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.
(Less)
- author
- 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
- organization
- publishing date
- 2018
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Physics
- volume
- 149
- issue
- 21
- article number
- 215101
- publisher
- American Institute of Physics (AIP)
- external identifiers
-
- scopus:85058109959
- pmid:30525714
- 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
- 2024-06-11 01:04:47
@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>}},
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 (AIP)}},
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}},
doi = {{10.1063/1.5051319}},
volume = {{149}},
year = {{2018}},
}