Macromolecules, Vol.46, No.16, 6659-6666, 2013
Equilibrium Statistics of a Surface-Pinned Semiflexible Polymer
Recently, looping probability of short double-stranded DNA (dsDNA) was measured from surface-tethered molecules and was shown to exceed the wormlike chain model prediction. However, it is not clear how the presence of a confining surface affects the structure of the polymer. Here, we investigate the conformational distribution of an isolated, surface-pinned dsDNA in the semiflexible regime. To obtain chain statistics, we randomly sampled chain conformations consistent with Boltzmann statistics and the confining surface. On the basis of comparison of simulated chain statistics to a theoretical wormlike chain model, we show that the effect of pinning can be analogous to a change in effective stiffness. In the semiflexible regime, middle pinning results in a 10-fold increase in looping probability and 100-fold increase in surface contact rate compared to end pinning. Our results highlight nontrivial effects of pinning a wormlike chain that cannot be deduced from the Gaussian chain model.