Current blockade in nanopores in the presence of double-stranded DNA and the microscopic mechanisms
Related Experiment Video
Updated: Jun 17, 2026

Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores
Published on: October 31, 2013
1Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996-2200, USA.
Abstract:
We have carried out Brownian Dynamics calculations to investigate the mechanism of current blockade by double-stranded DNA (dsDNA) in a nanopore. We find that the blockade current crosses over from negative to positive as the ionic concentration decreases, similar to experiment. In addition to the volume exclusion and the counterion condensation, we find that the electric double layer overlap is a significant factor in the current blockade. The electric double layer overlap causes the ionic concentration beyond the immediate neighborhood of dsDNA and the wall to be lower in a dsDNA-blocked nanopore than the plateau ionic concentration away from the wall in an open nanopore, thus contributing importantly to the blockade current. On the basis of the calculated ion distribution function in the nanopore, we examined the counterion condensation to the dsDNA. We find the excess counterion condensation to be about 60% of the charge on the dsDNA, which is within the range of percentages obtained from experiments. We performed equilibrium and nonequilibrium (under an applied electric field) Brownian dynamics simulations to calculate the average mobility of the ions in nanopores. The calculated ion mobility is found to be reduced in DNA-blocked nanopores.
More Related Videos
08:42Determination of Zeta Potential via Nanoparticle Translocation Velocities through a Tunable Nanopore: Using DNA-modified Particles as an Example
Published on: October 26, 2016
07:50Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks
Published on: November 25, 2015
Related Concept Videos
The DNA Replication Fork
Single-Strand DNA Binding Proteins
Restarting Stalled Replication Forks
Fixing Double-strand Breaks
DNA Topoisomerases
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...
The Replisome
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...