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Face of Tobias Ambjörnsson. Photo.

Tobias Ambjörnsson

Senior lecturer

Face of Tobias Ambjörnsson. Photo.

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

Author

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

Summary, in English

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.

Department/s

  • Computational Biology and Biological Physics
  • Solid State Physics
  • BioCARE: Biomarkers in Cancer Medicine improving Health Care, Education and Innovation
  • NanoLund

Publishing year

2018

Language

English

Publication/Series

Journal of Chemical Physics

Volume

149

Issue

21

Document type

Journal article

Publisher

American Institute of Physics (AIP)

Topic

  • Physical Chemistry

Status

Published

ISBN/ISSN/Other

  • ISSN: 0021-9606