Theory for spin-lattice relaxation of spin probes on weakly deformable DNA

Journal of Physical Chemistry B

Volumn 112, Issue 30, 2008, Pages 9219-9236

  Smith, Alyssa L ^a   Cekan, Pavol ^b   Rangel, David P ^a   Sigurdsson, Snorri Th ^b   Mailer, Colin ^c   Robinson, Bruce H ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF ICELAND   (Iceland)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DYNAMICS; ELECTRON RESONANCE; GENES; MAGNETISM; NUCLEIC ACIDS; ORGANIC ACIDS; PARAMAGNETIC RESONANCE; PARAMAGNETISM; SPIN-LATTICE RELAXATION;

DOUBLE-STRANDED DNA; ELECTRON PARAMAGNETIC RESONANCE; INTERNAL DYNAMICS; SPIN LATTICES; SPIN PROBES; SPIN-LATTICE RELAXATION RATES;

SPIN DYNAMICS;

EID: 49349101731     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp7111704     Document Type: Article

References (77)

1. Bloomfield, V. A.; Crothers, D. M.; Tinoco, I. Nucleic acids: structures, properties, and functions; University Science Books: Sausalito, CA, 2000.
2. Wahl, P.; Paoletti, J.; Le Pecq, J.-B. Proc. Natl. Acad. Sci. U.S.A. 1970, 65, 417.
3. Barkley, M. D.; Zimm, B. H. J. Chem. Phys. 1979, 70, 2991.
4. Allison, S. A.; Schurr, J. M. Chem. Phys. 1979, 41, 35.
5. Song, L. S.; Schurr, J. M. Biopolymers 1990, 30, 119.
6. Thomas, J. C.; Allison, S. A.; Appellor, C. J.; Schurr, J. M. Biophys. Chem. 1980, 12, 177.
7. Heath, P. J.; Clendenning, J. B.; Fujimoto, B. S.; Schurr, J. M. J. Mol. Biol. 1996, 260, 718.
8. Schurr, J. M.; Fujimoto, B. S.; Wu, P.; Song, L. S. Fluorescence studies of nucleic acids: dynamics, rigidities, and structures. In Topics in Fluorescence Spectroscopy; Lakowicz, J. R., Ed.; Plenum Press: New York, 1992; pp 137.
9. Wu, P.; Fujimoto, B. S.; Schurr, J. M. Biopolymers 1987, 26, 1463.
10. Robinson, B. H.; Mailer, C.; Drobny, G. Site-specific dynamics in DNA: experiments. In Annu. Rev. Biophys. Biomol. Struct.; Stroud, R. M., Hubbell, W. L., Olson, W. K., Eds.; Annual Reviews Inc.: Palo Alto, 1997; Vol. 26, pp 629.
11. Naimushin, A. N.; Fujimoto, B. S.; Schurr, J. M. Biophys. J. 2000, 78, 1498.
12. Allison, S. A.; Austin, R.; Hogan, M. J. Chem. Phys. 1989, 90, 3843.
13. Hagerman, P. J. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 265.
14. Robinson, B. H. In Stereodynamics of Molecular Systems; Sarma, R. H., Ed.; Pergamon: New York, 1979.
15. Robinson, B. H.; Forgacs, G.; Dalton, L. R.; Frisch, H. L. J. Chem. Phys. 1980, 73, 4688.
16. Robinson, B. H.; Lerman, L. S.; Beth, A. H.; Frisch, H. L.; Dalton, L. R.; Auer, C. J. Mol. Biol. 1980, 139, 19.
17. Spielmann, H. P.; Chi, D. Y.; Hunt, N. G.; Klein, M. P.; Hearst, J. E. Biochemistry 1995, 34, 14801.
18. Strobel, O. K.; Kryak, D. D.; Bobst, E. V.; Bobst, A. M. Bioconjug. Chem. 1991, 2, 89.
19. Hustedt, E. J.; Spaltenstein, A.; Kirschner, J. J.; Hopkins, P. B.; Robinson, B. H. Biochemistry 1993, 32, 1174.
20. Miller, T. R.; Alley, S. C.; Reese, A. W.; Solomon, M. S.; McCallister, W. V.; Mailer, C.; Robinson, B. H.; Hopkins, P. B. J. Am. Chem. Soc. 1995, 117, 9377.
21. Okonogi, T. M.; Reese, A. W.; Alley, S. C.; Hopkins, P. B.; Robinson, B. H. Biophys. J. 1999, 77, 3256.
22. Keyes, R. S.; Bobst, A. M. Biochemistry 1995, 34. 9265.
23. Strobel, O. K.; Keyes, R. S.; Sinden, R. R.; Bobst, A. M. Biochemistry 1995, 324, 357.
24. Eimer, W.; Williamson, J. R.; Boxer, S. G.; Pecora, R. Biochemistry 1990, 29, 799.
25. Alam, T. M.; Drobny, G. P. Chem. Rev. 1991, 91, 1545.
26. Mattiello, D. L.; Drobny, G. P. Investigating furanose ring dynamics in oligonucleotides with solid state 2H NMR. In NMR Probes of Molecular Dynamics; Tycko, R., Ed.; Kluwer Academic Press: Amsterdam, 1994; pp 335.
27. Nuutero, S.; Fujimoto, B. S.; Flynn, P. F.; Reid, B. R.; Ribeiro, N. S.; Schurr, J. M. Biopolymers 1994, 34, 463.
28. Hustedt, E. J.; Kirschner, J. J.; Spaltenstein, A.; Hopkins, P. B.; Robinson, B. H. Biochemistry 1995, 34, 4369.
29. Barhate, N.; Cekan, P.; Massey, A. P.; Sigurdsson, S. T. Angew. Chem., Int. Ed. 2007, 46, 2655.
30. Freed, J. H. Theory of slow tumbling ESR spectra for nitroxides. In Spin Labeling: Theory and Applications; Berliner, L. J., Ed.; Academic Press: New York, 1976; pp 53.
31. Hustedt, E. J.; Cobb, C. E.; Beth, A. H.; Beechem, J. M. Biophys. J. 1993, 64, 614.
32. Okonogi, T. M.; Alley, S. C.; Reese, A. W.; Hopkins, P. B.; Robinson, B. H. Biophys. J. 2000, 78, 2560.
33. Okonogi, T. M.; Alley, S. C.; Reese, A. W.; Hopkins, P. B.; Robinson, B. H. Biophys. J. 2002, 83, 3446.
34. Robinson, B. H.; Drobny, G. P. Site-specific dynamics in DNA: theory and experiment. In Methods in Enzymology; James, T. L., Ed.; Academic Press: San Diego, 1995; Vol. 261, pp 451.
35. Robinson, B. H.; Drobny, G. P. Site-specific dynamics in DNA: theory. In Annu. Rev. Biophys. Biomol. Struct.; Stroud, R. M. , Hubbell, W. L. , Olson, W. K. , Eds.; Annual Reviews Inc.: Palo Alto, 1995; Vol. 24, pp 523.
36. Nielsen, R.; Canaan, S.; Gladden, J. A.; Gelb, M. H.; Robinson, B. H. J. Magn. Reson. 2004, 169, 129.
37. Mailer, C.; Nielsen, R.; Robinson, B. H. J. Phys. Chem. A 2005, 109, 4049.
38. Hyde, J. S.; Dalton, L. R. Saturation-transfer spectroscopy. In Spin Labeling; Berliner, L. J., Eds.; Academic Press, Inc.: New York, 1979; Vol. II.
39. Altenbach, C.; Froncisz, W.; Hyde, J. S.; Hubbell, W. L. Biophys. J. 1989, 56, 1183.
40. Froncisz, W.; Hyde, J. S. J. Magn. Reson. 1982, 47, 515.
41. Huisjen, M.; Hyde, J. S. Rev. Sci. Instrum. 1974, 45, 669.
42. Hyde, J. S.; Yin, J. J.; Feix, J. B.; Hubbell, W. L. Pure Appl. Chem. 1990, 62, 255.
43. Subczynski, W. K.; Hyde, J. S.; Kusumi, A. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 4474.
44. Nielsen, R.; Che, K.; Gelb, M. H.; Robinson, B. H. J. Am. Chem. Soc. 2005, 127, 6430.
45. Columbus, L.; Hubbell, W. L. Trends Biochem. Sci. 2002, 27, 288.
46. Thomas, D. D.; Seidel, J. C.; Gergely, J.; Hyde, J. S. J. Supramol. Struct. 1975, 3, 376.
47. Lipari, G.; Szabo, A. Biochemistry 1981, 20, 6250.
48. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546.
49. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4559.
50. Schurr, J. M.; Babcock, H. P.; Fujimoto, B. S. J. Magn. Reson. B 1994, 105, 211.
51. Qin. P. Z.; Dieckmann, T. Curr. Opin. Struct. Biol. 2004, 14, 350.
52. Song, L. S.; Allison, S. A.; Schurr, J. M. Biopolymers 1990, 29, 1773.
53. Alvarez, F.; Alegria, A.; Colmenero, J. Phys. Rev. B 1991, 44, 7306.
54. Bergman, R. J. Appl. Phys. 2000, 88, 1356.
55. Lindsey, C. P.; Patterson, G. D. J. Chem. Phys. 1980, 73, 3348.
56. Provencher, S. W. J. Chem. Phys. 1976, 64, 2772.
57. Svanberg, C. J. Appl. Phys. 2003, 94, 4191.
58. Robinson, B. H.; Reese. A. W.; Gibbons, E.; Mailer, C. J. Phys. Chem. B 1999, 103, 5881.
59. Abragam, A. The Principles of Nuclear Magnetism; Clarendon Press: Oxford, 1961.
60. Hubbard, P. S. Phys. Rev. A 1974, 9.
61. Hubbard, P. S. Phys. Rev. A 1977, 15.
62. McClung, R. E. D. J. Chem. Phys. 1980, 73.
63. Hubbard, P. S. Phys. Rev. A 1973, 8.
64. Atkins, P. W.; Kivelson, D. J. Chem. Phys. 1966, 44, 169.
65. Torrey, H. C. Phys. Rev. 1953, 92, 962.
66. Robinson, B. H.; Haas, D. A.; Mailer, C. Science 1994, 263, 490.
67. de Gennes, P.-G. J. Phys. Chem. Solids 1958, 7, 345.
68. Schurr, J. M. J. Chem. Phys. 1984, 84, 11.
69. Zwanzig, R. Nonequilibrium statistical mechanics; Oxford University Press: New York, 2001.
70. Hubbard, P. S. Phys. Rev. 1963, 131.
71. Okonogi, T. M. Dynamics, thermodynamics, and structural investigations of nucleic acids using site-specific spin-labeling and electron paramagnetic resonance; University of Washington, 2000.
72. Tirado, M. M.; Torre, J. G. d. I. J. Chem. Phys. 1979, 71, 2581.
73. Tirado, M. M.; Torre, J. G. d. I. J. Chem. Phys. 1980, 73, 1986.
74. Schurr, J. M.; Fujimoto, B. S.; Nuutero, S. J. Magn. Reson. 1994, 106, 1.
75. Rangel, D. P.; Sucato, C. A.; Spink. C. H.; Fujimoto, B. S.; Schurr, J. M. Biopolymers 2004, 75, 291.
76. Barber, E. J. National Cancer Institute monograph 1966, 21, 219.
77. Fujimoto, B. S.; Schurr, J. M. Nature 1990, 344, 4055.