Hairpins in the conformations of a confined polymer
arXiv:1611.05736 · doi:10.1063/1.5018787
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.
Revised version. 22 pages, 7 figures, 2 tables, supplementary material
References in corpus (7)
- Scaling theory of DNA confined in nanochannels and nanoslits
- DNA Confined in Nanochannels: Hairpin Tightening by Entropic Depletion
- Conformations of confined biopolymers
- Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics
- Confined polymers in the extended de Gennes regime
- Scaling regimes of a semi-flexible polymer in a rectangular channel
- Free energy of a folded polymer under cylindrical confinement