Hairpins in the conformations of a confined polymer

E. Werner, A. Jain, A. Muralidhar, K. Frykholm, T. St Clere Smithe, J. Fritzsche, F. Westerlund, K. D. Dorfman, B. Mehlig

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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.

Original languageEnglish (US)
Article number024105
JournalBiomicrofluidics
Volume12
Issue number2
DOIs
StatePublished - Mar 1 2018

Bibliographical note

Funding Information:
The labeled RecA protein was a kind gift from Edwige B. Garcin and Mauro Modesti. E.W. and B.M. wish to thank Stefano Bo and Tobias Ambj?rnsson for discussions concerning Eq. (12). Financial support from Vetenskapsradet [Grant Nos. 2013-3992, 2017-3865 (BM) and 2011-4324 (FW)] and from the National Institutes of Health [R01-HG006851(KDD)] is gratefully acknowledged. The computational work was carried out in part using computing resources at the University of Minnesota Supercomputing Institute, and in part at the Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC).

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