After molecular dynamics simulations, the first two DNA duplex conformations in clustering results were subjected to quantum chemistry calculations. Subsequently, the mean value of the computed energy was selected for use. Interaction energies of 200 stacks and 32 dangles are shown in Table and, respectively. Energies of 400 stacks and 32 dangles are shown in Table , while energies of remaining dangles, loops and initiations were set to 0.