Theory of DNA translocation through narrow ion channels and nanopores with charged walls

TL;DR

This paper develops a theoretical model predicting how positively charged walls in engineered ion channels alter DNA translocation, affecting ion current, effective charge, and capture rate, with implications for nanopore-based DNA analysis.

Contribution

It introduces a theoretical framework for DNA translocation through charged nanopores, highlighting the impact of wall charge on transport properties, which was not previously modeled.

Findings

Ion current decreases with wall charge at low salt concentrations

Effective DNA charge increases with wall charge, reaching the bare charge at full charge

DNA capture rate exponentially increases with wall charge

Abstract

Translocation of a single stranded DNA through genetically engineered $\alpha$-hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral wild type $\alpha$-hemolysin channel. We assume that the wall charges compensate the fraction $x$ of the bare charge $q_{b}$ of the DNA piece residing in the channel. Our prediction are as follows (i) At small concentration of salt the blocked ion current decreases with $x$. (ii) The effective charge $q$ of DNA piece, which is very small at $x = 0$ (neutral channel) grows with $x$ and at $x=1$ reaches $q_{b}$. (iii) The rate of DNA capture by the channel exponentially grows with $x$. Our theory is also applicable to translocation of a double stranded DNA in narrow solid state nanopores with positively charged walls.