Contributions of Ordered Solvent to Long-Range DNA-Dendrimer Interactions

Abstract

Water is essential to nearly all biological reactions, and yet the role of solvent is often overlooked in studying such interactions. In particular, the ability of highly charged molecules to orient the dipole moments of water molecules has not been thoroughly explored. While short-range solvent ordering effects have been previously investigated, we report evidence of the existence of ordered waters between charged molecules at large distances and characterize the free energy contributions of this solvent ordering to the interaction. We present evidence from molecular dynamics simulations that the hydrogen bonding network in ordered waters between a strand of DNA and a highly charged nanoparticle, a generation 3 polyamidoamine (PAMAM) dendrimer, contribute significantly to the free energy and extend the interaction beyond the electrostatic range of the molecules. Such long-range water effects could potentially be of great importance to many biological systems, in which molecules appear to be able to recognize each other across significant distances, or for which the kinetic rates are too fast to be due to pure diffusion. Our results are in good agreement with experiments on the role of solvent in DNA condensation by multivalent cations.