MOLECULAR-DYNAMICS SIMULATIONS STUDY OF THE FREE-ENERGY OF ASSOCIATION OF 9-METHYLADENINE AND 1-METHYLTHYMINE BASES IN WATER

The results of molecular dynamics simulations on the free energy of association of adenine and thymine bases in water are presented. The influence of the solvent on the free energy surfaces (potentials of mean force) of the hydrogen-bonded and stacked interactions of these base pairs is determined with the use of molecular dynamics in conjunction with the statistical perturbation theory of Zwanzig.1 11The stacked-configuration potential of mean force in water is found to be more stable than the hydrogen-bonded configuration, in agreement with previous theoretical and experimental studies on these systems. The calculated ΔGb for base-pair association by stacking is-0.8 kcal/mol, in good agreement with the experiment value of-1.15 kcal/mol. © 1990, American Chemical Society. All rights reserved.