title: Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore.
abstract: The advent of solid state nanodevices allows for interrogating the physicochemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been recently characterized by theoretical and computational studies of model polymer chains free from self-entanglement. However, sufficiently long equilibrated chains are necessarily knotted. The impact of such topological "defects" on the translocation process is largely unexplored, and is addressed in this Letter. By using Brownian dynamics simulations on a coarse-grained polyelectrolyte model we show that knots, despite being trapped at the pore entrance, do not per se cause the translocation process to jam. Rather, knots introduce an effective friction that increases with the applied force, and practically halts the translocation above a threshold force. The predicted dynamical crossover, which is experimentally verifiable, ought to be relevant in applicative contexts, such as DNA nanopore sequencing.
authors.affiliation: SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy. anrosa@sissa.it
authors.forename: A
authors.initials: A
authors.lastname: Rosa
authors.forename: M
authors.initials: M
authors.lastname: Di Ventra
authors.forename: C
authors.initials: C
authors.lastname: Micheletti
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry; D004573:Electrolytes / Q000737:chemistry*; D004586:Electrophoresis; D008956:Models, Chemical; D008958:Models, Molecular; D058608:Nanopores / Q000648:ultrastructure*; D011108:Polymers / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D004573:Electrolytes; D011108:Polymers