Pulling DNA: The Effect of Chain Length on the Mechanical Stability of DNA Chain

Abstract

We have investigated the effect of chain length on the thermal denaturation as well as on mechanical unzipping of double stranded DNA (ds-DNA) molecule. We use a simple nonlinear Peyrard Bishop and Dauxois (PBD) model and calculate the melting temperature as well as the critical force as a function of chain length for different heterogeneous chains. We found that in mechanical unzipping, when a force is applied on an end, there is a length up-to which the effect of applied force sustains. The base pairs beyond this length can not feel the force that is applied on the end. We have studied the chain with other end to be open and with the other end to be restricted. By comparing the force required to unzip the chain in these two cases, we found a critical length above which the entropy contribution from the end is not significant to change the duplex state of the chain. For shorter chain, we found that the entropic forces due to open end have significant contribution to change the duplex state of DNA to single strand state of DNA chain.