Dynamics of Water and Ions Near DNA: Perspective from Time-Resolved Fluorescence Stokes Shift Experiments and Molecular Dynamics Simulation

Abstract

The fact that ubiquitous water and ions are important for biological functions of biomolecules is well established. However, understanding the dynamics of water and ions near biomolecules such as DNA, protein and phospholipid is difficult, but essential, for comprehending biomolecular functions. While significant progress has been made to apprehend the hydration structure and dynamics around proteins and phospholipids, understanding dynamics of water and ions near DNA remains challenging. Time-resolved fluorescence Stokes shift (TRFSS) experiments and molecular dynamics (MD) simulation have unraveled several new insights about perturbed water and counterion dynamics near poly-anionic DNA from femtoseconds to nanoseconds time-scales, although with debated explanations of the dispersed DNA dynamics. Here we review the advances of TRFSS experiments and MD simulation studies that unfolded several fascinating, but complex, dynamical features of perturbed water and counterions near different DNA structures in solution.