DNA stretching modeled at the base pair level: Overtwisting and shear instability in elastic linkages

Stretching experiments on single DNA molecules indicate that, counterintuitive to expectations, DNA overwinds when stretched and, at large forces, undergoes a transition into an overstretched form indicated by a plateau on the force–displacement diagrams. It is believed that these effects are the result of non-linearities in the elastic response of DNA. We use a discrete, base pair level model to simulate the behavior of short DNA molecules, taking into account the sequence dependent physical properties of DNA alongside with the coupling between the kinematical step parameters, yet retaining the quadratic form of local elastic energy function. By constructing bifurcation diagrams of equilibrium configurations and studying the dependence on base pair combinations we show that the quadratic model is capable of explaining the overtwisting as a result of coupling between modes of deformation and overstretching as a result of shear instability.