Modeling the Current Modulation of Bundled DNA Structures in Nanopores

TL;DR

This study models how bundled DNA nanostructures affect ionic current in nanopores, using four simulation approaches, revealing consistent salt-dependent conductivity but also highlighting discrepancies with experimental data.

Contribution

Introduces four progressively detailed simulation models for DNA nanostructures in nanopores, advancing understanding of current modulation mechanisms.

Findings

Consistent salt-dependent pore conductivity across models

Significant deviations from experimental results

Discussion of model limitations and future extensions

Abstract

We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2x2 origami structure with increasing level of detail: from the mean-field level to an all-atom representation of the DNA structure. We observe a consistent pore conductivity as a function of salt concentration for all four models. However, a comparison of our data to recent experimental investigations on similar systems displays significant deviations. We discuss possible reasons for the discrepancies and propose extensions to our models for future investigations.