Collect. Czech. Chem. Commun. 2008, 73, 161-174
https://doi.org/10.1135/cccc20080161

Correlation Between the Thermodynamic Stability of DNA Duplexes and the Interaction and Solvation Energies of DNA Building Blocks

Jan Řezáč and Pavel Hobza*

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic

References

1. Doktycz M. J., Morris M. D., Dormady S. J., Beattie K. L., Jacobson K. B.: J. Biol. Chem. 1995, 270, 8439. <https://doi.org/10.1074/jbc.270.15.8439>
2. Řezáč J., Hobza P.: Chem. Eur. J. 2007, 13, 2983. <https://doi.org/10.1002/chem.200601120>
3. Sugimoto N., Nakano S. I., Yoneyama M., Honda K. I.: Nucleic Acids Res. 1996, 24, 4501. <https://doi.org/10.1093/nar/24.22.4501>
4. Watkins J., SantaLucia J.: Nucleic Acids Res. 2005, 33, 6258. <https://doi.org/10.1093/nar/gki918>
5. Wang J. M., Cieplak P., Kollman P. A.: J. Comput. Chem. 2000, 21, 1049. <https://doi.org/10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F>
6. Cornell W. D., Cieplak P., Bayly C. I., Gould I. R., Merz K. M., Ferguson D. M., Spellmeyer D. C., Fox T., Caldwell J. W., Kollman P. A.: J. Am. Chem. Soc. 1996, 118, 2309. <https://doi.org/10.1021/ja955032e>
7. Case D. A., Darden T. A., Cheatham T. A., Simmerling C. L., Wang J., Duke R. E., Luo R., Merz K. M., Pearlman D. A., Crowley M., Walker R. C., Zhang W., Wang B., Hayik S., Roitberg A., Seabra G., Wong K. F., Paesani F., Wu X., Brozell S., Tsui V., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Beroza P., Mathews H. D., Schafmeister C., Ross W. S., Kollman P. A.: AMBER 9. University of California, San Francisco 2006.
8. Černý J., Jurečka P., Hobza P., Valdes H.: J. Phys. Chem. A 2007, 111, 1146. <https://doi.org/10.1021/jp066504m>
9. Jurečka P., Černý J., Hobza P., Salahub D. R.: J. Comput. Chem. 2007, 28, 555. <https://doi.org/10.1002/jcc.20570>
10. Staroverov V. N., Scuseria G. E., Tao J., Perdew J. P.: J. Chem. Phys. 2003, 119, 12129. <https://doi.org/10.1063/1.1626543>
11. Ahlrichs R., Bar M., Haser M., Horn H., Kolmel C.: Chem. Phys. Lett. 1989, 162, 165. <https://doi.org/10.1016/0009-2614(89)85118-8>
12. Barone V., Cossi M.: J. Phys. Chem. A 1998, 102, 1995. <https://doi.org/10.1021/jp9716997>
13. Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Montgomery J., Vreven T., Kudin K. N., Burant J. C., Millam J. M., Iyengar S. S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G. A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J. E., Hratchian H. P., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Ayala P. Y., Morokuma K., Voth G. A., Salvador P., Dannenberg J. J., Zakrzewski V. G., Dapprich S., Daniels A. D., Strain M. C., Farkas O., Malick D. K., Rabuck A. D., Raghavachari K., Foresman J. B., Ortiz J. V., Cui Q., Baboul A. G., Clifford S., Cioslowski J., Stefanov B. B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R. L., Fox D. J., Keith T., Al-Laham M. A., Peng C. Y., Nanayakkara A., Challacombe M., Gill P. M. W., Johnson B., Chen W., Wong M. W., Gonzalez C., Pople J. A.: Gaussian 03, Revision C.02, 2004.
14. Řezáč J., Harris S. A.: Unpublished results.