A minimal coarse-grained model to study the gelation of multi-armed DNA nanostars

Abstract

DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and five arms and study their self-assembly using molecular dynamics simulations. Our simulations show that the DNA nanostars form thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from the arrested gel phase to an unstructured liquid phase has been modelled using two-state theoretical model. We find that this transition is enthalpic driven and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends which is giving rise to gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using two-phase thermodynamic model, also substantiate the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature, demonstrating the phase transition to the gel phase. The detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, easily extensible to other polymeric systems, and has remarkable implications in the DNA nanotechnology field.