Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

Journal of Chemical Physics

Volumn 125, Issue 11, 2006, Pages

  Lee, Chewook ^a   Cho, Minhaeng ^a  

^a Korea University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION SPECTROSCOPY; AROMATIC COMPOUNDS; ATOMIC PHYSICS; DEUTERIUM; MOLECULAR DYNAMICS; PROBABILITY DENSITY FUNCTION; SPECTRUM ANALYSIS;

BASE DERIVATIVES; DENSITY FUNCTIONAL THEORY; DEUTERIUM ATOMS; WATSON-CRICK BASE PAIRS;

DNA;

DEUTERIUM; DNA; NUCLEOTIDE;

ARTICLE; BASE PAIRING; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; VIBRATION;

BASE PAIRING; COMPUTER SIMULATION; DEUTERIUM; DNA; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; VIBRATION;

EID: 33749032401     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2213258     Document Type: Article

References (59)

1. C. Lee, K.-H. Park, and M. Cho, J. Chem. Phys. 125, 114508 (2006), preceding paper.
2. F. Geinguenaud, J. Liquier, M. G. Bervnov, O. V. Petrauskene, Y. I. Alexeev, E. S. Gromova, and E. Taillandier, Biochemistry 39, 12650 (2000).
3. W. Pohle and H. Fritzsche, Nucleic Acids Res. 8, 2527 (1980).
4. G. J. Thomas, Jr., and J. M. Benevides, Biopolymers 24, 1101 (1985).
5. T. J. Thamann, R. C. Lord, A. H. J. Wang, and A. Rich, Nucleic Acids Res. 9, 5443 (1981).
6. J. A. Taboury and E. Taillandier, Nucleic Acids Res. 13, 4469 (1985).
7. J. Liquier, E. Taillandier, W. L. Peticolas, and G. A. Thomas, J. Biomol. Struct. Dyn. 8, 295 (1990).
8. J. Pilet and J. Brahms, Biopolymers 12, 387 (1973).
9. M. Semenov, T. Bolbukh, and V. Maleev, J. Mol. Struct. 408/409, 213 (1997).
10. E. Taillandier and J. Liquier, Methods Enzymol. 211, 307 (1992).
11. L. Urpi, J. P. Ridoux, J. Liquier, N. Verdaguer, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh-Dinh, J. Igolen, and E. Taillandier, Nucleic Acids Res. 17, 6669 (1989).
12. J. Šponer, J. Leszczyński, and P. Hobza, J. Phys. Chem. 100, 5590 (1996).
13. Y. Nishimura, M. Tsuboi, T. Sato, and K. Aoki, J. Mol. Struct. 146, 123 (1986).
14. H. T. Miles and J. Fraizier, Biochemistry 17, 2920 (1978).
15. E. Taillandier, J.-P. Ridoux, J. Liquier, W. Leupin, W. A. Denny, Y. Wang, G. A. Thomas, and W. L. Peticolas, Biochemistry 26, 3361 (1987).
16. M. J. Nowack, H. Rostkowska, L. Lapinski, J. S. Kwiatkowski, and J. Leszczynski, Spectrochim. Acta, Part A 50, 1081 (1994).
17. M.-C. Lin, P. Eid, P. T. T. Wong, and R. B. Macgregor, Jr., Biophys. Chem. 76, 87 (1999).
18. V. Hrouda, J. Florián, and P. Hobza, J. Phys. Chem. 97, 1542 (1993).
19. M.-P. Gaigeot and M. Sprik, J. Phys. Chem. B 107, 10344 (2003).
20. M. J. Nowak, L. Lapinski, J. S. Kwiatkowski, and J. Leszczynski, J. Phys. Chem. 100, 3527 (1996).
21. E. D. Radchenko, G. G. Sheina, N. A. Smorygo, and Yu. P. Blagoi, J. Mol. Struct. 116, 387 (1984).
22. K. Schoone, G. Maes, and L. Adamowicz, J. Mol. Struct. 480-481, 505 (1999).
23. B. Morzyk-Ociepa, M. J. Nowak, and D. Michalska, Spectrochim. Acta, Part A 60, 2113 (2004).
24. R. Santamaria, E. Charro, A. Zacarías, and M. Castro, J. Comput. Chem. 20, 511 (1999).
25. M. Banyay, M. Sarkar, and A. Gräslund, Biophys. Chem. 104, 477 (2003).
26. M. Tsuboi and S. Takahashi, in Physico-chemical Properties of Nucleic Acids, edited by J. Duchesne (Academic, London, 1973), Vol. 2, p. 91.
27. F. B. Howard, J. Frazier, and H. T. Miles, Proc. Natl. Acad. Sci. U.S.A. 64, 451 (1969).
28. A. T. Krummel, P. Mukherjee, and M. T. Zanni, J. Phys. Chem. B 107, 9165 (2003).
29. Y. Zhang, H. Zhou, and Z.-C. Ou-Yang, Biophys. Chem. 81, 1133 (2001).
30. A. V. Kabanov, V. M. Komarov, L. V. Yakushevich, and A. V. Teplukhin, Int. J. Quantum Chem. 100, 595 (2004).
31. A. Pelmenschikov, D. M. Hovorun, and J. Leszczynski, J. Chem. Phys. 113, 5986 (2000).
32. F. Moroni, A. Famulari, and M. Raimondi, J. Phys. Chem. A 105, 1169 (2001).
33. D. Sivanesan, I. Sumathi, and W. Welsh, Chem. Phys. Lett. 367, 351 (2003).
34. A. A. Maevski and B. I. Sukhorukov, Nucleic Acids Res. 8, 3029 (1980).
35. S. L. Zhang, K. H. Michaelian, and G. R. Loppnow, J. Phys. Chem. A 102, 461 (1998).
36. M. Egli, V. Tereshko, M. Teplova et al., Biopolymers 48, 234 (1998).
37. C. Mayer-Jung, D. Moras, and Y. Timsit, EMBO J. 17, 2709 (1998).
38. A. Pevsner and M. Diem, Biopolymers 72, 282 (2003).
39. M. Kabeláč, L. Zendlová, D. Řeha, and P. Hobza, J. Phys. Chem. B 109, 12206 (2005).
40. M. Kabeláč, F. Ryjáček, and P. Hobza, Phys. Chem. Chem. Phys. 2, 4906 (2000).
41. S. L. Lee, P. G. Debenedetti, J. R. Errington, B. A. Pethica, and D. J. Moore, J. Phys. Chem. B 108, 3098 (2004).
42. T. van Mourik, Phys. Chem. Chem. Phys. 3, 2886 (2001).
43. E. Gonzalez-Jiménes, I. Castro-Valdez, E. Lopez-Apresa, S. V. Filippov, A. V. Teplukhin, and V. I. Poltev, J. Mol. Struct.: THEOCHEM 493, 301 (1999).
44. S. A. Trygubenko, T. V. Bogdan, M. Rueda, M. Orozco, F. J. Luque, J. Šponer, P. Slavíček, and P. Hobza, Phys. Chem. Chem. Phys. 4, 4192 (2002).
45. M. Hanus, F. Ryjáček, M. Kabeláč, T. Kubař, T. V. Bogdan, S. A. Trygubenko, and P. Hobza, J. Am. Chem. Soc. 125, 7678 (2003).
46. M. Hanus, M. Kabeláč, J. Rejnek, F. Ryjáček, and P. Hobza, J. Phys. Chem. B 108, 2087 (2004).
47. J. Rejnek, M. Hanus, M. Kabeláč, F. Ryjáček, and P. Hobza, Phys. Chem. Chem. Phys. 7, 2006 (2005).
48. J. Liquier and E. Taillandier, in Infrared Spectroscopy of Biomolecules, edited by H. H. Mantsch and D. Chapman, (Wiley-Liss, New York, 1996), p. 131.
49. M. Tsuboi, in Applied Spectroscopy Reviews, edited by E. G. Brame, Jr., (Dekker, New York, 1969), Vol. 3, p. 45.
50. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 03, Revision C.02, Gaussian, Inc., Wallingford, CT, 2004.
51. A. P. Scott and L. Radom, J. Phys. Chem. 100, 16502 (1996).
52. S. Ham and M. Cho, J. Chem. Phys. 118, 6915 (2003).
53. S. Ham, S. Cha, J.-H. Choi, and M. Cho, J. Chem. Phys. 119, 1451 (2003).
54. J.-H. Choi and M. Cho, J. Chem. Phys. 120, 4383 (2004).
55. S. Ham, S. Hahn, C. Lee, T.-K. Kim, K. Kwak, and M. Cho, J. Phys. Chem. B 108, 9333 (2004).
56. J.-H. Choi, S. Ham, and M. Cho, J. Phys. Chem. B 107, 9132 (2003).
57. C. Lee and M. Cho, J. Phys. Chem. B 108, 20397 (2004).
58. J.-H. Choi, S. Hahn, and M. Cho, Int. J. Quantum Chem. 104, 616 (2005).
59. C. Lee, K.-H. Park, J.-A. Kim, S. Hahn, and M. Cho, J. Chem. Phys. 125, 114510 (2006), following paper.