title: Extension of nanoconfined DNA: Quantitative comparison between experiment and theory.
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.
authors.affiliation: Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden.
authors.forename: V
authors.initials: V
authors.lastname: Iarko
authors.affiliation: Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden.
authors.forename: E
authors.initials: E
authors.lastname: Werner
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden.
authors.forename: L K
authors.initials: LK
authors.lastname: Nyberg
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden.
authors.forename: V
authors.initials: V
authors.lastname: Müller
authors.affiliation: Department of Applied Physics, Chalmers University of Technology, 412 96 Göteborg, Sweden.
authors.forename: J
authors.initials: J
authors.lastname: Fritzsche
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, 22 100 Lund, Sweden.
authors.forename: T
authors.initials: T
authors.lastname: Ambjörnsson
authors.affiliation: Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden.
authors.forename: J P
authors.initials: JP
authors.lastname: Beech
authors.affiliation: Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden.|NanoLund, Lund University, 22 100 Lund, Sweden.
authors.forename: J O
authors.initials: JO
authors.lastname: Tegenfeldt
authors.affiliation: Department of Public Health and Community Medicine, University of Gothenburg, 413 46 Göteborg, Sweden.
authors.forename: K
authors.initials: K
authors.lastname: Mehlig
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden.
authors.forename: F
authors.initials: F
authors.lastname: Westerlund
authors.affiliation: Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden.
authors.forename: B
authors.initials: B
authors.lastname: Mehlig
mesh_terms: D010582:Bacteriophage lambda; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D036103:Nanotechnology
chemical_list: D004247:DNA