Abstract
We present a detailed investigation of the ionic current in a cylindrical model nanopore in the absence and the presence of a double stranded DNA homopolymer. Our atomistic simulations are capable of reproducing almost exactly the experimental data obtained by Smeets etal., including notably the crossover salt concentration that yields equal current measurements in both situations. We can rule out that the observed current blockade is due to the steric exclusion of charge carriers from the DNA, since for all investigated salt concentrations the charge carrier density is higher when the DNA is present. Calculations using a mean-field electrokinetic model proposed by van Dorp etal. fail quantitatively in predicting this effect. We can relate the shortcomings of the mean-field model to a surface related molecular drag that the ions feel in the presence of the DNA. This drag is independent of the salt concentration and originates from electrostatic, hydrodynamic, and excluded volume interactions.
Highlights
Nanopores are holes in membranes that can range from one to a few hundred nanometers
Macromolecules, in this Letter we consider doublestranded DNA, induce short modulations in the electric current when traversing the pore. These events are the main observable in the experiments
In this Letter we investigate the problem with the help of atomistic molecular dynamics simulations
Summary
Nanopores are holes in membranes that can range from one to a few hundred nanometers. Our results show quantitative agreement with the experiments of Smeets et al [6], and a detailed comparison of our results to an electrokinetic continuum model reveals that the ions in the vicinity of the DNA are slowed down considerably when compared to the bulk. For electrolyte concentrations above 0:8 mol=l the number of ions excluded from the pore due to the volume of the DNA exceeds the number of extra ions in the counterion cloud.
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