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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics

Alizadehheidari, Mohammadreza; Werner, Erik; Noble, Charleston LU ; Reiter-Schad, Michaela LU ; Nyberg, Lena K.; Fritzsche, Joachim; Mehlig, Bernhard; Tegenfeldt, Jonas LU ; Ambjörnsson, Tobias LU and Persson, Fredrik, et al. (2015) In Macromolecules 48(3). p.871-878
Abstract
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results... (More)
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations. (Less)
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publishing date
type
Contribution to journal
publication status
published
subject
in
Macromolecules
volume
48
issue
3
pages
871 - 878
publisher
The American Chemical Society
external identifiers
  • wos:000349574100046
  • scopus:84922593842
ISSN
0024-9297
DOI
10.1021/ma5022067
language
English
LU publication?
yes
id
e20a5103-01ae-48a3-bf5d-93f79b9ea1b7 (old id 5160190)
date added to LUP
2015-03-25 08:32:49
date last changed
2017-08-27 03:33:24
@article{e20a5103-01ae-48a3-bf5d-93f79b9ea1b7,
  abstract     = {Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.},
  author       = {Alizadehheidari, Mohammadreza and Werner, Erik and Noble, Charleston and Reiter-Schad, Michaela and Nyberg, Lena K. and Fritzsche, Joachim and Mehlig, Bernhard and Tegenfeldt, Jonas and Ambjörnsson, Tobias and Persson, Fredrik and Westerlund, Fredrik},
  issn         = {0024-9297},
  language     = {eng},
  number       = {3},
  pages        = {871--878},
  publisher    = {The American Chemical Society},
  series       = {Macromolecules},
  title        = {Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics},
  url          = {http://dx.doi.org/10.1021/ma5022067},
  volume       = {48},
  year         = {2015},
}