Promoting single-file DNA translocations through nanopores using electroosmotic flow

TL;DR

This study demonstrates that electroosmotic flow can be used to promote single-file DNA translocations through nanopores by adjusting electrolyte conditions, improving the accuracy of nanopore sensing.

Contribution

It reveals how electrolyte concentration, pH, and PEG content influence DNA folding and translocation mode, highlighting the role of electroosmotic flow in controlling DNA conformation during nanopore sensing.

Findings

Over 90% of translocations are single-file at specific ionic conditions.

Electroosmotic flow influences DNA entry orientation and folding.

Control of DNA folding enhances nanopore sensing accuracy.

Abstract

Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be controlled by changing the electrolyte concentration, pH and PEG content of the measurement buffer. At 1 M LiCl or 0.35 M KCl in neutral pH, single-file translocations make up more than 90% of the total. We attribute the effect to the onset of electroosmotic flow from the pore at low ionic strength. Our hypothesis on the critical role of flows is supported by the preferred orientation of entry of a strand that has been folded into a multi-helix structure at one end. Control over DNA folding is critical for nanopore sensing approaches that use modifications along a DNA strand and the associated secondary current drops to encode information.