Topological patterns in two-dimensional gel electrophoresis of DNA knots
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Publication:2962297
DOI10.1073/PNAS.1506907112zbMATH Open1355.92082arXiv1504.02327OpenAlexW2141328247WikidataQ36155180 ScholiaQ36155180MaRDI QIDQ2962297FDOQ2962297
Authors: Davide Michieletto, Davide Marenduzzo, E. Orlandini 
Publication date: 16 February 2017
Published in: Proceedings of the National Academy of Sciences (Search for Journal in Brave)
Abstract: Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel, and in particular on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an "entanglement number", and yield a non-monotonic mobility at moderate fields. Consequently, in two-dimensional electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.
Full work available at URL: https://arxiv.org/abs/1504.02327
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Cites Work
Cited In (6)
- Topology in soft and biological matter
- Rate dependence of current and fluctuations in jump models with negative differential mobility
- Title not available (Why is that?)
- Topological Process of Splitting DNA-Links
- Statics and dynamics of DNA knotting
- Monte-Carlo simulations of gel-electrophoresis of DNA knots
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