Force induced unzipping of dsDNA: The solvent effect

Abstract

The salt concentration of the solution plays an important role in the stabilization of double stranded DNA (dsDNA) molecule. In our work, the Hamiltonian in Peyrard-Bishop Dauxois (PBD) model of a heterogeneous chain has been modified with a stabilizing solvent interaction term. This term strengthens the base pair dissociation energy and stabilizes the hydrogen bonds between complementary strands of dsDNA. To study the effect of salt concentration we have modified the potentials appearing in this model. We investigated the influence of salt concentration on the force required to unzip the chain. The force induced unzipping is studied in both constant extension ensemble (CEE) and constant force ensemble (CFE). We found that the results are independent of choice of the ensembles and are in good agreement with the experimental results