Force and kinetic barriers to initiation of DNA unzipping

A semimicroscopic model of the binding of the two nucleotide strands in a double-stranded DNA is used to describe the effects of applied tension on strand unpairing. We show that the model describes strand separation by elevated temperature, applied torque, and applied force. In particular, we show how the interactions responsible for stabilizing the double helix against thermal denaturation determine the ≈12 pN force threshold for DNA strand separation. The larger rigidity of the strands when formed into double-stranded DNA, relative to that of isolated strands, gives rise to a potential barrier to unzipping. We show that this barrier results in a ≈250 pN force barrier opposing the beginning of strand separation. The thermal-fluctuation-assisted “tunnelling” through the barrier is then analyzed using instanton calculations. The resulting kinetics of unzipping initiation is shown to be consistent with solution-phase strand dissociation experiments, and can explain results of two recent unzipping experiments done using atomic-force microscopy.