Enhanced tetrahedral ordering of water molecules in minor grooves of DNA: Relative role of DNA rigidity, nanoconfinement, and surface specific interactions

Journal of Physical Chemistry B

Volumn 114, Issue 10, 2010, Pages 3633-3638

  Jana, Biman ^a   Pal, Subrata ^b   Bagchi, Biman ^a,c  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b INDIAN INSTITUTE OF TECHNOLOGY GANDHINAGAR   (India)

^c JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA SEQUENCES; DYNAMICS; GENES; MOLECULAR DYNAMICS; NUCLEIC ACIDS; SCANDIUM; THERMOANALYSIS;

ADAM-GIBBS RELATION; ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS; CONFIGURATIONAL ENTROPY; DNA DUPLEXES; MINOR GROOVES; NANOCONFINEMENTS; SELF-DIFFUSION COEFFICIENTS; SPECIFIC INTERACTION; TETRAHEDRAL ORDERING; THERMO DYNAMIC ANALYSIS; WATER DYNAMICS; WATER MOLECULE; X-RAY STRUCTURE;

MOLECULES;

DNA; WATER;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; NANOTECHNOLOGY; THERMODYNAMICS;

DNA; MOLECULAR DYNAMICS SIMULATION; NANOTECHNOLOGY; THERMODYNAMICS; WATER;

EID: 77953729667     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp907513w     Document Type: Article

References (36)

1. Bagchi, B. Chem. Rev. 2005, 105, 3197.
2. Park, S.; Fayer, M. D. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 16731.
3. Meilanen, D. E.; Levinger, N.; Spry, D. B.; Payer, M. D. J. Am. Chem: Soc. 2007, 129, 14311.
4. Tan, H.-S.; Piletic, I. R.; Riter, R. E.; Levinger, N. E.; Payer, M. D. Phys. Rev. Lett. 2005, 94, 057405.
5. Faeder, J.; Ladanyi, B. M. J. Phys. Chem. B 2005, 109, 6732.
6. Senapati, S.; Berkowitz, M. L. J. Phys. Chem. A 2004, 108, 9768;
7. J. Phys. Chem. B 2003, 107, 12906.
8. Bhattacharyya, K. Acc. Chem. Res. 2003, 36, 95;
9. Chem. Commun., 2008, 2848.
10. Pant, D.; Levinger, N. E. Langmuir 2000, 16, 10123.
11. Kurita, R.; Tanaka, H. Phys. Rev. Lett. 2007, 98, 235701.
12. Royall, C. P.; Williams, S. R.; Ohtsuka, T.; Tanaka, H. Nat. Mater. 2008, 7, 556.
13. Shintani, H.; Tanaka, H. Nat. Phys. 2006, 2, 200.
14. Ohtsuka, T.; Royall, C. P.; Tanaka, H. Eur. Phys. Lett. 2008, 84, 46002.
15. Mukherjee, A.; Lavery, R.; Bagchi, B.; Hynes, J. T. J. Am. Chem. Soc. 2008, 130, 9747.
16. Nguyen, B.; Neidle, S.; Wilson, W. D. Acc. Chem. Res. 2008, 42, 11.
17. Flatters, D.; Lavery, R. Biophys. J. 1998, 75, 372.
18. 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.
19. Berg, M. A.; Coleman, R. S.; Murphy, C. J., phys. Chem. Chem. Phys. 2008, 10, 1229.
20. Pal, S.; Maiti, P. K.; Bagchi, B.; Hynes, J. T. J. Phys. Chem. B 2006, 110, 26396.
21. Furse, K. E.; Corcelli, S. A. J. Am. Chem. Soc. 2008, 130, 13103.
22. Lin, S. T.; Blanco, M.; Goddard, W. A. J. Chem. Phys. 2003, 119, 11792.
23. Jana, B.; Pal, S.; Maiti, P. K.; Lin, S. T.; Hynes, J. T.; Bagchi, B. J. Phys. Chem. B 2006. 110. 10611.
24. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E.; Wang, J.; Ross, W. S.; Simmerling, C.; Darden, T.; Merz, K. M.; Stanton, R. V. AMBER, 7th ed.; University of California: San Francisco, 1999.
25. 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.
26. Feig, M.; Pettitt, B. M. Biophys. J. 1998, 75, 134;
27. J. Mol. Biol. 1999, 286, 1075.
28. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
29. Giguen, P. A. J. Raman Spectrosc. 1984, 15, 354.
30. Chau, P.-L.; Hardwick, A. J. Mol. Phys. 1998, 93, 511.
31. Nave, E. L.; Sastry, S.; Sciortino, F. Phys. Rev. E. 2006, 74, 050501.
32. Alexeev, D. G.; Lipanov, A. A.; Skuratovskii, I. Y. Nature 1987, 325, 821.
33. Yakishevich, L. V. Nonlinear Physics of DNA: Wiley-VCH: Weinheim, 2004; p 6.
34. Senapati, S.; Chandra, A. J. Phys. Chem. B 2001, 105, 5106.
35. Senapati, S.; Chandra, A. J. Chem. Phys. 1999, 111, 1223.
36. Hansen, J.-P.; McDonald, I. R. Theory of Simple Liquids, 2nd ed.; Academic Press: New York, 1968.