Hairpins in the conformations of a confined polymer

TL;DR

This paper investigates the extension behavior of confined semiflexible polymers with intermediate hairpin formation, using experiments on RecA-coated DNA and Monte Carlo simulations, revealing non-Gaussian extension distributions influenced by hairpins.

Contribution

It provides the first experimental and theoretical analysis of polymer extension statistics in the intermediate hairpin regime, bridging the gap between known limiting cases.

Findings

Extension distribution is highly non-Gaussian.

Monte Carlo simulations agree with experimental results.

Hairpins significantly influence the distribution tail.

Abstract

If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, 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.