Energetics of complex formation of the DNA hairpin structure d(GCGAAGC) with aromatic ligands

Biophysics

Volumn 56, Issue 1, 2011, Pages 28-39

  Kostyukov, V V ^a  

^a SEVASTOPOL STATE UNIVERSITY   (Russian Federation)

Author keywords

aromatic ligands; complex formation; DNA hairpin d(GCGAAGC); energy contributions

Indexed keywords

EID: 79955931733     PISSN: 00063509     EISSN: 15556654     Source Type: Journal    
DOI: 10.1134/S000635091101012X     Document Type: Article

References (43)

1. M. F. Brana, M. Cacho, A. Gradillas, et al., Curr. Pharm. Des. 7, 1745 (2001).
2. E. Chu and V. T. DeVita, Physician's Cancer Chemotherapy Drug Manual (Jones and Bartlett Publ., London, 2003).
3. R. D. Wells, J. Biol. Chem. 263, 1095 (1988).
4. S.-H. Chou, K.-H. Chin, and A. H.-J. Wang, Nucleic Acids Res. 31, 2461 (2003).
5. A. N. Veselkov, V. I. Pakhomov, L. N. Djimant, et al., Mol. Biol. 32, 639 (1998).
6. A. N. Veselkov, R. D. Eaton, A. V. Semanin et al., Mol. Biol. 36, 880 (2002).
7. I. Hirao, G. Kawai, S. Yoshizawa, et al., Nucleic Acid Res. 22, 576 (1994).
8. K. Arai, R. Low, J. Kobori, et al., J. Biol. Chem. 256, 5273 (1981).
9. P. Elias and I. R. Lehman, Proc. Natl. Acad. Sci. USA 85, 2959 (1988).
10. D. W. Cowing, J. C. A. Bardwell, E. A. Craig, et al., Proc. Natl. Acad. Sci. USA 82, 2679 (1985).
11. V. V. Kostjukov, V. I. Pahomov, M. P. Evstigneev, et al., J. Mol. Struct. 843, 78 (2007).
12. V. V. Kostjukov, A. O. Lantushenko, M. P. Evstigneev, et al., Biophys. Chem. 129, 56 (2007).
13. V. V. Kostjukov, N. M. Khomytova, and M. P. Evstigneev, Biopolymers 91, 773 (2009).
14. H. M. Berman, J. Westbrook, Z. Feng, et al., Nucleic Acids Res. 28, 235 (2000).
15. Gaussian, Inc., 2004. Gaussian 03. Gaussian, Wallingford, CT.
16. G. J. Kleywegt, News from Uppsala Software Factory 5 (1998).
17. P. Padrta, R. Stefl, L. Kralik, et al., J. Biomol. NMR 24, 1 (2002).
18. W. D. Cornell, P. Cieplak, C. I. Bayly, et al., J. Am. Chem. Soc. 117, 5179 (1995).
19. A. T. Brunger, X-PLOR. A System for X-ray Crystallography and NMR (Univ. Press, Yale, 1992).
20. A. V. Teplukhin, V. I. Poltev, and V. P. Chuprina, Biopolymers 31, 1445 (1991).
21. M. Baginski, F. Fogolari, and J. M. Briggs, J. Mol. Biol. 274, 253 (1997).
22. V. K. Misra and B. Honig, Proc. Natl. Acad. Sci. USA 92, 4691 (1995).
23. G. I. Makhatadze and P. L. Privalov, Adv. Protein Chem. 47, 307 (1995).
24. P. Kollman, Chem. Rev. 93, 2395 (1993).
25. R. Elber, A. Roitberg, C. Simmerling, et al., Comp. Phys. Commun. 91, 159 (1995).
26. W. Rocchia, E. Alexov, and B. Honig, J. Phys. Chem. B 105, 6507 (2001).
27. V. V. Kostjukov, N. M. Khomytova, M. P. Evstigneev, et al., Biopolymers 89, 680 (2008).
28. J. B. Chaires, Anti-Cancer Drug Des. 11, 569 (1996).
29. G. J. Quigley, A. H.-J. Wang, G. Ughetto et al., Proc. Natl. Acad. Sci. USA 77, 7204 (1980).
30. W. Fuller and M. J. Waring, Ber. Bunsen Ges. Phys. Chem. 68, 805 (1964).
31. K.-X. Chen, N. Gresh, and B. Pullman, Nucl. Acids Res. 14, 3799 (1986).
32. A. Aggarwal, S. A. Islam, R. Kuroda, et al., Biopolymers 23, 1025 (1984).
33. K. A. Sharp, A. Nicholls, R. F. Fine, et al., Science 252, 106 (1991).
34. B. Lee and F. M. Richards, J. Mol. Biol. 55, 379 (1971).
35. B. Tidor and M. Karplus, J. Mol. Biol. 238, 405 (1994).
36. A. Maczek, Statistical Thermodynamics (Univ. Press, Oxford, 1998).
37. I. Z. Steinberg and H. A. Scheraga, J. Biol. Chem. 238, 172 (1963).
38. V. V. Kostyukov, N. M. Khomutova, and M. P. Evstigneev, Biofizika 54, 606 (2009).
39. J. J. SantaLucia, Proc. Natl. Acad. Sci. USA 95, 1460 (1998).
40. R. A. Friedman and B. Honig, Biophys. J. 69, 1528 (1995).
41. K. J. Breslauer, D. P. Remeta, W.-Y. Chou, et al., Proc. Natl. Acad. Sci. USA 84, 8922 (1987).
42. S. Wang, T. Peng, and C. F. Yang, J. Biochem. Biophys. Methods 55, 191 (2003).
43. M. Aslanoglu, Analyt. Sci. 22, 439 (2006).