Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies

Journal of Biomolecular Structure & Dynamics
D L BeveridgeM Mezei

Abstract

Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distribution functions based on the Proximity Criterion, and partitioned into hydrophobic, hydrophilic and ionic contributions. Color stereo views of selected hydration complexes are also presented. A preliminary discussion of the transferability of functional group coordination numbers is given. The results enable to comment on two current problems related to the hydration of nucleic acids: a) the theory of Dickerson and coworkers on the role of water in the relative stability of the A and B form of DNA and b) the idea of water bridges and filaments emerging from the computer simulation results on the hydration of DNA fragments by Clementi.

References

Oct 1, 1979·Biopolymers·E Clementi, G Corongiu
Aug 17, 1977·Journal of the American Chemical Society·E ClementiR Scordamaglia
Nov 1, 1967·Journal of Theoretical Biology·S Lewin
Jan 1, 1983·Progress in Biophysics and Molecular Biology·S Neidle, H M Berman
Oct 1, 1983·Journal of Biomolecular Structure & Dynamics·B TidorM Karplus
Oct 1, 1983·Journal of Biomolecular Structure & Dynamics·K S KimE Clementi
Oct 1, 1983·Journal of Biomolecular Structure & Dynamics·M MezeiS Neidle
Aug 1, 1984·Journal of Biomolecular Structure & Dynamics·M MezeiD L Beveridge
Oct 1, 1983·Journal of Biomolecular Structure & Dynamics·M PrabhakaranJ A McCammon
Sep 25, 1981·Journal of Molecular Biology·H R Drew, R E Dickerson
Jan 1, 1984·Journal of the American Chemical Society·A PohorilleR D MacElroy

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Citations

Feb 1, 1989·International Journal of Biological Macromolecules·F VovelleJ M Goodfellow
Apr 8, 2000·Current Opinion in Structural Biology·D L Beveridge, K J McConnell
Mar 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·P S SubramanianD L Beveridge
Oct 1, 1983·Journal of Biomolecular Structure & Dynamics·S L ForniliP L San Biagio
Mar 1, 1984·Journal of Biomolecular Structure & Dynamics·A PohorilleR D MacElroy
Jun 21, 2006·The Journal of Chemical Physics·Hendrik HeinzB L Farmer
Aug 21, 1987·Journal of Theoretical Biology·R J Elliott, J M Goodfellow
Jun 1, 1987·Journal of Biomolecular Structure & Dynamics·A R Srinivasan, W K Olson
Apr 1, 1988·Journal of Biomolecular Structure & Dynamics·H M BermanD Beveridge
Mar 4, 2009·Biological Research for Nursing·Jennifer R DunganCarolyn B Yucha
Jan 1, 1989·Annals of the New York Academy of Sciences·Y Ben David, A Bernstein
Aug 25, 2006·The Journal of Physical Chemistry. B·Jana Chocholousová, Michael Feig
Oct 18, 2012·Chemical Reviews·Hashem A TahaTodd L Lowary

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