Interaction of double-stranded DNA with a nanosphere: a coarse-grained molecular dynamics simulation study

Abstract

Using coarse-grained molecular dynamics simulations, we study the behavior of a DNA-nanosphere complex in the absence and presence of an external stretching force exerted on two ends of DNA chain. In this work, we use an accurate coarse-grained model for double-stranded DNA chain recently developed by Savelyev and Papoian [Biophys. J. 96, 4044 (2009)]. Charged particles are uniformly distributed on the surface of the sphere. Without a stretching force, an ordered or disordered complex is formed depending on the surface charge density and the salt concentration. It is found that DNA wraps randomly around the sphere only at an intermediate salt concentration and high surface charge density. Additionally, the DNA folding around the sphere induces a reduced distance between DNA monomers close to the spherical surface. When an external force is applied, the force-extension relation reveals a discontinuous transition of DNA stretching during the unwrapping process. Moreover, the discrete change becomes more obvious for a higher salt concentration.