On the origin of the long-range attraction between surface-confined DNA bases

Abstract

Surface forces apparatus measurements (Phys. Rev. Lett., 73 (1994) 2780) have established strongly attractive long-range forces between thymine- and adenine-terminated ester monolayers approaching in an aqueous environment. The origin of these forces has not yet been completely understood. We report here a molecular modelling investigation of the forces between single adenine and thymine DNA bases and a molecular dynamics simulation of monolayers of the same amphiphilic esters. The tail regions of the monolayers are in a fluid, disordered state. However, the thymidine- and adenosine-terminated head groups show a tendency toward aggregation and domain formation. The simulation reveals that the orientation of the water molecules is well expressed only at close distances to the DNA bases. The hydrogen bonds between the nucleotides themselves, and with water, are explicitly considered in the performed simulations.