Concepedia

Slowing down DNA Translocation through a Nanopore in Lithium Chloride

Stefan W. Kowalczyk, David B. Wells, Aleksei Aksimentiev, Cees Dekker

Nano Letters · 2012 · 447 citations · 36 references

TL;DR

The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab‑on‑a‑chip applications. The study investigates how counterion binding reduces DNA charge using nanopore translocation experiments and all‑atom MD simulations. The authors used nanopore translocation experiments and all‑atom MD simulations to examine how counterion binding alters DNA charge and to reveal that Li⁺ and Na⁺ bind more strongly than K⁺. The experiments and simulations show that translocation time increases dramatically as counterions shrink from K⁺ to Na⁺ to Li⁺, enabling at least a ten‑fold improvement in nanopore resolution.

Abstract

The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial reduction of the DNA charge due to counterion binding by means of nanopore translocation experiments and all-atom molecular dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA molecule through a solid-state nanopore strongly increases as the counterions decrease in size from K(+) to Na(+) to Li(+), both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li(+) and Na(+) bind DNA stronger than K(+). These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resolution in nanopore applications.