The SIRAH force-field and interactions between short DNA duplexes

Abstract

In recent years, short DNA duplexes have been studied as an interesting self-assembling system and a building block for DNA-based nanotechnologies. Numerical simulation studies for the determination of the full phase diagram of short duplexes require, as an input ingredient, a simplified but reliable force-field able to capture the main features of duplex-duplex interaction. We used the coarse-grained SIRAH force field in the implicit solvent approximation to study the interaction between two short duplexes of double-strand DNA as a function of the relative positions and orientations and the salt concentration, in the cases of 8 and 20 base pairs. We discuss the consequences of our study to determine new simple but qualitatively reliable model potentials.