Hairpins in the conformations of a confined polymer

Abstract

If a semiflexible polymer confined to a narrow channel bends around by 180°, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here, we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte-Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.

Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis

“…The resulting conformations are thus quite different from those considered in Ref. [47]. Second, immediately after the loop is cut, the unfolding process starts from both open ends.…”

“…[46] In general the dynamics of confined DNA is subject to diffusive fluctuations, originating from the molecular motion in the fluid. [47] considered a single hairpin in the conformation of a confined semiflexible polymer. Entropic repulsion causes the hairpin to unfold.…”

“…This process is described by a generalized diffusion equation that takes into account the competition between the deterministic entropic force and the stochastic molecular dynamics. [47] [48] measured the unfolding dynamics of circular DNA to its linear form. Several different types of biological DNA molecules are circular, such as mitochondrial DNA in eukaryotic cells and chromosomal and plasmid DNA in bacteria.…”

“…There are three main aspects that distinguish our system from those in Refs. [43,44,45,46,47]. First, the persistence length of the DNA molecules is of the same order as the channel size, so that the DNA molecule can fold back upon itself several times.…”

Distribution of label spacings for genome mapping in nanochannels

“…We further expect that the tails are sensitive to flexibility of the DNA backbone, providing a probe for sequence-specific effects on confined DNA conformations, an emerging area of interest 41. Finally, an entirely open question is to understand the conformational dynamics [42][43][44][45][46]. While the results described here show that the equilibrium conformation statistics of strongly confined DNA molecules are now well understood, much less is known about the dynamics.…”