The effect of solvent dynamics on the low frequency collective motions of DNA in solution and unoriented films

Journal of Chemical Physics

Volumn 124, Issue 22, 2006, Pages

  Woods, K N ^a   Lee, S A ^b   Holman, H Y N ^a   Wiedemann, H ^c,d  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF TOLEDO   (United States)

^c STANFORD UNIVERSITY   (United States)

^d SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FAR-INFRARED SPECTRA; GLASS FORMING POLYMERS; SOLVENT DYNAMICS; UNORIENTED FILMS;

GLASS; HYDRATION; INFRARED SPECTROSCOPY; SOLUTIONS; SOLVENT EXTRACTION; THIN FILMS;

DNA;

ALCOHOL; DNA; GLASS; POLYMER; SOLVENT;

ANIMAL; ARTICLE; BIOPHYSICS; CATTLE; CHEMISTRY; CONFORMATION; HYDROGEN BOND; INFRARED SPECTROPHOTOMETRY; METABOLISM; METHODOLOGY; PHYSICAL CHEMISTRY; TEMPERATURE; THYMUS;

ANIMALS; BIOPHYSICS; CATTLE; CHEMISTRY, PHYSICAL; DNA; ETHANOL; GLASS; HYDROGEN BONDING; MOLECULAR CONFORMATION; POLYMERS; SOLVENTS; SPECTROPHOTOMETRY, INFRARED; TEMPERATURE; THYMUS GLAND;

EID: 33745172796     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2200349     Document Type: Article

References (63)

1. E. W. Prohofsky, Phys. Rev. A 1050-2947 10.1103/PhysRevA.38.1538 38, 1538 (1988); E. W. Prohofsky, Comments Mol. Cell. Biophys. 2, 65 (1983).
2. E. W. Prohofsky, Phys. Rev. A 1050-2947 10.1103/PhysRevA.38.1538 38, 1538 (1988); E. W. Prohofsky, Comments Mol. Cell. Biophys. 2, 65 (1983).
3. H. Urabe and Y. Tominaga, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.50.3543 50, 3543 (1981); H. Urabe and Y. Tominaga, Biopolymers 0006-3525 10.1002/bip.360211212 21, 2477 (1982); S. M. Lindsay, S. A. Lee, J. W. Powell, T. Weidlich, C. DeMarco, G. D. Lewen, N. J. Tao, and A. Rupprecht, Biopolymers 0006-3525 10.1002/bip.360270610 27, 1015 (1988); T. Wiedlech and S. M. Lindsay, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.61.1674 61, 1674 (1988); T. Wiedlech and S. M. Lindsay, J. Phys. Chem. 92, 6479 (1988).
4. H. Urabe and Y. Tominaga, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.50.3543 50, 3543 (1981); H. Urabe and Y. Tominaga, Biopolymers 0006-3525 10.1002/bip.360211212 21, 2477 (1982); S. M. Lindsay, S. A. Lee, J. W. Powell, T. Weidlich, C. DeMarco, G. D. Lewen, N. J. Tao, and A. Rupprecht, Biopolymers 0006-3525 10.1002/bip.360270610 27, 1015 (1988); T. Wiedlech and S. M. Lindsay, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.61.1674 61, 1674 (1988); T. Wiedlech and S. M. Lindsay, J. Phys. Chem. 92, 6479 (1988).
5. H. Urabe and Y. Tominaga, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.50.3543 50, 3543 (1981); H. Urabe and Y. Tominaga, Biopolymers 0006-3525 10.1002/bip.360211212 21, 2477 (1982); S. M. Lindsay, S. A. Lee, J. W. Powell, T. Weidlich, C. DeMarco, G. D. Lewen, N. J. Tao, and A. Rupprecht, Biopolymers 0006-3525 10.1002/bip.360270610 27, 1015 (1988); T. Wiedlech and S. M. Lindsay, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.61.1674 61, 1674 (1988); T. Wiedlech and S. M. Lindsay, J. Phys. Chem. 92, 6479 (1988).
6. H. Urabe and Y. Tominaga, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.50.3543 50, 3543 (1981); H. Urabe and Y. Tominaga, Biopolymers 0006-3525 10.1002/bip.360211212 21, 2477 (1982); S. M. Lindsay, S. A. Lee, J. W. Powell, T. Weidlich, C. DeMarco, G. D. Lewen, N. J. Tao, and A. Rupprecht, Biopolymers 0006-3525 10.1002/bip.360270610 27, 1015 (1988); T. Wiedlech and S. M. Lindsay, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.61.1674 61, 1674 (1988); T. Wiedlech and S. M. Lindsay, J. Phys. Chem. 92, 6479 (1988).
7. H. Urabe and Y. Tominaga, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.50.3543 50, 3543 (1981); H. Urabe and Y. Tominaga, Biopolymers 0006-3525 10.1002/bip.360211212 21, 2477 (1982); S. M. Lindsay, S. A. Lee, J. W. Powell, T. Weidlich, C. DeMarco, G. D. Lewen, N. J. Tao, and A. Rupprecht, Biopolymers 0006-3525 10.1002/bip.360270610 27, 1015 (1988); T. Wiedlech and S. M. Lindsay, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.61.1674 61, 1674 (1988); T. Wiedlech and S. M. Lindsay, J. Phys. Chem. 92, 6479 (1988).
8. H. Urabe, M. Kato, Y. Tominaga, and K. Kajiwara, J. Chem. Phys. 92, 768 (1990).
9. H. Urabe, Y. Sugawara, M. Tsukakoshi, and T. Kasuya, J. Chem. Phys. 95, 5519 (1991).
10. H. Urabe, Y. Sugawara, M. Ataka, and A. Rupprecht, Biophys. J. 74, 1533 (1998).
11. N. J. Tao, S. M. Lindsay, and A. Rupprecht, Biopolymers 27, 1655 (1988).
12. T. Weidlich, S. M. Lindsay, O. Rui, A. Rupprecht, W. L. Peticolas, and G. A. Thomas, J. Biomol. Struct. Dyn. 8, 139 (1990).
13. A. Wittlin, L. Genzel, F. Kremer, S. Haeseler, A. Poglitsch, and A. Rupprecht, Phys. Rev. A 1050-2947 10.1103/PhysRevA.34.493 34, 493 (1986); J. W. Powell, G. S. Edwards, L. Genzel, F. Kremer, A. Wittlin, W. Kubasek, and W. Peticolas, Phys. Rev. A 1050-2947 10.1103/PhysRevA.35.3929 35, 3929 (1987); T. Weidlich, J. Powell, L. Genzel, and A. Rupprecht, Biopolymers 30, 477 (1990).
14. A. Wittlin, L. Genzel, F. Kremer, S. Haeseler, A. Poglitsch, and A. Rupprecht, Phys. Rev. A 1050-2947 10.1103/PhysRevA.34.493 34, 493 (1986); J. W. Powell, G. S. Edwards, L. Genzel, F. Kremer, A. Wittlin, W. Kubasek, and W. Peticolas, Phys. Rev. A 1050-2947 10.1103/PhysRevA.35.3929 35, 3929 (1987); T. Weidlich, J. Powell, L. Genzel, and A. Rupprecht, Biopolymers 30, 477 (1990).
15. A. Wittlin, L. Genzel, F. Kremer, S. Haeseler, A. Poglitsch, and A. Rupprecht, Phys. Rev. A 1050-2947 10.1103/PhysRevA.34.493 34, 493 (1986); J. W. Powell, G. S. Edwards, L. Genzel, F. Kremer, A. Wittlin, W. Kubasek, and W. Peticolas, Phys. Rev. A 1050-2947 10.1103/PhysRevA.35.3929 35, 3929 (1987); T. Weidlich, J. Powell, L. Genzel, and A. Rupprecht, Biopolymers 30, 477 (1990).
16. Y. Gao, K. V. Devi-Prasad, and E. W. Prohofsky, J. Chem. Phys. 80, 6291 (1984).
17. Y. Z. Chen and E. W. Prohofsky, Biopolymers 35, 573 (1995).
18. T. Weidlich, S. M. Lindsay, and A. Rupprecht, Phys. Rev. Lett. 61, 1674 (1988).
19. P. Kung, H. C. Lihn, D. Bocek, and H. Wiedemann, Phys. Rev. Lett. 73, 967 (1994).
20. H. C. Lihn, D. Bocek, M. Hernandez, P. Kung, C. Settakorn, and H. Wiedemann, Phys. Rev. E 1063-651X 10.1103/PhysRevE.53.6413 53, 6413 (1996); H. Wiedemann, D. Bocek, M. Hernandez, and C. Settakorn, J. Nucl. Mater. 248, 374 (1997).
21. H. C. Lihn, D. Bocek, M. Hernandez, P. Kung, C. Settakorn, and H. Wiedemann, Phys. Rev. E 1063-651X 10.1103/PhysRevE.53.6413 53, 6413 (1996); H. Wiedemann, D. Bocek, M. Hernandez, and C. Settakorn, J. Nucl. Mater. 248, 374 (1997).
22. M. N. Afsar and J. B. Hasted, Infrared Phys. 18, 835 (1978).
23. J. R. Birch and M. Bennouna, Infrared Phys. 21, 229 (1981).
24. M. C. Martin and W. R. McKinney, Proc. Mater. Res. Soc. 524, 11 (1998); H.-Y. N. Holman, M. C. Martin, and W. R. McKinney, Spectroscopy-An International Journal 17, 139 (2003).
25. M. C. Martin and W. R. McKinney, Proc. Mater. Res. Soc. 524, 11 (1998); H.-Y. N. Holman, M. C. Martin, and W. R. McKinney, Spectroscopy-An International Journal 17, 139 (2003).
26. D. A. Pearlman, D. A. Case, J. W. Caldwell, W. R. Ross, I. T. E. Cheatham, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman, Comput. Phys. Commun. 91, 1 (1995).
27. S. Cocco, J. Chem. Phys. 112, 10017 (2000).
28. W. Gotze, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/11/10A/ 002 11, A1 (1999); W. Gotze and L. Sjogren, Rep. Prog. Phys. 55, 241 (1992).
29. W. Gotze, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/11/10A/ 002 11, A1 (1999); W. Gotze and L. Sjogren, Rep. Prog. Phys. 55, 241 (1992).
30. L. Wu, Phys. Rev. B 0163-1829 10.1103/PhysRevB.43.9906 43, 9906 (1991); A. Arbe, D. Richter, J. Colmenero, and B. Farago, Phys. Rev. E 54, 3853 (1996).
31. L. Wu, Phys. Rev. B 0163-1829 10.1103/PhysRevB.43.9906 43, 9906 (1991); A. Arbe, D. Richter, J. Colmenero, and B. Farago, Phys. Rev. E 54, 3853 (1996).
32. G. P. Johari and M. Goldstein, J. Chem. Phys. 0021-9606 10.1063/1.1674335 53, 2372 (1970); G. P. Johari and M. Goldstein, J. Chem. Phys. 55, 4245 (1971).
33. G. P. Johari and M. Goldstein, J. Chem. Phys. 0021-9606 10.1063/1.1674335 53, 2372 (1970); G. P. Johari and M. Goldstein, J. Chem. Phys. 55, 4245 (1971).
34. C. A. Angell, J. Non-Cryst. Solids 73, 1 (1985); in Relaxation in Complex Systems, edited by, K. Nagai, and, G. B. Wright, (National Technical Information Service, U.S. Department of Commerce, Springfield, 1985).
35. C. A. Angell, J. Non-Cryst. Solids 73, 1 (1985); in Relaxation in Complex Systems, edited by, K. Nagai, and, G. B. Wright, (National Technical Information Service, U.S. Department of Commerce, Springfield, 1985).
36. M. Kruger, M. Soltwisch, I. Petscherizin, and D. Quitmann, J. Chem. Phys. 96, 7352 (1992).
37. A. Sjolander, in Static and Dynamic Properties in Liquids, edited by, M. Davidovic, and, A. K. Soper, (Springer, Berlin, 1989), p. 90.
38. G. Meier, F. Fujara, and W. Petrys, Macromolecules 22, 4421 (1989).
39. M. Billeter, P. Guntert, P. Luginbuhl, and K. Wuthrich, Cell 85, 1057 (1996).
40. A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, and W. A. Eatron, Science 0036-8075 256, 1796 (1992); D. Beece, L. Eisenstein, H. Frauenfelder, D. Good, M. C. Marden, L. Reinisch, A. H. Reynolds, and K. T. Yue, Biochemistry 0006-2960 10.1021/bi00564a001 19, 5147 (1980); S. J. Hagen, J. Hofrichter, and W. A. Eaton, J. Phys. Chem. 100, 12008 (1996).
41. A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, and W. A. Eatron, Science 0036-8075 256, 1796 (1992); D. Beece, L. Eisenstein, H. Frauenfelder, D. Good, M. C. Marden, L. Reinisch, A. H. Reynolds, and K. T. Yue, Biochemistry 0006-2960 10.1021/bi00564a001 19, 5147 (1980); S. J. Hagen, J. Hofrichter, and W. A. Eaton, J. Phys. Chem. 100, 12008 (1996).
42. A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, and W. A. Eatron, Science 0036-8075 256, 1796 (1992); D. Beece, L. Eisenstein, H. Frauenfelder, D. Good, M. C. Marden, L. Reinisch, A. H. Reynolds, and K. T. Yue, Biochemistry 0006-2960 10.1021/bi00564a001 19, 5147 (1980); S. J. Hagen, J. Hofrichter, and W. A. Eaton, J. Phys. Chem. 100, 12008 (1996).
43. P. W. Fenimore, H. Frauenfelder, B. H. McMahon, and R. D. Young, Proc. Natl. Acad. Sci. U.S.A. 101, 14408 (2004).
44. S. K. Pal, L. Zhao, and A. H. Zewail, Proc. Natl. Acad. Sci. U.S.A. 100, 2003 (2003);
45. S. K. Pal, L. Zhao, T. Xia, and A. H. Zewail, Proc. Natl. Acad. Sci. U.S.A. 100, 13746 (2003).
46. W. Saenger, W. N. Hunter, and O. Kennard, Nature (London) 324, 385 (1986).
47. C. R. Robinson and S. G. Sligar, J. Mol. Biol. 234, 302 (1993).
48. P. W. Fenimore, H. Frauenfelder, B. H. McMahon, and F. G. Parak, Proc. Natl. Acad. Sci. U.S.A. 99, 16047 (2002).
49. T. Kleinert, W. Doster, H. Leyser, W. Petry, V. Schwarz, and M. Settles, Biochemistry 0006-2960 10.1021/bi971508q 37, 717 (1998); C. Andreani, A. Filabozzi, F. MEnzinger, A. Desideri, A. Deriu, and D. D. Cola, Biophys. J. 68, 2519 (1995).
50. T. Kleinert, W. Doster, H. Leyser, W. Petry, V. Schwarz, and M. Settles, Biochemistry 0006-2960 10.1021/bi971508q 37, 717 (1998); C. Andreani, A. Filabozzi, F. MEnzinger, A. Desideri, A. Deriu, and D. D. Cola, Biophys. J. 68, 2519 (1995).
51. G. Caliskan, D. Mehtani, J. H. Roh, A. Kisliuk, A. P. Sokolov, S. Azzam, M. T. Cicerone, S. Lin-Gibson, and I. Peral, J. Chem. Phys. 121, 1978 (2004).
52. M. Sun, S. Pejanovic, and J. Mijovic, Macromolecules 38, 9854 (2005).
53. I. Bahar, B. Badur, and P. Donuker, J. Chem. Phys. 0021-9606 99, 2235 (1993); Y. E. Ryabov, Y. Feldman, N. Shinyashiki, and S. Yagihara, J. Chem. Phys. 116, 8610 (2002).
54. I. Bahar, B. Badur, and P. Donuker, J. Chem. Phys. 0021-9606 99, 2235 (1993); Y. E. Ryabov, Y. Feldman, N. Shinyashiki, and S. Yagihara, J. Chem. Phys. 116, 8610 (2002).
55. M. Banyay, M. Sarkar, and A. Graslund, Biophys. J. 104, 477 (2003).
56. 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.
57. L. Yang, I. Lee, C. Wang, Q. Li, and C. Bai, J. Mol. Struct. 442, 275 (1998).
58. S. Flock, R. Labarbe, and C. Houssier, J. Biomol. Struct. Dyn. 0739-1102 13, 87 (1995); J. L. Sikorav, J. Pelta, and F. Livolant, Biophys. J. 0006-3495 67, 1387 (1994); P. G. Arscott, C. Ma, J. R. Wenner, and V. A. Bloomfield, Biopolymers 36, 345 (1995).
59. S. Flock, R. Labarbe, and C. Houssier, J. Biomol. Struct. Dyn. 0739-1102 13, 87 (1995); J. L. Sikorav, J. Pelta, and F. Livolant, Biophys. J. 0006-3495 67, 1387 (1994); P. G. Arscott, C. Ma, J. R. Wenner, and V. A. Bloomfield, Biopolymers 36, 345 (1995).
60. S. Flock, R. Labarbe, and C. Houssier, J. Biomol. Struct. Dyn. 0739-1102 13, 87 (1995); J. L. Sikorav, J. Pelta, and F. Livolant, Biophys. J. 0006-3495 67, 1387 (1994); P. G. Arscott, C. Ma, J. R. Wenner, and V. A. Bloomfield, Biopolymers 36, 345 (1995).
61. B. M. Ladanyi and M. Skaf, J. Phys. Chem. 100, 1368 (1996).
62. R. Bohmer, G. Hinze, T. Jorg, F. Qui, and H. Sillescu, J. Phys.: Condens. Matter 12, A383 (2000);
63. R. Richert, Europhys. Lett. 54, 767 (2001).