Tensile force in a single-stranded DNA gap

We recently measured the melting (or dehybridization) rate of a short DNA duplex in the presence of small tensile forces in the range of 1-5 pN and found that the melting rate decays exponentially with force even in this small force range. Interestingly, we also observed that the dehybridization rate of a short oligo from a single-stranded DNA (ssDNA) gap is significantly faster than that from an isolated duplex. This result is consistent with the presence of ~1pN of tensile force in the ssDNA gap. We hypothesized that this tensile force arises from the steric repulsion between the double-stranded DNA (dsDNA) segments flanking the gap. We used a simple model to calculate the mutually excluded volume between two dsDNA segments as a function of distance, which produces a force of a similar magnitude. Coarse-grained simulations of our system also reveal a similar force of entropic origin.