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Extension of nanoconfined DNA: Quantitative comparison between experiment and theory

Iarko, V.; Werner, E.; Nyberg, L. K.; Muller, V.; Fritzsche, J.; Ambjörnsson, Tobias LU ; Beech, Jason LU ; Tegenfeldt, Jonas LU ; Mehlig, K. and Westerlund, F., et al. (2015) In Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)2001-01-01+01:002016-01-01+01:00 92(6).
Abstract
The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic... (More)
The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution. (Less)
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Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)2001-01-01+01:002016-01-01+01:00
volume
92
issue
6
publisher
American Physical Society
external identifiers
  • wos:000365872700009
  • pmid:26764721
  • scopus:84951031282
ISSN
1539-3755
DOI
10.1103/PhysRevE.92.062701
language
English
LU publication?
yes
id
a1b7f8f0-81a2-4cae-8e50-b8812825729d (old id 8560194)
date added to LUP
2016-01-26 08:53:17
date last changed
2017-08-27 03:22:51
@article{a1b7f8f0-81a2-4cae-8e50-b8812825729d,
  abstract     = {The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.},
  articleno    = {062701},
  author       = {Iarko, V. and Werner, E. and Nyberg, L. K. and Muller, V. and Fritzsche, J. and Ambjörnsson, Tobias and Beech, Jason and Tegenfeldt, Jonas and Mehlig, K. and Westerlund, F. and Mehlig, B.},
  issn         = {1539-3755},
  language     = {eng},
  number       = {6},
  publisher    = {American Physical Society},
  series       = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)2001-01-01+01:002016-01-01+01:00},
  title        = {Extension of nanoconfined DNA: Quantitative comparison between experiment and theory},
  url          = {http://dx.doi.org/10.1103/PhysRevE.92.062701},
  volume       = {92},
  year         = {2015},
}