Chain persistency in single-stranded DNA

Abstract

We develop a theoretical approach to hairpin-loop formation of single-stranded (ss) DNA by treating the strand as a two-state system in which bases are either “stacked” or “unstacked.” The looping kinetics of ssDNA is shown to be intrinsically different from that of a wormlike chain; it is mainly controlled by stacking-breakage probability, not by the mean curvature of loops, and highly sensitive to the composition of the loop as seen in recent experiments. Our estimate of a stacking energy for poly$\left(dA\right)$, $-3.9\text{kcal}∕\mathrm{mol}$, is consistent with known results.