Simulation of adenine-thymine base pair hydration using the Monte-Carlo method

A Monte Carlo method was used to simulate the hydration of separate molecules and four possible hydrogen-bonded (H-bonded) pair of nucleic acid bases, adenine and thymine. Hydration energies and hydration shell characteristics for separate bases and base pairs have been determined. The new method, the computation of the volume accessible for H-bond formation, is used to estimate the hydration changes after base pair formation. The computations demonstrate changes in accessible volumes of atoms involved in H-bonding between bases. Good correlation exists between accessible volumes and hydration indices of hydrophilic atoms of bases. This correlation will be used to elaborate new simplified method of estimation of hydration energy change on biomolecular complexing or conformational transitions.