Extension of nanoconfined DNA: Quantitative comparison between experiment and theory

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Vitalii IarkoB Mehlig

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.

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Citations

Jan 7, 2017·Soft Matter·Mattia MarendaCristian Micheletti
Jul 1, 2017·Integrative Biology : Quantitative Biosciences From Nano to Macro·Karolin FrykholmFredrik Westerlund
Jan 13, 2018·Physical Review Letters·E WernerB Mehlig
Dec 12, 2018·Small·Saroj Dangi, Robert Riehn
Jan 15, 2016·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Toby St Clere SmitheBernhard Mehlig
Jul 4, 2018·Scientific Reports·Maedeh RoushanRobert Riehn
Mar 17, 2017·Physical Review. E·Guo Kang CheongKevin D Dorfman
Dec 12, 2018·The Journal of Chemical Physics·Jens KrogTobias Ambjörnsson
Jun 24, 2017·PloS One·Paola C TorcheTobias Ambjörnsson
Feb 27, 2018·Physical Review. E·Guo Kang CheongKevin D Dorfman
Sep 23, 2019·The Journal of Chemical Physics·Hui-Min ChuangKevin D Dorfman
Sep 17, 2018·The Journal of Chemical Physics·Aditya Bikram BhandariKevin D Dorfman
Mar 31, 2018·Macromolecules·Damini GuptaKevin D Dorfman

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