Local THz time domain spectroscopy of duplex DNA via fluorescence of an embedded probe

Journal of Physical Chemistry B

Volumn 113, Issue 47, 2009, Pages 15619-15628

  Dallmann, André ^a   Pfaffe, Matthias ^a   Mügge, Clemens ^a   Mahrwald, Rainer ^a   Kovalenko, Sergey A ^a   Ernsting, Nikolaus P ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; NUCLEIC ACIDS; OPTICAL PUMPING;

BASE PAIRS; BOUND WATERS; DNA DUPLEXES; DUPLEX DNA; DYNAMIC SHIFT; EFFECTIVE LENGTH; EMBEDDED PROBES; EMISSION BANDS; FEMTOSECONDS; FLUORENE MOIETY; FREE WATER; HYDRATION WATER; LONG AXIS; MOLECULAR PROBES; OPTICAL PUMPS; SOLUTION STRUCTURES; SPECTRAL OSCILLATIONS; STOKES SHIFT; SUPRAMOLECULAR STRUCTURE; THZ TIME DOMAIN SPECTROSCOPY; TIME-RESOLVED; TIME-SCALES; VIBRATIONAL ACTIVITIES;

PROBES;

EID: 71549116385     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp906037g     Document Type: Article

References (86)

1. Wang, Q.; Schoenlein, R. W.; Peteanu, L. A.; Mathies, R. A.; Shank, C. V. Science 1994, 266, 422.
2. Klug, D. D.; Zgierski, M. Z.; Tse, J. S.; Liu, Z.; Kincaid, J. R.; Czarnecki, K.; Hemley, R. J. Proc Natl. Acad Sci. U.S.A. 2002, 99, 12526.
3. Austin, R. H.; Roberson, M. W.; Mansky, P. Phys. Rev. Lett. 1989, 62, 1912.
4. Xie, A.; van der Meer, A. F. G.; Austin, R. H. Phys. Rev. Lett. 2002, 88, 018102.
5. Prohofsky, E. W.; Lu, K. C.; Van Zandt, L. L.; Putnam, B. E. Phys. Lett. 1979, 70A, 492.
6. Cocco, S.; Monasson, R. J. Chem. Phys. 2000, 112, 10017.
7. Leipinsh, E.; Otting, G.; Wüthrich, K. Nucleic Acids Res. 1992, 20, 6549.
8. Shui, X.; McFail-Isom, L.; Hu, G. G.; Williams, L. D. Biochemistry 1998, 37, 8341.
9. Tavenier, H. L.; Fayer, M. D. J. Phys. Chem. 2000, 104, 1154.
10. Young, M. A.; Jayaram, B.; Beveridge, D. L. J. Am. Chem. Soc. 1997, 119, 59.
11. Manning, G. S.; Ray, J. J. Biomol. Struct. Dyn. 1998, 16, 461.
12. Gelbart, W. M. Phys. Today 2000, 53, 38.
13. Siriwong, K.; Voityuk, A. A.; Newton, M. D.; Rösch, N. J. Phys. Chem. B 2003, 107, 2595.
14. Auffinger, P.; Hshem, Y. Curr. Opin. Struct. Biol. 2007, 17, 325.
15. Grimm, H.; Rupprecht, A. Physica B 1997, 183, 234.
16. Maret, G.; Oldenbourg, R.; Winterling, G.; Dransfeld, K.; Rupprecht, A. Colloid Polym. Sci.. 1979, 257, 1017.
17. Urabe, H.; Hayashi, H.; Tominaga, Y.; Nishimura, Y.; Kubota, K.; Tsuboi, M. J. Chem. Phys. 1985, 82, 531.
18. Weidlich, T.; Lindsay, S. M.; Rui, Q.; Rupprecht, A.; Peticolas, W. L.; Thomas, G. A. J. Biomol. Struct. Dyn. 1990, 8, 139.
19. Edwards, G.; Liu, C. Phys. Rev. A 1991, 44, 2709.
20. Chen, Y. Z.; Prohofsky, E. W. Biopolymers 1995, 35, 573.
21. Globus, T.; Woolard, D.; Crowe, T. W.; Khromoval, T.; Gelmont, B.; Hesler, J. J. Phys. D: Appl. Phys. 2006, 39, 3405. and previous publications by these authors cited therein.
22. Jazerba, J.; Walker, G. C.; Johnson, A. E.; Barbara, P. F. Chem. Phys. 1991, 152, 57.
23. Brauns, E. B.; Madaras, M. L.; Coleman, R. S.; Murphy, C.. J.; Berg, M. A. Phys. Rev. Lett. 2002, 88, 158101.
24. Pal, S. K.; Zhao, L.; Zewail, A. H. Proc. Natl. Acad. Sci.. U.S.A. 2003, 100, 8113.
25. Pal, S. K.; Zhao, L.; Xia, T.; Zewail, A. H. Proc. Natl. Acad. Sci.. U.S.A. 2003, 100, 13746.
26. Andreatta, D.; Pérez Lustres, J. L.; Kovalenko, S. A.; Ernsting, N. P.; Murphy, C.. J.; Coleman, R. S.; Berg, M. A. J. Am. Chem. Soc. 2005, 127, 7270.
27. Andreatta, D.; Sen, S.; Pérez; Lustres, J. L.; Kovalenko, S. A.; Ernsting, N. P.; Murphy, C.. J.; Coleman, R. S.; Berg, M. A. J. Am. Chem. Soc. 2006, 128, 6885.
28. Bonvin, A. M. J. J.; Sunnerhagen, M.; Otting, G.; van Gunsteren, W. F. J. Mol. Biol. 1998, 282, 859.
29. Makarov, V.; Pettitt, B. M.; Feig, M. Acc. Chem. Res. 2002, 35, 376.
30. Nilsson, L.; Halle, B. Proc. Natl. Acad Sci.. U.S.A. 2005, 102, 13867.
31. Pal, S.; Maiti, P. K.; Bagchi, B.; Hynes, J. T. J. Phys. Chem. B 2006, 110, 26396.
32. (a) Pal, S.; Maiti, P. K.; Bagchi, B. J. Chem. Phys. 2006, 125, 234903.
33. (b) Pal, S.; Maiti, P. K.; Bagchi, B. J. Phys.: Condens. Matter 2005, 17, S4317.
34. Golosov, A. A.; Karplus, M. J. Phys. Chem. B 2007, 111, 1482.
35. Sen, S.; Andreatta, D.; Ponomarev, S. Y.; Beveridge, D. L.; Berg, M. A. J. Am. Chem. Soc. 2009, 131, 1724.
36. Furse, K. E.; Corcelli, S. A. J. Am. Chem. Soc. 2008, 130, 13103.
37. Horng, M. L.; Gardecki, J. A.; Papazyan, A.; Maroncelli, M. J. Phys. Chem. 1995, 99, 17311.
38. Zhao, L.; Pérez Lustres, J. L.; Farztdinov, V.; Ernsting, N. P. Phys. Chem. Chem. Phys. 2005, 7, 1716.
39. Ruthmann, J.; Kovalenko, S. A.; Ernsting, N. P.; Ouw, D. J. Chem. Phys. 1998, 109, 5466.
40. Karunakaran, V.; Pfaffe, M.; Ioffe, I.; Senyushkina, T.; Kovalenko, S. A.; Mahrwald, R.; Fartzdinov, V.; Sklenar, H.; Ernsting, N. P. J. Phys. Chem. A 2008, 112, 4294.
41. Pérez Lustres, J. L.; Kovalenko, S. A.; Mosquera, M.; Senyushkina, T.; Flasche, W.; Ernsting, N. P. Angew. Chem., Int. Ed. 2005, 44, 5635.
42. Generally, standard (68%) confidence intervals are given.
43. Freier, S. M.; Hill, K. O.; Dewey, T. G.; Marky, L. A.; Breslauer, K. J.; Turner, D. H. Biochemistry 1981, 20, 1419, and references therein.
44. Ivanov, V.; Zeng, Y; Zocchi, G. Phys. Rev. E 2004, 70, 051907.
45. Comparison of standard hybridization enthalpies, assuming a common standard hybridization entropy of-1.2 kJ/(mol K) from the nearestneighbor model. SantaLucia, J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1460.
46. Chen, J.; Dupradeau, F.-Y.; Case, D. A.; Turner, C. J.; Stubbe, J. Nucleic Acids Res. 2008, 36, 253.
47. Chen, J.; Dupradeau, F.-Y.; Case, D. A.; Turner, C. J.; Stubbe, J. Biochemistry 2007, 46, 3096.
48. Hoehn, S. T.; Turner, C. J.; Stubbe, J. Nucleic Acids Res. 2001, 29, 3413.
49. Lin, Z.; de los Santos, C. J. Mol. Biol. 2001, 308, 341.
50. Lin, Z.; Hung, K.-H.; Grollmann, A. P.; de los Santos, C. Nucleic Acids Res. 1998, 26, 2385.
51. Coppel, Y.; Berthet, N.; Coulombeau, C.; Coulombeau, C.; Garcia, J.; Lhomme, J. Biochemistry 1997, 36, 4817.
52. Gueron, M.; Kochoyan, M.; Leroy, J.-L. Nature 1987, 328, 89.
53. Blackledge, M. Prog. Nucl. Magn. Reson. Spectrosc. 2005, 46, 23.
54. Matray, T. J.; Kool, E. T. Nature 1999, 399, 704.
55. Smirnov, S.; Matray, T. J.; Kool, E. T.; de los Santos, C. Nucleic Acids Res. 2002, 30, 5561.
56. Singh, I.; Hecker, W.; Prasad, A. K.; Parmar, V. S.; Seitz, O. Chem Commun. 2002, 500.
57. Dobryakov, A. L.; Kovalenko, S. A.; Ernsting, N. P. J. Chem. Phys. 2003, 119, 988.
58. Dobryakov, A. L.; Kovalenko, S. A.; Ernsting, N. P. J. Chem. Phys. 2005, 123, 044502.
59. The inverted absorption spectrum.
60. cool = 1/312 ps.
61. -3, and 56%.
62. Siano, D. B.; Metzler, D. E. J. Chem. Phys. 1969, 51, 1856.
63. The time dependence of the other parameters is provided in the Supporting Information.
64. Sajadi, M.; Obernhuber, T.; Kovalenko, S. A.; Mosquera, M.; Dick, B.; Ernsting, N. P. J. Phys. Chem. A 2009, 113, 44.
65. -1 for DNA-HNF in water. In both cases, the blue flank of the early SE band is being monitored.
66. Elsaesser, T.; Huse, N.; Dreyer, J.; Dwyer, J. R.; Heyne, K.; Nibbering, E. T. J. Chem. Phys. 2007, 341, 175.
67. Dwyer, J. R.; Szyc, L.; Nibbering, E. T. J.; Elsaesser, T. J. Phys. Chem. B 2008, 112, 11194.
68. Kozich, V.; Szyc, £L.; Nibbering, E. T. J.; Werncke, W.; Elsaesser, T. Chem. Phys. Lett. 2009, 473, 171.
69. Rønne, C.; Keiding, S. R. J. Mol. Liq. 2002, 101, 199.
70. Zelsmann, H. R. J. Mol. Struct. 1995, 350, 95.
71. Bertie, J. E.; Lan, Z. Appl. Spectrosc. 1996, 50, 1047.
72. Yada, H.; Nagai, M.; Tanaka, K. Chem. Phys. Lett. 2008, 464, and references therein.
73. Bertie, J. E.; Ahmed, M. K.; Eysel, H. H. J. Phys. Chem. 1989, 93, 2210.
74. Cohen, G.; Rabani, E. private communication.
75. A dipole in a spherical cavity has almost the same solvation relaxation curves, only very slightly faster (for example, by 25 fs at half point).
76. The frequency resolution of a FM experiment involves the slope of the emission band and the photometric accuracy. It can be much higher than the resolution of the spectrograph.
77. The susceptibility is obtained from the AFA/T-T curve in Figure 8, ref 39, by division through Ṽ.
78. Pal, S.; Balasubramanian, S.; Bagchi, B. J. Phys. Chem. B 2003, 107, 5194.
79. Rieveschl., G., Jr.; Earl Ray, F. Chem. Rev. 1938, 23, 287.
80. Jones Jr., W. D.; Albrecht, W. L.; Palopoli, F. P. J. Org. Chem. 1977, 42, 4144.
81. Bryant, H.; Sawicki, E. J. Org. Chem. 1956, 21, 1322.
82. Dahlgard, M. J. Org. Chem. 1960, 25, 469.
83. Bloomfield, V. A.; Crothers, D. M.; Tinoco Jr, I.; Nucleic Acids; University Science: Sausalito, CA, 2000.
84. Breneman, C. M.; Wiberg, K. B. J. Comput. Chem. 1990, 11, 361.
85. Kovalenko, S. A.; Dobryakov, A. L.; Ruthmann, J.; Ernsting, N. P. Phys. Rev. A 1999, 59, 2369.
86. Ernsting, N. P.; Kovalenko, S. A.; Senyushkina, T.; Saam, J.; Farztdinov, V. J. Phys. Chem. A 2001, 105, 3443.