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

Journal article
Authors J. Krog
M. Alizadehheidari
Erik Werner
S. K. Bikkarolla
J. O. Tegenfeldt
Bernhard Mehlig
M. A. Lomholt
F. Westerlund
T. Ambjornsson
Published in Journal of Chemical Physics
Volume 149
Issue 21
ISSN 0021-9606
Publication year 2018
Published at Department of Physics (GU)
Language en
Links dx.doi.org/10.1063/1.5051319
Keywords single-molecule, resistance plasmids, compaction, identification, elongation, chains, knots, Chemistry, Physics
Subject categories Chemical physics

Abstract

Nanochannels provide a means for detailed experiments on the effect of confinement on biomacro-molecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of -mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis. Published by AIP Publishing.

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