Molecular dynamics simulations and adaptive biasing force analysis of the quadruplex DNA dynamics in an explicit solvent reveal fundamentally different mechanisms of Na(+) transport in xanthine- and guanine-based DNA systems. The barrier to the transport of K(+) through the xanthine-based quadruplex is significantly lower than those reported for the guanine-based analogs.
Keywords: adaptive biasing force; free-energy; guanine; ion transport; molecular dynamics.