Y-DNA melting: a short tale of three scales

We address some aspects of the thermal denaturation of Y-DNA-the three-way junction-on three different length scales: the effect of chain concentration on the extrinsic melting behaviour within a simple kinetic approach, the exponent of the loop entropy in intrinsic melting as it appears in statistical mechanics models, and the microscopics of stacking within the junction from molecular dynamics simulations. Our results suggest that a multiscale approach is needed to properly describe the denaturation properties of these systems. We propose experiments which can also shed light on the melting of short and long duplex DNA sequences.