Molecular Dynamics Simulations of DNA Solvation Dynamics

Abstract

Time-dependent Stokes shift experiments of fluorescent probe molecules incorporated into DNA have uncovered a broad range of time scales from femtoseconds to tens of nanoseconds. A series of recent molecular dynamics simulations have investigated the longest solvation dynamics time scales with sometimes conflicting interpretations. The conclusions of these computational studies are reviewed along with the theoretical methodologies that are utilized to decompose calculated solvation responses in terms of the components present in the system: water, DNA, and ions. Extensive validation of one such decomposition procedure for the dye molecule Hoechst 33258 bound to DNA reveals that the long time scale measured experimentally, 19 ps, is due to DNA. Future opportunities and challenges from both a theoretical and experimental perspective are also briefly highlighted.