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

Krog, Jens LU ; Alizadehheidari, Mohammadreza; Werner, Erik; Bikkarolla, Santosh Kumar; Tegenfeldt, Jonas O. LU ; Mehlig, Bernhard; Lomholt, Michael A.; Westerlund, Fredrik and Ambjörnsson, Tobias LU (2018) In Journal of Chemical Physics 149(21).
Abstract

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... (More)

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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Physics
volume
149
issue
21
publisher
American Institute of Physics
external identifiers
  • scopus:85058109959
ISSN
0021-9606
DOI
10.1063/1.5051319
language
English
LU publication?
yes
id
a904d04c-1176-4a41-91fe-980809562a8f
date added to LUP
2018-12-18 13:35:04
date last changed
2019-10-15 06:52:46
@article{a904d04c-1176-4a41-91fe-980809562a8f,
  abstract     = {<p>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.</p>},
  articleno    = {215101},
  author       = {Krog, Jens and Alizadehheidari, Mohammadreza and Werner, Erik and Bikkarolla, Santosh Kumar and Tegenfeldt, Jonas O. and Mehlig, Bernhard and Lomholt, Michael A. and Westerlund, Fredrik and Ambjörnsson, Tobias},
  issn         = {0021-9606},
  language     = {eng},
  number       = {21},
  publisher    = {American Institute of Physics},
  series       = {Journal of Chemical Physics},
  title        = {Stochastic unfolding of nanoconfined DNA : Experiments, model and Bayesian analysis},
  url          = {http://dx.doi.org/10.1063/1.5051319},
  volume       = {149},
  year         = {2018},
}