Vibrational dynamics of DNA: IV. Vibrational spectroscopic characteristics of A-, B-, and Z-form DNA's

Journal of Chemical Physics

Volumn 126, Issue 14, 2007, Pages

  Lee, Chewook ^c   Cho, Minhaeng ^a,b  

^a Korea University   (South Korea)

^b Korea Basic Science Institute (KBSI)   (South Korea)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DENSITY FUNCTIONAL THEORY; INFRARED SPECTROSCOPY; MOLECULAR SPECTROSCOPY; MOLECULAR VIBRATIONS; NUCLEIC ACIDS;

COUPLING CONSTANTS; VIBRATIONAL COUPLINGS; VIBRATIONAL DYNAMICS; VIBRATIONAL SPECTROSCOPIC CHARACTERISTICS;

DNA SEQUENCES;

DNA;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; KINETICS; STRUCTURE ACTIVITY RELATION; ULTRASTRUCTURE; VIBRATION;

COMPUTER SIMULATION; DNA; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP; VIBRATION;

EID: 34247279814     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2715602     Document Type: Article

References (65)

1. R. E. Dickerson, Methods Enzymol. 211, 67 (1992).
2. A. H. J. Wang, G. J. Quigley, F. J. Kolpak, J. L. Crawford, J. H. Vanboom, G. Vandermarel, and A. Rich, Nature (London) 282, 680 (1979).
3. S. Adam, P. Bourtayre, J. Liquier, and E. Taillandier, Nucleic Acids Res. 14, 3501 (1986).
4. J. A. Taboury, S. Adam, E. Taillandier, J. M. Neumann, S. Tran-Dinh, T. Huynh-Dinh, B. Langlois d'Estaintot, M. Conti, and J. Igolen, Nucleic Acids Res. 12, 6291 (1984).
5. J. A. Taboury, P. Bourtayre, J. Liquier, and E. Taillandier, Nucleic Acids Res. 12, 4247 (1984).
6. J. A. Taboury and E. Taillandier, Nucleic Acids Res. 13, 4469 (1985).
7. E. Taillandier, S. Adam, J. P. Ridoux, and J. Liquier, Nucleic Acids Res. 16, 5621 (1988).
8. E. Taillandier and J. Liquier, Methods Enzymol. 211, 307 (1992).
9. E. Taillandier, J. Liquier, and J. A. Taboury, Adv. Infrared Raman Spectrosc., 12, 65 (1985).
10. 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).
11. E. Taillandier, J. A. Taboury, S. Adam, and J. Liquier, Biochemistry 23, 5703 (1984).
12. L. Urpi, J. P. Ridoux, J. Liquier, N. Verdaguer, I. Fita, J. A. Subirana, F. Iglesias, T. Huynhdinh, J. Igolen, and E. Taillandier, Nucleic Acids Res. 17, 6669 (1989).
13. S. Adam, J. Liquier, J. A. Taboury, and E. Taillandier, Biochemistry 25, 3220 (1986).
14. M. Banyay, M. Sarkar, and A. Graslund, Biophys. Chem. 104, 477 (2003).
15. V. Hrouda, J. Florian, and P. Hobza, J. Phys. Chem. 97, 1542 (1993).
16. Y. Nishimura, M. Tsuboi, T. Sato, and K. Aoki, J. Mol. Struct. 146, 123 (1986).
17. M. J. Nowak, H. Rostkowska, L. Lapinski, J. S. Kwiatkowski, and J. Leszczynski, Spectrochim. Acta, Part A 50, 1081 (1994).
18. J. Pilet and M. Leng, Proc. Natl. Acad. Sci. U.S.A. 79, 26 (1982).
19. A. V. Kabanov, V. M. Komarov, L. V. Yakushevich, and A. V. Teplukhin, Int. J. Quantum Chem. 100, 595 (2004).
20. R. Santamaria, E. Charro, A. Zacarias, and M. Castro, J. Comput. Chem. 20, 511 (1999).
21. K. Schoone, G. Maes, and L. Adamowicz, J. Mol. Struct. 481, 505 (1999).
22. J. Sponer, J. Leszczynski, and P. Hobza, J. Phys. Chem. 100, 5590 (1996).
23. T. J. Thamann, R. C. Lord, A. H. J. Wang, and A. Rich, Nucleic Acids Res. 9, 5443 (1981).
24. G. J. Thomas and J. M. Benevides, Biopolymera 24, 1101 (1985).
25. L. J. Wang and T. A. Keiderling, Biochemistry 31, 10265 (1992).
26. F. M. Pohl, A. Ranade, and M. Stockbur, Biochim. Biophys. Acta 335, 85 (1974).
27. V. Andrushchenko, H. Wieser, and P. Bour, J. Phys. Chem. B 106, 12623 (2002).
28. P. Bour, V. Andrushchenko, M. Kabelac, V. Maharaj, and H. Wieser, J. Phys. Chem. B 109, 20579 (2005).
29. A. T. Krummel and M. T. Zanni, J. Phys. Chem. B 110, 13991 (2006).
30. C. Lee, K.-H. Park, and M. Cho, J. Chem. Phys. 125, 114508 (2006).
31. C. Lee and M. Cho, J. Chem. Phys. 125, 114509 (2006).
32. C. Lee, K.-H. Park, J.-A. Kim, S. Hahn, and M. Cho, J. Chem. Phys. 125, 114510 (2006).
33. C. Lee and M. Cho, J. Phys. Chem. B 108, 20397 (2004).
34. J.-H. Choi, S. Hahn, and M. Cho, Int. J. Quantum Chem. 104, 616 (2005).
35. J.-H. Choi, S. Ham, and M. Cho, J. Phys. Chem. B 107, 9132 (2003).
36. J.-H. Choi and M. Cho, J. Chem. Phys. 120, 4383 (2004).
37. S. Ham, S. Cha, J.-H. Choi, and M. Cho, J. Chem. Phys. 119, 1451 (2003).
38. S. Ham and M. Cho, J. Chem. Phys. 118, 6915 (2003).
39. S. Ham, S. Hahn, C. Lee, T.-K. Kim, K. Kwak, and M. Cho, J. Phys. Chem. B 108, 9333 (2004).
40. A. T. Krummel, P. Mukherjee, and M. T. Zanni, J. Phys. Chem. B 107, 9165 (2003).
41. J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, J. Phys. Chem. B 107, 8654 (2003).
42. C. Fang and R. M. Hochstrasser, J. Phys. Chem. B 109, 18652 (2005).
43. C. Fang, J. Wang, Y. S. Kim, A. K. Charnley, W. Barber-Armstrong, A. B. Smith, S. M. Decatur, and R. M. Hochstrasser, J. Phys. Chem. B 108, 10415 (2004).
44. S. Gnanakaran and R. M. Hochstrasser, J. Am. Chem. Soc. 123, 12886 (2001).
45. P. Hamm, M. Lim, W. F. DeGrado, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. 96, 2036 (1999).
46. P. Hamm, M. H. Lim, and R. M. Hochstrasser, J. Phys. Chem. B 102, 6123 (1998).
47. Y. S. Kim, J. Wang, and R. M. Hochstrasser, J. Phys. Chem. B 109, 7511 (2005).
48. A. Piryatinski, S. Tretiak, V. Chernyak, and S. Mukamel, J. Raman Spectrosc. 31, 125 (2000).
49. J. P. Wang, J. X. Chen, and R. M. Hochstrasser, J. Phys. Chem. B 110, 7545 (2006).
50. M. T. Zanni, S. Gnanakaran, J. Stenger, and R. M. Hochstrasser, J. Phys. Chem. B 105, 6520 (2001).
51. C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, Nature (London) 444, 469 (2006).
52. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 03, Revision C.02, Gaussian, Inc., Wallingford, CT, 2004.
53. A. P. Scott and L. Radom, J. Phys. Chem. 100, 16502 (1996).
54. J. Avery, J. Mol. Struct.: THEOCHEM 48, 225 (1988).
55. A. S. Davydov, Theory of Molecular Excitons (Plenum, New York, 1971).
56. A. Asensio, N. Kobko, and J. J. Dannenberg, J. Phys. Chem. A 107, 6441 (2003).
57. J. Florian and J. Leszczynski, J. Am. Chem. Soc. 118, 3010 (1996).
58. N. Kurita, V. I. Danilov, and V. M. Anisimov, Chem. Phys. Lett. 404, 164 (2005).
59. N. A. Richardson, S. S. Wesolowski, and H. F. Schaefer, J. Phys. Chem. B 107, 848 (2003).
60. O. V. Shishkin, J. Sponer, and P. Hobza, J. Mol. Struct. 477, 15 (1999).
61. M. K. Shukla and J. Leszczynski, J. Phys. Chem. A 106, 4709 (2002).
62. J. Sponer, J. Leszczynski, and P. Hobza, J. Phys. Chem. 100, 1965 (1996).
63. T. E. Cheatham and P. A. Kollman, J. Mol. Biol. 259, 434 (1996).
64. R. Stefl, L. Trantirek, M. Vorlickova, J. Koca, V. Sklenar, and J. Kypr, J. Mol. Biol. 307, 513 (2001).
65. L. Trantirek, R. Stefl, M. Vorlickova, J. Koca, V. Sklenar, and J. Kypr, J. Mol. Biol. 297, 907 (2000).