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Hairpins in the conformations of a confined polymer

Journal article
Authors Erik Werner
A. Jain
A. Muralidhar
K. Frykholm
Toby St Clere Smithe
J. Fritzsche
F. Westerlund
K. D. Dorfman
Bernhard Mehlig
Published in Biomicrofluidics
Volume 12
Issue 2
ISSN 1932-1058
Publication year 2018
Published at Department of Physics (GU)
Language en
Keywords Conformations, Intelligent systems, Monte Carlo methods, Confined polymers, DNA molecules, Narrow channel, Non-Gaussian, Semi-flexible polymers, Simple modeling, Wormlike chain, Polymers
Subject categories Microbiology, Polymer Chemistry


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. © 2018 Author(s).

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