Simulation of dissociation of DNA duplexes attached to the surface

Abstract

Abstract:We present Monte Carlo simulations of dissociation of duplexes formed of complementary single-stranded DNAs with one of the strands attached to the surface. To describe the transition from the bound state to the unbound state of two strands located nearby, we use a lattice model taking DNA base-pair interactions and comformational changes into account. The results obtained are employed as a basis for a more coarse-grained model including strand backward association and diffusion resulting in complete dissociation. The distribution of the dissociation time is found to be exponential. This finding indicates that the non-exponential kinetic features observed in the corresponding experiments seem to be related to extrinsic factors, e.g., to the surface heterogeneity.

Force induced DNA melting in the presence of an attractive surface

“…21 Recently, theoretical efforts have been made to explore the simultaneous adsorption and melting of dsDNA in the presence of surfaces. [22][23][24][25] From a theoretical point of view, the loss of conformational entropy of DNA near the surface is compensated by the attractive interaction between the DNA and the surface. This subtle competition between entropy and attractive surface energy makes free energy a minimum, making the problem complex but worth exploring.…”