Anomalous scaling in nanopore translocation of structured heteropolymers

TL;DR

This paper investigates how the translocation time of structured RNA molecules through nanopores scales with length, revealing a power law with an exponent influenced by temperature, due to diffusion in a complex energy landscape.

Contribution

It introduces a model for RNA translocation that accounts for secondary structure breaking, showing anomalous scaling behavior beyond simple diffusion expectations.

Findings

Translocation time follows a power law with respect to RNA length.

The scaling exponent varies with temperature and exceeds the diffusive limit.

Diffusion occurs in a one-dimensional energy landscape with a logarithmic barrier.

Abstract

Translocation through a nanopore is a new experimental technique to probe physical properties of biomolecules. A bulk of theoretical and computational work exists on the dependence of the time to translocate a single unstructured molecule on the length of the molecule. Here, we study the same problem but for RNA molecules for which the breaking of the secondary structure is the main barrier for translocation. To this end, we calculate the mean translocation time of single-stranded RNA through a nanopore of zero thickness and at zero voltage for many randomly chosen RNA sequences. We find the translocation time to depend on the length of the RNA molecule with a power law. The exponent changes as a function of temperature and exceeds the naively expected exponent of two for purely diffusive transport at all temperatures. We interpret the power law scaling in terms of diffusion in a one-dimensional energy landscape with a logarithmic barrier.