ArticleProceedings of the National Academy of Sciences of the United States of America2015
Topological patterns in two-dimensional gel electrophoresis of DNA knots.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A parallel algorithm for the computation of the Jones polynomial.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Phosphoglycerate Kinase Can Adopt Topologically Misfolded Forms That Are More Stable Than Its Native State.Journal of the American Chemical Society · 2026Article
- Geometric learning of knot topology.Soft matter · 2023Article
- A Trefoil Knot Polymer Chain Translocates through a Funnel-like Channel: A Multi-Particle Collision Dynamics Study.Polymers · 2022Article
- Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.Polymers · 2021Article
- A review on nonlinear DNA physics.Royal Society open science · 2020Review
- The bacterial condensin MukB compacts DNA by sequestering supercoils and stabilizing topologically isolated loops.The Journal of biological chemistry · 2017Article
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3 authors.
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Abstract
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that 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 nonmonotonic mobility at moderate fields. Consequently, in 2D 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.
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