DNA melting in small-molecule-DNA-hybrid dimer structures: Experimental characterization and coarse-grained molecular dynamics simulations

When DNA hybridization is used to link together nanoparticles or molecules, the melting transition of the resulting DNA-linked material often is very sharp. In this paper, we study a particularly simple version of this class of material based on a small-molecule-DNA-hybrid (SMDH) structure that has three DNA strands per l, 3, 5-tris(phenylethynyl)benzene core. By varying the concentration of the SMDHs, it is possible to produce either SMDH dimers or bulk aggregates, with the former having highly packed duplex DNA while the latter has an extended network. Melting measurements that we present show that the dimers exhibit sharp melting while the extended aggregates show broad melting. To interpret these results, we have performed coarsegrained molecular dynamics (CGMD) studies of the dimer melting and also of isolated duplex melting using CGMD potentials that have either implicit or explicit ions. Details of the melting simulation technology demonstrate that the simulations properly describe equilibrium transitions in isolated duplexes. The results show that the SMDH dimer has much sharper melting than the isolated duplex. Both implicit and explicit ion calculations show this effect, but the explicit ion results are sharper. An analytical model of the melting thermodynamics is developed which shows that the sharp melting is entropically driven and can be understood primarily in terms of the differences between the effective concentrations of the DNA strands for intracomplex hybridization events compared to intermolecular hybridization.