Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G3T4G4)]2 G-Quadruplex DNA Structure

We have used both adaptive biasing force (ABF) and regular molecular dynamics (MD) simulations to investigate the asymmetrical NH4+ ion movement inside of a bimolecular G-quadruplex DNA structure [d(G(3)T(4)G(4))](2). The free-energy landscapes obtained from ABF MD simulations suggest that the NH4+ ion exiting the [d(G(3)T(4)G(4))](2) G-quadruplex stem in the direction toward the edge-type loop (denoted as the upper direction) experiences a lower free-energy barrier than that toward the diagonal loop (denoted as the lower direction) by approximately 3-4 kcal mol(-1). This result is in qualitative agreement with the previous discovery made by Sket and Plavec on the same G-quadruplex structure from N-15 NMR experiments (J. Am. Chem. Soc. 2007, 129, 8794). In the Na+ form of the same G-quadruplex, Na+ ion movement was found to be symmetrical, with a free-energy barrier of only 5-7 kcal mol(-1) to cross all three G-quartets, that is, [d(G(3)T(4)G(4))](2) still exhibits ion-channel-like behaviors for Na+ ions. On the basis of the new computational results, we hypothesize that the stiffness of a G-quartet is primarily determined by the base stacking interactions within the G-quadruplex stem. Therefore, the structural origin for the asymmetrical NH4+ ion movement in [d(G(3)T(4)G(4))](2) is the presence of two different modes of base stacking around the NH4+ binding sites, a more stable 5'-syn-anti mode between lower and central G-quartets and a less stable 5'-anti-anti mode between upper and central G-quartets. Simulations also suggest that loop topology at the end of a G-quadruplex stem only controls the direction at which an exiting NH4+ ion reaches bulk solution but does not impose significant free-energy barriers.