(698b) Backfolding and Hairpin Formation of DNA and Other Semiflexible Polymers in Nanochannel Confinement

There has been a recent surge of interest in understanding the properties of confined semiflexible polymers owing to the development of nanochannel-based genomics technology. Odijk's seminal theory (Macromolecules, 1983) for the properties of confined semiflexible polymers has been extensively used to explain outcomes from both experiments and simulations where the confinement size is much smaller than the persistence length of the molecule. However, this theory does not account for backfolding or hairpin formation of the confined chain, which is possible in the practical situation when the confinement size is of the order of the persistence length. More recently, Odijk (Phys. Rev. E, 2008) proposed a Flory theory for the statistics of such backfolded chains in confinement. In this talk, we present results from large scale Pruned-Enriched Rosenbluth Method (PERM) simulations of a coarse-grained discrete wormlike chain model that demonstrate that Odijk's scaling theory for backfolding of semiflexible polymers is indeed correct for confinement in square channels. Furthermore, we show results for the more experimentally relevant case of confinement in rectangular channels. We then discuss the implications of our work to experiments and genome mapping technology.