Origin of Current Blockades in Nanopore Translocation Experiments

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 et al., 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 et al. 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.

Figure 1

Left panel: Sketch of a typical DNA translocation experiment. DNA (blue contour) is driven through the pore by applying a voltage. Right panel: We model only the central region of an long cylindrical pore. It contains a DNA homopolymer centered on the axis, a variable KCl concentration, and is filled with explicit water molecules.

Figure 2

Left panel: Comparison of the ion concentration as a function of the distance $r$ from the pore axis at around $0.3\mathrm{mol}/\mathrm{l}$ of the atomistic data (points) to the continuum model (broken lines). The long distance decay of the second peak at $r=1.25\mathrm{nm}$ is well described by the continuum model. Right panel: Comparison of the measured ion and water velocities as a function of $r$.

Figure 3

Left panel: position dependent ion mobility normalized by the bulk mobility $(v-u)/{\mu }_{D}E$ for five different salt concentration. Near the DNA and the wall a significant reduction is observed. Right panel: Observed current densities as a function of $r$. We distinguish the direct current $j_D$, the advective current $j_W$, and the (negative) frictional current $j_F$. The direct current near the DNA is largely canceled by friction.

Figure 4

Relative current modulation caused by the DNA as a function of salt concentration for the experiments (diamonds) and simulations (circles). The quantitative agreement between simulations and experiments is good, especially the location of the crossover point between enhancement and reduction. We decomposed the total current into direct current (downward triangles), advective current (upward triangles), and friction (squares) and consider their contribution to the modulation independently. The current reduction due to friction is responsible for observing an overall current reduction at large salt concentrations.