Inter and intrastrand vibrational coupling in DNA studied with heterodyned 2D-IR spectroscopy

Journal of Physical Chemistry B

Volumn 107, Issue 35, 2003, Pages 9165-9169

  Krummel, Amber T ^a   Mukherjee, Prabuddha ^a   Zanni, Martin T ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ELECTRON TRANSITIONS; EXCITONS; HYDROGEN BONDS; INFRARED SPECTROSCOPY; LASER PULSES; LIGHT POLARIZATION; MOLECULAR STRUCTURE; PHOTONS;

CYTIDINE; GUANOSINE; INTERSTRAND VIBRATIONAL COUPLING; INTRASTRAND VIBRATIONAL COUPLING;

MOLECULAR VIBRATIONS;

EID: 0141794723     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp035473h     Document Type: Letter

References (36)

1. Hamm, P.; Lim, M.; Hochstrasser, R. M. J. Phys. Chem. B 1998, 102, 6123.
2. Iwaki, L. K.; Dlott, D. D. J. Phys. Chem. A 2000, 104, 9101.
3. Zhao, W.; Wright, J. C. Phys. Rev. Lett. 2000, 84, 1411.
4. Golonzka, O.; Khalil, M.; Demirdöven, N.; Tokmakoff, A. Phys. Rev. Lett. 2001, 86, 2154.
5. Hybl, J. D.; Albrecht Ferro, A.; Jonas, D. M. J. Chem. Phys. 2001, 115, 6606.
6. Stenger, J.; Madsen, D.; Hamm, P.; Nibbering, E. T. J.; Elsaesser, T. Phys. Rev. Lett. 2001, 87, 027401.
7. Thompson, D. E.; Merchant, K. A.; Fayer, M. D. J. Chem. Phys. 2001, 115, 317.
8. Zanni, M. T.; Gnanakaran, S.; Stenger, J.; Hochstrasser, R. M. J. Phys. Chem. B 2001, 105, 6520.
9. Kaufman, L. J.; Heo, J.; Ziegler, L. D.; Fleming, G. R. Phy. Rev. Lett. 2002, 88, 207402/1.
10. Piryatinski, A.; Tretiak, S.; Chernyak, V.; Mukamel, S. J. Raman Spectrosc. 2000, 31, 125.
11. Cho, M. J. Chem. Phys. 2001, 115, 4424.
12. Herzberg, G. Infrared and Raman spectra of polyatomic molecules; D. Van Nostrand Co.: New York, 1945.
13. Torii, H.; Tasumi, M. J. Chem. Phys. 1993, 96, 3379.
14. Taillandier, E.; Liquier, J. Methods Enzymol, 1992, 211, 307.
15. Liquier, J.; Taillandier, E. Infrared Spectroscopy of nucleic acids. In Infrared Spectroscopy of Biomolecules; Mantsch, H. H., Chapman, D., Eds.; Wiley-Liss: New York, 1996; p 131.
16. Howard, F. B.; Frazier, J.; Miles, H. T. Proc. Natl. Acad. Sci. U.S.A. 1969, 64, 451.
17. Tsuboi, M.; Takahashi, S. Infrared and Raman spectra of nucleic acids - vibrations in the base-residues. In Physicochemical properties of nucleic acids; 1973; Vol. 2, p 91.
18. Manuscript in preparation.
19. 3 delays were scanned 2000 and 3000 fs, respectively, in 18 fs steps. The signal-to-noise ratio is approximately 150:1.
20. 2 plates spaced 25 μm apart resulting in optical densities near 0.1.
21. 4 is A-form (Eisenstein, E.; Shakked, Z. J. Mol. Biol. 1995, 248, 662).
22. The ratio of the G diagonal peaks in <0°,0°0°0°> and <0°,90°,-90°,0°> is 2.5. The theoretical ratio is 3.0 for single oscillators, but cross-peaks are also present, as discussed with regard to <45°,-45°,90°,0°>.
23. Zanni, M. T.; Asplund, M. C.; Hochstrasser, R. M. J. Chem. Phys. 2001, 114, 4579.
24. Golonzka, O.; Tokmakoff, A. J. Chem. Phys. 2001, 115, 297.
25. Zanni, M. T.; Ge, N.-H.; Kim, Y. S.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11265.
26. Arnott, S.; Hukins, D. W. L. Biochem. Biophys. Res. Commun. 1972, 47, 1504.
27. Higgs, P. W. Proc. R. Soc. (London) 1953, A220, 472.
28. Miyazawa, T. J. Chem. Phys. 1960, 32, 1647.
29. Moffitt, W. J. Chem. Phys. 1956, 25, 467.
30. Geometry optimization and frequency calculations were performed with Gaussian 98 using density functional theory with B3LYP functionals and 6-31+G(d) basis functions.
31. 1, respectively.
32. Clockwise and counterclockwise, respectively, in structure I.
33. Cθ by 10° gave a significantly poorer fit.
34. Santamaria, R.; Charro, E.; Zacarías, A.; Castro, M. J. Comput. Chem. 1999, 20, 511.
35. Ge, N.-H.; Zanni, M. T.; Hochstrasser, R. M. J. Phys. Chem. A 2002, 106, 962.
36. Demirdoven, N.; Khalil, M.; Tokmakoff, A. Phy. Rev. Lett. 2002, 89, 237401/1.