Unrestrained Molecular Dynamics Simulations of [d(AT)5]2Duplex in Aqueous Solution: Hydration and Binding of Sodium Ions in the Minor Groove

Abstract

The results of unrestrained particle mesh Ewald molecular dynamics simulations of the [d(AT)5]2 duplex in aqueous solution are presented here. Two trajectories starting from A (10 ns) and B (5 ns) canonical forms were carried out. Both trajectories converged within about 500 ps and produced stable and similar conformational ensembles, which exhibit the qualitative features of B-DNA. Surprisingly, the convergence of hydration patterns is much slower than the convergence of the solute structure. We observed intrusions of sodium ions into the minor groove of the ApT steps with residence times of about 1−2 ns. The sodium ions were coordinated by the electronegative potential of O2 atoms of thymines, which induce a large negative propeller twist. The propeller twist change is related to the repulsion between a sodium ion and H2 atoms of adenines in the minor groove. It simultaneously leads to rather close mutual amino group contacts of adenine amino groups in ApT steps frequently occurring in nucleotide crysta...