Topological patterns in two-dimensional gel electrophoresis of DNA knots.
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.
Department of Physics and Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom; d.michieletto@warwick.ac.uk.
Davide
D
Michieletto
School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom;
Davide
D
Marenduzzo
Dipartimento di Fisica e Astronomia and Sezione, Istituto Nazionale di Fisica Nucleare, Universitá di Padova, 35131 Padova, Italy.
Enzo
E
Orlandini
D000180:Acrylic Resins / Q000737:chemistry* / Q000378:metabolism; D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D057446:Hydrodynamics; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
D000180:Acrylic Resins; C016680:polyacrylamide gels; D004247:DNA
DNA knots; gel electrophoresis; topology