Topology Sorting and Characterization of Folded Polymers Using Nano-pores

TL;DR

This study uses molecular dynamics simulations to explore how folded polymers translocate through nano-pores, revealing potential for topology-based molecule characterization and sorting.

Contribution

It introduces a novel approach to analyze polymer topology during nano-pore translocation, including unfolding effects and contact site detection.

Findings

Nano-pore translocation dynamics vary with polymer topology.

Nano-pores can distinguish pure topological states.

Contact site positions can be read during translocation.

Abstract

Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the molecule passes through the nano-pore. The topology of a folded polymer chain is defined as the arrangement of the intramolecular contacts, known as circuit topology. In the case where intramolecular contacts remain intact, we show that the dynamics of passage through a nano-pore varies for molecules with differing topologies: a phenomenon that can be exploited to enrich certain topologies in mixtures. We find that the nano-pore allows reading of topology for short chains. Moreover, when the passage is coupled with unfolding, the nano-pore enables discrimination between pure states, i.e., states for which the majority of contacts are arranged identically. In this case, as we show here, it is also possible to read the positions of the contact sites along a chain. Our results demonstrate the applicability of nano-pore technology to characterize and sort molecules based on their topology.