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

Artikel i vetenskaplig tidskrift
Författare J. Krog
M. Alizadehheidari
Erik Werner
S. K. Bikkarolla
J. O. Tegenfeldt
Bernhard Mehlig
M. A. Lomholt
F. Westerlund
T. Ambjornsson
Publicerad i Journal of Chemical Physics
Volym 149
Nummer/häfte 21
ISSN 0021-9606
Publiceringsår 2018
Publicerad vid Institutionen för fysik (GU)
Språk en
Länkar dx.doi.org/10.1063/1.5051319
Ämnesord single-molecule, resistance plasmids, compaction, identification, elongation, chains, knots, Chemistry, Physics
Ämneskategorier Kemisk fysik

Sammanfattning

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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