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