Biopolymers and cell. 1985. Volume 1. № 2. 59 - 69
V. I. Danilov, I. S. Tolokh
NATURE OF NUCLEOTIDE BASE ASSOCIATIONS IN WATER: THE MONTE CARLO SIMULATION OF THE HYDRATION OF PYRIMIDINE BASES AND THEIR MOLECULAR ASSOCIATES
Summary
Results of the Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It is shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It is found that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the slack. The simulation of the hydration of different stacked thymine dimers has shown that the most favourable of them is the one for which base methyl groups are close to each other.