Water clustering and percolation in low hydration DNA shells

Journal of Physical Chemistry B

Volumn 111, Issue 12, 2007, Pages 3258-3266

  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

DNA SEQUENCES; HYDRATION; HYDROGEN; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; PHASE TRANSITIONS; POLYMORPHISM;

DNA SHELLS; HYDROGEN-BONDED NETWORKS; POLYMORPHIC TRANSITIONS; WATER CLUSTERS;

PERCOLATION (FLUIDS);

EID: 34147187253     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp068776v     Document Type: Article

References (56)

1. Gascoyne, P. R.; Pethig, R.; Szent-Gyorgyi, A. Proc. Natl. Acad. Sei. U.S.A. 1981, 78, 261-265.
2. Careri, G.; Giansanti, A.; Rupley, J. A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 6810-6814.
3. Careri, G.; Giansanti, A.; Rupley, J. A. Phys. Rev. A 1988, 37, 2703-2705.
4. Rupley, J. A.; Siemankowski, L.; Careri, G.; Bruni, F. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 9022-9025.
5. Bruni, F.; Careri, G.; Leopold, A. C. Phys. Rev. A 1989, 40, 2803-2805.
6. Bruni, F.; Careri, G.; Clegg, J. S. Biophys. J. 1989, 55, 331-338.
7. Rupley, J. A.; Careri, G. Adv. Protein Chem. 1991, 41, 37-172.
8. Klammler, F.; Kimmich, R. Croat. Chem. Acta 1992, 65, 455-470.
9. Konsta, A. A.; Laudat, J.; Pissis, P. Solid State Ionics 1997, 97, 97-104.
10. Haranczyk, H. On water in extremely dry biological systems; Jagiellonian University Press: Krakow, Poland, 2003.
11. Sokolowska, D.; Krol-Otwinowska, A.; Moscicki, J. K. Phys. Rev. E 2004, 70, 052901.
12. Oleinikova, A.; Smolin, N.; Brovchenko, I.; Geiger, A.; Winter, R. J. Phys. Chem. B 2005, 109, 1988-1998.
13. Kuntz, I. D.; Kauzmann, W. Adv. Protein Chem. 1974, 28, 239-345.
14. Brovchenko, I.; Oleinikova, A. In Handbook of Theoretical and Computational Nanotechnology; Rieth, M., Schommers, W., Eds.; American Scientific Publishers: Stevenson Ranch, CA, 2006; Vol. 9, Chapter 3, pp 109-206.
15. Oleinikova, A.; Brovchenko, L; Geiger, A. Physica A 2006, 364, 1-12.
16. Oleinikova, A.; Brovchenko, I. Mol. Phys. 2006, 104, 3841-3855.
17. Smolin, N.; Oleinikova, A.; Brovchenko, I.; Geiger, A.; Winter, R. J. Phys. Chem. B 2005, 109, 10995-11005.
18. Brovchenko, I.; Krukau, A.; Smolin, N.; Oleinikova, A.; Geiger, A.; Winter, R. J. Chem. Phys. 2005, 123, 224905.
19. Oleinikova, A.; Smolin, N.; Brovchenko, I. J. Phys. Chem. B 2006, 110, 19619-19624.
20. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
21. Leslie, A. G. W.; Arnott, S.; Chandrasekaran, R.; Ratliff, R. L. J. Mol. Biol. 1980, 143, 49-72.
22. Saenger, W.; Hunter, W. N.; Kennard, O. Nature 1986, 324, 385-388.
23. Texter, J. Prog. Biophys. Mot. Biol. 1979, 33, 83-97.
24. van Dam, L.; Korolev, N.; Nordenskild, L. Nucleic Acids Res. 2002, 30, 419-428.
25. van Dam, L.; Levitt, M. H. J. Mol. Biol. 2000, 304, 541-561.
26. Fuller, W.; Forsyth, T.; Mahendrasingam, A. Philos. Trans. R. Soc. London, Ser. B 2004, 359, 1237-48.
27. Mazur, A. K. J. Am. Chem. Soc. 2003, 125 (26), 7849-7859.
28. Mazur, A. K. J. Chem. Theory Comput. 2005, 1, 325-336.
29. Ivanov, V. I.; Minchenkova, L. E.; Minyat, E. E.; Sehyolkina, A. K. Cold Spring Harbor Symp. Quant. Biol. 1983, 47, 243-250.
30. Malenkov, G.; Minchenkova, L.; Minyat, E.; Sehyolkina, A.; Ivanov, V. FEBS Lett. 1975, 51, 38-42.
31. Brovchenko, I.; Krukau, A.; Oleinikova, A.; Mazur, A. K. Phys. Rev. Lett. 2006, 97 (13), 137801(4).
32. Warman, J. M.; de Haas, M. P.; Rupprecht, A. Chem. Phys. Lett. 1996, 249, 319-322.
33. Arnott, S.; Hukins, D. W. L. Biochem. Biophys. Res. Commun. 1972, 47, 1504-1509.
34. 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 (19), 5179-5197.
35. Jorgensen, W. L.; Chandreskhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
36. Mazur, A. K. J. Am. Chem. Soc. 2002, 124 (49), 14707-14715.
37. Mazur, A. K. J. Am. Chem. Soc. 1998, 120 (42), 10928-10937.
38. Mazur, A. K. J. Chem. Phys. 1999, 111 (4), 1407-1414.
39. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
40. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
41. Geiger, A.; Stillinger, F.; Rahman, A. J. Chem. Phys. 1979, 70, 4185-4193.
42. Oleinikova, A.; Brovchenko, I.; Geiger, A.; Guillot, B. J. Chem. Phys. 2002, 117, 3296-3304.
43. Stauffer, D. Introduction to percolation theory; Taylor and Francis: London and Philadelphia, PA, 1985.
44. Pártay, L. P.; Jedlovszky, P.; Oleinikova, A.; Brovchenko, I. Phys. Chem. Chem. Phys., in press.
45. Cheatham, T. E., Ill; Crowley, M. F.; Fox, T.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 9626-9630.
46. Ivanov, V. I.; Minchenkova, L. E.; Minyat, E. E.; Frank-Kametetskii, M. D.; Sehyolkina, A. K. J. Mol. Biol. 1974, 87, 817-833.
47. Zimmerman, S. B.; Pheiffer, B. H. J. Mol. Biol. 1980, 142, 315-330.
48. Zhurkin, V. B.; Lysov, Y. P.; Ivanov, V. I. Nucleic Acids Res. 1979, 6(3), 1081-1096.
49. Brovchenko, I.; Geiger, A.; Oleinikova, A. J. Chem. Phys. 2004, 120, 1958-1972.
50. Oleinikova, A.; Brovchenko, I.; Smolin, N.; Krukau, A.; Geiger, A.; Winter, R. Phys. Rev. Lett. 2005, 95, 247802.
51. Becker, M. M.; Wang, Z. J. Biol. Chem. 1989, 265, 4163-4167.
52. Tolstorukov, M. Y.; Ivanov, V. I.; Malenkov, G. G.; Jernigan, R. L.; Zhurkin, V. B. Biophys. J. 2001, 87, 3409-3421.
53. Dougan, L.; Bates, S. P.; Hargreaves, R.; Fox, J. P.; Crain, J.; Finney, J. L.; Reat, V.; Soper, A. K. J. Chem. Phys. 2004, 121, 6456-6462.
54. Xu, Q.; Shoemaker, R. K.; Braunlin, W. H. Biophys. J. 1993, 65, 1039-1049.
55. Robinson, H.; Gao, Y.-G.; Sanishvili, R.; Joachimiak, A.; Wang, A. H.-J. Nucleic Acids Res. 2000, 28, 1760-1766.
56. Schultz, J.; Rupprecht, A.; Song, Z.; Piskur, J.; Nordenskiold, L.; Lahajnar, G. Biophys. J. 1994, 66, 810-819.