jiri ^b,c   Jurecka, Petr ^b,c   Hobza, Pavel ^c   Luque, F Javier ^d   Orozco, Modesto ^a,d  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b INSTITUTE OF BIOPHYSICS   (Czech Republic)

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

^d UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Density functional calculations; DNA; Hydrogen bonds; Quantum mechanics; RNA

Indexed keywords

CARRIER CONCENTRATION; CONFORMATIONS; DNA; PHASE INTERFACES; PROBABILITY DENSITY FUNCTION; QUANTUM THEORY; RNA; TOPOLOGY;

DENSITY FUNCTIONAL CALCULATIONS; ELECTRON DENSITY TOPOLOGY; REACTIVITY INDEXES; SOLVATION;

HYDROGEN BONDS;

DNA; RNA;

ARTICLE; CHEMISTRY; HYDROGEN BOND; QUANTUM THEORY;

DNA; HYDROGEN BONDING; QUANTUM THEORY; RNA;

EID: 24344439730     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/chem.200500255     Document Type: Article

References (33)

1. a) V. A. Bloomfield, D. M. Crothers, I. Tinoco, Nucleic Acids: Structure, Properties and Functions, University Science Books, Sausalito, CA. 2000;
2. b) M. Riley, B. Maling, M. J. Chanberlin, J. Mol. Biol. 1966, 20, 359;
3. K. J. Breslauer, J. M. Sturtevant, I. Tinoco, J. Mol. Biol. 1975, 99, 549;
4. S. Nakano, T. Kanzaki, N. Sugimoto, J. Am. Chem. Soc. 2004, 126, 1088.
5. P. Acharya, S. Cheruku, S. Chatterjee, S. Acharya, J. Chattopadhyaya, J. Am. Chem. Soc. 2004, 126, 2862.
6. I. Vakonakis, A. C. LiWang, J. Am. Chem. Soc. 2004, 126, 5688.
7. a) J. Sponer, P. Hobza, Chem. Rev. 1999, 99, 3247;
8. b) C. Fonseca-Guerra, F. M. Bickelhaupt, J. G. Snijders, E. J. Baerends, J. Am. Chem. Soc. 2000, 122, 4117.
9. M. Swart, C. Fonseca-Guerra, F. M. Bickelhaupt, J. Am. Chem. Soc. 2004, 126, 16718.
10. a) R. Ahlrichs, M. Bär, M. Häser, H. Horn, C. Kölmel, Chem. Phys. Lett. 1989, 162, 165;
11. b) F. Weigend, M. Häser, Theor. Chem. Acc. 1997, 97, 331;
12. A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, H. Koch, J. Olsen, Chem. Phys. Lett. 1999, 302, 437;
13. A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, H. Koch, J. Olsen, A. K. Wilson, Chem. Phys. Lett. 1998, 256, 243;
14. e) P. Jureèka, P. Hobza, Chem. Phys. Lett. 2002, 365, 89;
15. f) S. F. Boys, F. Bernardi, Mol. Phys. 1970, 19, 553.
16. a) R. F. W. Bader, Atoms in Molecules: A Quantum Theory, Oxford University Press, Oxford, UK, 1990;
17. b) R. F. W. Bader, Chem. Rev. 1991, 91, 983;
18. J. Muñoz, J. Sponer, P. Hobza, M. Orozco, F. J. Luque, J. Phys. Chem. B 2001, 105, 6051;
19. I. Alkorta, I. Rozas, J. Elguero, Chem. Soc. Rev. 1998, 27, 167;
20. e) I. Alkorta, I. Rozas, J. Elguero, Struct. Chem. 1998, 9, 243.
21. a) E. Cubero, F. J. Luque, M. Orozco, Proc. Natl. Acad. Sci. USA 1998, 95, 5976;
22. b) F. J. Luque, M. Orozco, J. Comput. Chem, 1998, 19, 866, The interacting probe was N(+0.4) for O4 and N(-0.4) for N3.
23. a) T. Helgaker, T. A. Ruden, P. Jørgensen, J. Olsen, W. Klopper, J. Phys. Org. Chem. 2004, 17, 913;
24. b) P. Jurecka, P. Hobza, J. Am. Chem. Soc. 2003, 125, 15608.
25. a) W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 11946;
26. b)T. E. Cheatham, P. Cieplak, P. A. Kollman, J. Biomol. Struct. Dyn. 1999, 16, 845.
27. A. Perez, A. Noy, F. Lankas, F. J. Luque, M. Orozco, Nucleic Acids Res. 2004, 32, 6144.
28. A. Noy, A. Pérez, F. Lankas, F. J. Luque, M. Orozco, J. Mol. Biol. 2004, 343, 627.
29. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R.W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926.
30. R. Ahlrichs, M. Bär, M. Häser, H. Horn, C. Kölmel, Chem. Phys. Lett. 1989, 162, 165.
31. 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. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, 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, 2004.
32. F.W. Biegler-König, R.F.W. Bader, T. Tang, J. Comput. Chem. 1982, 3, 317.
33. M. Orozco, C. Alhambra, F. J. Luque, MOPETE/MOPFIT computer programs, University of Barcelona, 1992.