  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.
