Direction- and Salt-Dependent Ionic Current Signatures for DNA Sensing with Asymmetric Nanopores

TL;DR

This study explores how the geometry and salt concentration of asymmetric nanopores influence ionic current signatures during DNA translocation, revealing complex behaviors driven by ion polarization and geometric effects.

Contribution

It provides a comprehensive analysis combining experiments and finite element modeling to explain ionic current variations in asymmetric nanopores, advancing DNA sensing technology.

Findings

Current blockade levels depend on translocation direction at high salt concentrations.

Unexpected current decreases and increases occur at lower salt concentrations during DNA exit.

Finite element calculations successfully explain observed ionic current behaviors.

Abstract

Solid-state nanopores are promising tools for single molecule detection of both DNA and proteins. In this study, we investigate the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of such conically shaped pores. We studied how the geometry of a nanopore affects the detected ionic current signal of a translocating DNA molecule over a wide range of salt concentration. The blockade level in the ionic current depends on the translocation direction at a high salt concentration, and at lower salt concentrations we find a non-intuitive ionic current decrease and increase within each single event for the DNA translocations exiting from confinement. We use recently developed DNA rulers with markers and finite element calculations to explain our observations. Our calculations explain the shapes of the signals observed at all salt concentrations and show that the unexpected current decrease and increase are due to the competing effects of ion concentration polarization and geometric exclusion of ions. Our analysis shows that over a wide range of geometry, voltage and salt concentrations we are able to understand the ionic current signals of DNA in asymmetric nanopores enabling signal optimization in molecular sensing applications.