Topological Patterns in Two-dimensional Gel Electrophoresis of DNA Knots

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.

To appear in PNAS; 12 pages: text+SI

References in corpus (4)

• Threading Dynamics of Ring Polymers in a Gel
• Dynamics of Self-Threading Ring Polymers in a Gel
• Rings in Random Environments: Sensing Disorder Through Topology
• Sedimentation of Knotted Polymers

Cited by in corpus (6)

• On the Tree-Like Structure of Rings in Dense Solutions
• Periodic motion of sedimenting flexible knots
• A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
• Geometric Learning of Knot Topology
• Rate dependence of current and fluctuations in jump models with negative differential mobility
• Topological Sieving of Rings According to their Rigidity