Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore

TL;DR

This study investigates how knots in long polyelectrolyte chains affect their translocation through nanopores, revealing that knots increase friction and can halt translocation at high forces, with implications for DNA sequencing.

Contribution

It demonstrates through simulations that knots cause frictional effects rather than jamming, and identifies a force-dependent dynamical crossover affecting translocation.

Findings

Knots increase effective friction during translocation.

High applied force can halt translocation due to knots.

The dynamical crossover is experimentally verifiable.

Abstract

The advent of solid state nanodevices allows for interrogating the physico-chemical 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 study. 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, is of relevance in applicative contexts, such as DNA nanopore sequencing.