Solution influence on biomolecular equilibria: nucleic acid base associations

Journal of Biomolecular Structure & Dynamics
A PohorilleR D MacElroy

Abstract

This paper consists of two parts. In the first part, the general problem of biomolecular equilibria in solution is considered, stressing that molecular interactions ultimately determine the answer to this problem. It is discussed how computer simulation techniques can reliably treat the problem and several pitfalls of computer simulation to be avoided are pointed out. Other approaches based on modeling and conceptual simplifications such as perturbative methods, long-range interaction approximations, surface thermodynamic approaches, and hydration shell models are discussed. In the second part, the results of Monte Carlo calculations on the associations of nucleic acid bases in water and carbon tetrachloride are presented. Stacked self-associations are found to be preferred in water and hydrogen-bonded complexes are favored in nonpolar solutions, in agreement with experimental data. The influence of the solvent on base associations is explained in terms of solute-solvent and solvent-solvent contributions to the total energy. No enthalpic stabilization of the complexes by the solvent was found. The results are used to examine the validity of various approximations discussed in the first part of the paper.

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Citations

Feb 1, 1996·Journal of Biomolecular Structure & Dynamics·V I PoltevJ H Miller
Oct 1, 1990·The International Journal of Supercomputer Applications·A PohorilleI Tinoco
Feb 16, 2007·Physical Chemistry Chemical Physics : PCCP·Martin Kabelác, Pavel Hobza
May 14, 2011·Physical Chemistry Chemical Physics : PCCP·Raphael F RibeiroDonald G Truhlar
Sep 13, 2012·The Journal of Physical Chemistry. B·Akshaya ShankarJeetain Mittal

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