Ion dynamics and water percolation effects in DNA polymorphism

Journal of the American Chemical Society

Volumn 130, Issue 1, 2008, Pages 121-131

  Brovchenko, Ivan ^a   Krukau, Aliaksei ^a   Oleinikova, Alla ^a   Mazur, Alexey K ^b  

^a TU DORTMUND UNIVERSITY   (Germany)

^b INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DNA; IONS; WATER;

DIELECTRIC PERMITTIVITY; PERCOLATION TRANSITION; WATER PERCOLATION;

POLYMORPHISM;

DNA; WATER;

ARTICLE; COMPUTER SIMULATION; DNA DETERMINATION; DNA STRUCTURE; DYNAMICS; HYDRATION; HYDROGEN BOND; STRUCTURE ANALYSIS;

COMPUTER SIMULATION; DNA; DNA, A-FORM; HYDROGEN BONDING; IONS; NUCLEIC ACID CONFORMATION; PHASE TRANSITION; WATER;

EID: 38349002577     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0732882     Document Type: Article

References (69)

1. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
2. Ivanov, V. I.; Minchenkova, L. E. Mol. Biol. 1995, 28, 780-788.
3. Lu, X. J.; Shakked, Z.; Olson, W. K. J. Mol. Biol. 2000, 300, 819-840.
4. Rich, A.; Zhang, S. Nat. Rev. Genet. 2003, 4, 566-72.
5. Tolstorukov, M. Y.; Ivanov, V. I.; Malenkov, G. G.; Jernigan, R. L.; Zhurkin, V. B. Biophys. J. 2001, 81, 3409-3421.
6. Ng, H.-L.; Kopka, M. L.; Dickerson, R. E. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2035-2039.
7. Franklin, R. E.; Gosling, R. G. Nature 1953, 171, 740-741.
8. Tunis-Schneider, M. J.; Maestre, M. F. J. Mol. Biol. 1970, 52, 521-541.
9. Leslie, A. G. W.; Arnott, S.; Chandrasekaran, R.; Ratliff, R. L. J. Mol. Biol. 1980, 143, 49-72.
10. Piskur, J.; Rupprecht, A. FEBS Lett. 1995, 375, 174-178.
11. Malenkov, G.; Minchenkova, L.; Minyat, E.; Schyolkina, A.; Ivanov, V. FEBS Lett. 1975, 51, 38-42.
12. Ivanov, V. I.; Minchenkova, L. E.; Schyolkina, A. K.; Poletaev, A. I. Biopolymers 1973, 12, 89-110.
13. Calladine, C. R.; Drew, H. R. J. Mol. Biol. 1984, 178, 773-782.
14. Saenger, W.; Hunter, W. N.; Kennard, O. Nature 1986, 324, 385-388.
15. Fuller, W.; Mahensdasingam, A.; Forsyth, V. T. Nature 1988, 335, 596.
16. Hunter, C. A. J. Mol. Biol. 1993, 230, 1025-1054.
17. Cheatham, T. E., III; Crowley, M. F.; Fox, T.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 9626-9630.
18. Cheatham, T. E., III; Kollman, P. A. Structure 1997, 5, 1297-1311.
19. Mazur, A. K. J. Am. Chem. Soc. 2003, 125, 7849-7859.
20. Mazur, A. K. J. Chem. Theory Comput. 2005, 1, 325-336.
21. Brovchenko, I.; Krukau, A.; Oleinikova, A.; Mazur, A. K. Phys. Rev. Lett. 2006, 97, 137801(4).
22. Brovchenko, I.; Krukau, A.; Oleinikova, A.; Mazur, A. K. J. Phys. Chem. B 2007, 111, 3258-3266.
23. Kuntz, I. D.; Kauzmann, W. Adv. Protein Chem. 1974, 28, 239-345.
24. Rupley, J. A.; Careri, G. Adv. Protein Chem. 1991, 41, 37-172.
25. Gascoyne, P. R.; Pethig, R.; Szent-Gyorgyi, A. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 261-265.
26. Careri, G.; Giansanti, A.; Rupley, J. A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 6810-6814.
27. Careri, G.; Giansanti, A.; Rupley, J. A. Phys. Rev. A 1988, 37, 2703-2705.
28. Rupley, J. A.; Siemankowski, L.; Careri, G.; Bruni, F. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 9022-9025.
29. Bruni, F.; Careri, G.; Leopold, A. C. Phys. Rev. A 1989, 40, 2803-2805.
30. Bruni, F.; Careri, G.; Clegg, J. S. Biophys. J. 1989, 55, 331-338.
31. Oleinikova, A.; Brovchenko, I. Mol. Phys. 2006, 104, 3841-3855.
32. Oleinikova, A.; Smolin, N.; Brovchenko, I.; Geiger, A.; Winter, R. J. Phys. Chem. B 2005, 109, 1988-1998.
33. Brovchenko, I.; Oleinikova, A. In Handbook of Theoretical and Computational Nanotechnology, Volume I; Rieth, M., Schommers, W., Eds.; American Scientific Publishers: Stevenson Ranch, CA, 2006; pp 1-98.
34. Oleinikova, A.; Brovchenko, I.; Geiger, A. Physica A 2006, 364, 1-12.
35. Smolin, N.; Oleinikova, A.; Brovchenko, I.; Geiger, A.; Winter, R. J. Phys. Chem. B 2005, 109, 10995-11005.
36. Brovchenko, I.; Krukau, A.; Smolin, N.; Oleinikova, A.; Geiger, A.; Winter, R. J. Chem. Phys. 2005, 123, 224905.
37. Oleinikova, A.; Smolin, N.; Brovchenko, I. J. Phys. Chem. B 2006, 110, 19619-19624.
38. Texter, J. Prog. Biophys. Molec. Biol. 1979, 33, 83-97.
39. van Dam, L.; Korolev, N.; Nordenskiöld, L. Nucleic Acids Res. 2002, 30, 419-428.
40. Warman, J. M.; de Haas, M. P.; Rupprecht, A. Chem. Phys. Lett. 1996, 249, 319-322.
41. Arnott, S.; Hukins, D. W. L. Biochem. Biophys. Res. Commun. 1972, 47, 1504-1509.
42. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
43. Jorgensen, W. L.; Chandreskhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys 1983, 79, 926-935.
44. Åqvist, J. J. Phys. Chem. 1990, 94, 8021-8024.
45. Mazur, A. K. J. Am. Chem. Soc. 2002, 124, 14707-14715.
46. Cheatham, T. E., III; Kollman, P. A. Annu. Rev. Phys. Chem. 2000, 51, 435-471.
47. Oleinikova, A.; Smolin, N.; Brovchenko, I. Biophys. J. 2007, 93, 2986-3000.
48. Zimmerman, S. B.; Pheiffer, B. H. J. Mol. Biol. 1980, 142, 315-330.
49. Cooper, P. J.; Hamilton, L. D. J. Mol. Biol. 1966, 16, 562-563.
50. Ivanov, V. I.; Minchenkova, L. E.; Minyat, E. E.; Schyolkina, A. K. Cold Spring Harbor Symp. Quant. Biol. 1983, 47, 243-250.
51. Mazur, A. K. J. Comput. Chem. 1997, 18, 1354-1364.
52. Mazur, A. K. In Computational Biochemistry and Biophysics; Becker, O. M., MacKerell, A. D., Jr., Roux, B., Watanabe, M., Eds.; Marcel Dekker: New York, 2001; pp 115-131.
53. Mazur, A. K. J. Phys. Chem. B 1998, 102, 473-479.
54. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
55. Oleinikova, A.; Brovchenko, I.; Smolin, N.; Krukau, A.; Geiger, A.; Winter, R. Phys. Rev. Lett. 2005, 95, 247802.
56. Geiger, A.; Stillinger, F.; Rahman, A. J. Chem. Phys. 1979, 70, 4185-4193.
57. Oleinikova, A.; Brovchenko, I.; Geiger, A.; Guillot, B. J. Chem. Phys. 2002, 117, 3296-3304.
58. Stauffer, D. Introduction to percolation theory; Taylor and Francis: London and Philadelphia, 1985.
59. Brovchenko, I.; Geiger, A.; Oleinikova, A.; Paschek, D. Eur. Phys. J. E 2003, 12, 69-76.
60. Settles, M.; Doster, W. Faraday Discuss. 1996, 103, 269-279.
61. Bizzarri, A. R.; Cannistraro, S. Phys. Rev. E 1996, 53, R3040-R3043.
62. Lee, R. S.; Bone, S. Faraday Discuss. 1996, 103, 59-69.
63. Rosen, D. Trans. Faraday Soc. 1963, 59, 2178-2191.
64. Tomaselli, V. P.; Shamos, M. H. Biopolymers 1973, 12, 353-366.
65. Bone, S.; Pethig, R. J. Mol. Biol. 1982, 157, 571-575.
66. Ivanov, V. I.; Minchenkova, L. E.; Minyat, E. E.; Frank-Kametetskii, M. D.; Schyolkina, A. K. J. Mol. Biol. 1974, 87, 817-833.
67. Lee, S. A.; Lindsay, S. M.; Powell, J. W.; Weidlich, T.; Tao, N. J.; Lewen, G. D. Biopolymers 1987, 26, 1637-65.
68. Fornells, M.; Campos, J. L.; Subirana, J. A. J. Mol. Biol. 1983, 166, 249-252.
69. van Dam, L.; Levitt, M. H. J. Mol. Biol. 2000, 304, 541-561.