Restructuring of hydration shells rules the low-temperature dynamics of B-DNA via its two conformer substates

Journal of Physical Chemistry B

Volumn 106, Issue 12, 2002, Pages 3263-3274

  Pichler, Arthur ^a   Rüdisser, Simon ^a   Rauch, Christine ^a   Flader, Wolfgang ^a   Wellenzohn, Bernd ^a   Winger, Rudolf H ^a   Liedl, Klaus R ^a   Hallbrucker, Andreas ^a   Mayer, Erwin ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMER SUBSTRATES; HYDRATION SHELLS;

BAND STRUCTURE; CONFORMATIONS; FOURIER TRANSFORM INFRARED SPECTROSCOPY; HYDRATION; HYDROGEN BONDS; NEUTRON SCATTERING; RELAXATION PROCESSES; X RAY DIFFRACTION ANALYSIS;

DNA;

EID: 0037188035     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp013121+     Document Type: Article

References (96)

1. Texter, J. Prog. Biophys. Mol. Biol. 1978, 33, 83-97.
2. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
3. Westhof, E. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 125-144.
4. Jeffrey, G.A.; Saenger, W. Hydrogen Bonding in Biological Structures; Springer-Verlag: New York, 1994.
5. Berman, H.M. Curr. Opin. Struct. Biol. 1994, 4, 345-350.
6. Berman, H.M.; Schneider, B. Nucleic acid hydration. In Nucleic Acid Structure; Neidle, S., Ed.; Oxford University Press: Oxford, U.K., 1999; pp 295-312.
7. Rüdisser, S.; Hallbrucker, A.; Mayer, E. J. Am. Chem. Soc. 1997, 119, 12251-12256.
8. Pichler, A.; Rüdisser, S.; Mitterböck, M.; Huber, C.G.; Winger, R.H.; Liedl, K.R.; Hallbrucker, A.; Mayer, E. Biophys. J. 1999, 77, 398-409.
9. Rüdisser, S.; Pichler, A.; Winger, R.H.; Liedl, K.R.; Hallbrucker, A.; Mayer, E. J. Mol. Liquids 2000, 86, 137-149.
10. 2 Dodekamer und in DNA aus Lachshoden, University of Innsbruck, 1999.
11. Pichler, A.; Hallbrucker, A.; Winger, R.H.; Liedl, K.R.; Mayer, E. J. Phys. Chem. B 2000, 104, 11354-11359.
12. Pichler, A.; Rüdisser, S.; Winger, R.H.; Liedl, K.R.; Hallbrucker, A.; Mayer, E. Chem. Phys. 2000, 258, 391-404.
13. Pichler, A.; Rüdisser, S.; Winger, R.H.; Wellenzohn, B.; Flader, W.; Liedl, K.R.; Hallbrucker, A.; Mayer, E. Appl. Spectrosc. 2001, 55, 9-22.
14. Winger, R.H.; Liedl, K.R.; Rüdisser, S.; Pichler, A.; Hallbrucker, A.; Mayer, E. J. Phys. Chem. B 1998, 102, 8934-8940.
15. Winger, R.H.; Liedl, K.R.; Pichler, A.; Hallbrucker, A.; Mayer, E. J. Biomol. Struct. Dynamics 1999, 17, 223-235.
16. Winger, R.H.; Liedl, K.R.; Pichler, A.; Hallbrucker, A.; Mayer, E. J. Phys. Chem. B 2000, 104, 11349-11353.
17. Hong, M.K.; Braunstein, D.; Cowen, B.; Frauenfelder, H.; Iben, I.E.T.; Mourant, J.R.; Ormos, P.; Scholl, R.; Schulte, A.; Steinbach, P.J.; Xie, A.-H.; Young, R.D. Biophys. J. 1990, 58, 429-436.
18. Potter, W.T.; Hazzard, J.H.; Choc, M.G.; Tucker, M.P.; Caughey, W.S. Biochemistry 1990, 29, 6283-6295.
19. Hogan, M.E.; Jardetzky, O. Proc. Natl. Acad. Sci. 1979, 76, 6341-6345.
20. Chou, S.-H.; Cheng, J.-W.; Reid, B.R. J. Mol. Biol. 1992, 228, 138-155.
21. Gorenstein, D.G. Chem. Rev. 1994, 94, 1315-1338.
22. Tisne, C.; Hantz, E.; Hartmann, B.; Delepierre, M. J. Mol. Biol. 1998, 279, 127-142.
23. Rüdisser, S.; Hallbrucker, A.; Mayer, E. J. Phys. Chem. 1996, 100, 458-461.
24. Rüdisser, S.; Hallbrucker, A.; Mayer, E.; Johari, G.P. J. Phys. Chem. 1997, 101, 266-277.
25. Rüdisser, S.; Fleissner, G.; Pichler, A.; Hallbrucker, A.; Mayer, E. J. Mol. Struct. 1999, 479, 237-243.
26. Dickerson, R.E.; Drew, H.R. J. Mol. Biol. 1981, 149, 761-786.
27. Drew, H.R.; Dickerson, R.E. J. Mol. Biol. 1981, 151, 535-556.
28. Drew, H.R.; Wing, R.M.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.; Dickerson, R.E. Proc. Natl. Acad. Sci. 1982, 78, 2179-2183.
29. Wing, R.; Drew, H.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.; Dickerson, R.E. Nature 1980, 287, 755-758.
30. Dickerson, R.E. Helix structure and molecular recognition by B-DNA. In Nucleic Acid Structure; Neidle, S., Ed.; Oxford University Press: Oxford, U.K., 1998; pp 145-197.
31. Pichler, A.; Rüdisser, S.; Winger, R.H.; Liedl, K.R.; Hallbrucker, A.; Mayer, E. J. Am. Chem. Soc. 2000, 122, 716-717.
32. Whitka, J.M.; Swaminathan, S.; Srinivasan, J.; Beveridge, D.L.; Bolton, P.H. Science 1992, 255, 597-599.
33. Denisov, V.P.; Carlstöm, G.; Venu, K.; Halle, B. J. Mol. Biol. 1997, 268, 118-136.
34. Lane, A.N.; Jenkins, T.C.; Brown, T.; Neidle, S. Biochemistry 1991, 30, 1372-1385.
35. Robinson, B.H.; Mailer, C.; Drobny, G. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 629-658.
36. Hatcher, M.E.; Mattiello, D.L.; Meints, G.A.; Orban, J.; Drobny, G.P. J. Am. Chem. Soc. 1998, 120, 9850-9862.
37. Weidlich, T.; Lindsay, S.M.; Rui, Q.; Rupprecht, A.; Peticolas, W.L.; Thomas, G.A. J. Biomol. Struct. Dyn. 1990, 8, 139-171.
38. Kubasek, W.L.; Wang, Y.; Thomas, G.A.; Patapoff, T.W.; Schoenwaelder, K.-H.; Van der Sande, J.H.; Peticolas, W.L. Biochemistry 1986, 25, 7440-7445.
39. Peticolas, W.L.; Thomas, G.A.; Wang, Y. J. Mol. Liquids 1989, 41, 367-388.
40. Taillandier, E. Nucleic Acid Conformations Studied by Vibrational Spectroscopy; Adenine Press: Schenectady, NY, 1990; Vol. 3.
41. Taillandier, E.; Liquier, J. Methods Enzymol. 1992, 211, 307-335.
42. Poncin, M.; Hartmann, B.; Lavery, R. J. Mol. Biol. 1992, 226, 775-794.
43. Hartmann, B.; Piazolla, D.; Lavery, R. Nucleic Acids Res. 1993, 21, 561-568.
44. Bertrand, H.-O.; Ha-Duong, T.; Fermandjian, S.; Hartmann, B. Nucleic Acids Res. 1998, 26, 1261-1267.
45. Young, M.A.; Ravishanker, G.; Beveridge, D.L. Biophys. J. 1997, 73, 2313-2336.
46. Young, M.A.; Jayaram, B.; Beveridge, D.L. J. Am. Chem. Soc. 1997, 119, 59-69.
47. Duan, Y.; Wilkosz, P.; Crowley, M.; Rosenberg, J.M. J. Mol. Biol. 1997, 272, 553-572.
48. Fratini, A.V.; Kopka, M.L.; Drew, H.R.; Dickerson, R.E. J. Biol. Chem. 1982, 257, 14686-14707.
49. Cruse, W.B.T.; Salisbury, S.A.; Brown, T.; Cosstick, R.; Eckstein, F.; Kennard, O. J. Mol. Biol. 1986, 192, 891-905.
50. Privé, G.G.; Heinemann, U.; Chandrasegaran, S.; Kan, L.-S.; Kopka, M.L.; Dickerson, R.E. Science 1987, 238, 498-504.
51. Grzeskowiak, K.; Yanagi, K.; Prive, G.G.; Dickerson, R.E. J. Biol. Chem. 1991, 266, 8861-8883.
52. Dickerson, R.E.; Goodsell, D.S.; Kopka, M.L.; Pjura, R.E. J. Biomol. Struct. Dyn. 1987, 5, 557-579.
53. Clark, G.R.; Squire, C.J.; Baker, L.J.; Martin, R.F.; White, J. Nucleic Acids Res. 2000, 28, 1259-1265.
54. van Dam, L.; Levitt, M.H. J. Mol. Biol. 2000, 304, 541-561.
55. Sokolov, A.P.; Grimm, H.; Kahn, R. J. Chem. Phys. 1999, 110, 7053-7057.
56. Taillandier, E.; Liquier, J.; Taboury, J.A. Infrared Spectral Studies Of DNA Conformations. In Advances in Infrared and Raman Spectroscopy; Clark, R.J.H., Hester, R.E., Eds.; Wiley: New York, 1985; Vol. 12, pp 65-114.
57. Huber, C.G.; Oefner, P.J.; Bonn, G.K. Anal. Chem. 1995, 67, 578-585.
58. Falk, M.; Hartman Jr., K.A.; Lord, R.C. J. Am. Chem. Soc. 1962, 85, 391-394.
59. Falk, M.; Poole, A.G.; Goymour, C.G. Can. J. Chem. 1970, 48, 1536-1539.
60. Bertie, J.E.; Labbe, H.J.; Whalley, E. J. Chem. Phys. 1969, 10, 4501-4520.
61. Walrafen, G.E.; Yang, W.-H.; Chu, Y.C. J. Phys. Chem. B 1999, 103, 1332-1338.
62. Kuntz, J.I.D.; Brassfield, D.S.; Law, G.D.; Purcell, G.V. Science 1969, 163, 1329-1331.
63. Bloomfield, V.A.; Crothers, D.M.; Tinoco, J.I. Nucleic Acids. Structures, Properties, and Functions; University Science Books: Sausalito, CA, 2000.
64. Wolf, B.; Hanlon, S. Biochemistry 1975, 14, 1661-1670.
65. 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; pp 131-158.
66. Morozov, V.N.; Gevorkian, S.G. Biopolymers 1985, 24, 1785-1799.
67. Frauenfelder, H.; Gratton, E. Methods Enzymol. 1986, 127, 207-216.
68. Parak, F. Methods Enzymol. 1986, 127, 196-206.
69. Duster, W.; Bachleitner, A.; Dunau, R.; Hiebl, M.; Lüscher, E. Biophys. J. 1986, 50, 213-219.
70. Doster, W.; Cusack, S.; Petry, W. Nature 1989, 337, 754-756.
71. Doster, W.; Cusack, S.; Petry, W. Phys. Rev. Lett. 1990, 65, 1080-1084.
72. Nienhaus, G.U.; Heinzl, J.; Huenges, E.; Patak, F. Nature 1989, 338, 665-666.
73. Goldanskii, V.I.; Krupyanskii, Y.F. Q. Rev. Biophys. 1989, 22, 39-92.
74. Smith, J.; Kuczera, K.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 1601-1605.
75. Rupley, J.A.; Careri, G. Adv. Protein Chem. 1991, 41, 37-172.
76. Srajer, V.; Reinisch, L.; Champion, P.M. Biochemistry 1991, 30, 4886-4893.
77. Champion, P.M. J. Raman Spectrosc. 1992, 23, 557-567.
78. Pethig, R. Annu. Rev. Phys. Chem. 1992, 43, 177-205.
79. Pissis, P.; Anagnostopoulou-Konsta, A.; Apekis, L.; Daoukaki-Diamanti, D.; Christodoulides, C. IEEE Trans. Elect. Insulation 1992, 27, 820-825.
80. Mayer, E. Biophys. J. 1994, 67, 862-873.
81. Tengroth, C.; Börjesson, L.; Kagunya, W.W.; Middendorf, H.D. Physica B 1999, 266, 27-34.
82. Sartor, G.; Hallbrucker, A.; Hofer, K.; Mayer, E. J. Phys. Chem. 1992, 96, 5133-5138.
83. Sartor, G.; Mayer, E.; Johari, G.P. Biophys. J. 1994, 66, 249-258.
84. Green, J.L.; Fan, J.; Angell, C.A. J. Phys. Chem. 1994, 98, 13780-13790.
85. Sartor, G.; Johari, G.P. J. Phys. Chem. 1996, 100, 10450-10463.
86. Johari, G.P.; Sartor, G. J. Chem. Soc., Faraday Trans. 1996, 92, 4521-4531.
87. Sokolov, A.P.; Hurst, J.; Quitmann, D. Phys. Rev. B 1995, 51, 12865-12868.
88. Goldstein, M. J. Chem. Phys. 1969, 51, 3728-3739.
89. Stillinger, F.H. Science 1995, 267, 1935-1939.
90. Debenedetti, P.G.; Stillinger, F.H. Nature 2001, 410, 259-267.
91. Angell, C.A. Science 1995, 267, 1924-1935.
92. Frauenfelder, H.; Sligar, S.G.; Wolynes, P.G. Science 1991, 254, 1598-1603.
93. Denisov, V.P.; Halle, B. Faraday Discuss. 1996, 103, 227-244.
94. Denisov, V.P.; Carlström, G.; Venu, K.; Halle, B. J. Mol. Biol. 1997, 268, 118-136.
95. Wang, Y.-X.; Freedberg, D.I.; Grzesiek, S.; Torchia, D.A.; Wingfield, P.T.; Kaufman, J.D.; Stahl, S.J.; Chang, C.-H.; Hodge, C.N. Biochemistry 1996, 35, 12694-12704.
96. Bizzarri, A.R.; Paciaroni, A.; Cannistraro, S. Phys. Rev. E 2000, 62, 3991-3999.