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

Jens Krog, Mohammadreza Alizadehheidari, Erik Werner, Santosh Bikkarolla, Jonas O. Tegenfeldt, Bernhard Mehlig, Michael A. Lomholt, Fredrik Westerlund, Tobias Ambjörnsson

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, 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.

Original languageEnglish
Article number215101
Pages (from-to)1-13
Number of pages13
JournalJournal of Chemical Physics
Issue number21
Publication statusPublished (in print/issue) - 4 Dec 2018

Bibliographical note

Funding Information:
J.K. and M.A.L. acknowledge the support from the Danish Council for Independent Research (Grant No. 4002-00428B). F.W., B.M., and T.A. acknowledge funding from the Swedish Research Council (Grant Nos. 2015-5062, 2017-03865, and 2014-4305). The circular DNA was a kind gift from Alex Hastie and Denghong Zhang at BioNanoGenomics.

Publisher Copyright:
© 2018 Author(s).

Copyright 2018 Elsevier B.V., All rights reserved.


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