Molecular Dynamics Simulations of DNA Solvation Dynamics

Time-dependent Stokes shift experiments of flourescent 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 some times conflicting interpretations. The conclusions of these computational studies are reviewed along with the theoretical methodologies that are utilized to decomposed 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.