Trapping DNA near a solid-state nanopore

Abstract

We demonstrate that voltage-biased solid-state nanopores can transiently localize DNA in an electrolyte solution. A double-stranded DNA (dsDNA) molecule is trapped when the electric field near the nanopore attracts and immobilizes a non-end segment of the molecule across the nanopore orifice without inducing a folded molecule translocation. In this demonstration of the phenomenon, the ionic current through the nanopore decreases when the dsDNA molecule is trapped by the nanopore. By contrast, a translocating dsDNA molecule under the same conditions causes an ionic current increase. We also present finite-element modeling results that predict this behavior for the conditions of the experiment.

Figure 1

Schematic of the experimental setup. (Orange arrow) Electric-field-induced trapping force. (Inset, top right) Transmission electron micrograph of a typical nanopore.

Figure 2

Current trace of a trapping event followed by translocation. The current in region B decreases from the open pore level in regions A and E. Briefly, the current returns to the open pore level, in region C, before the translocating dsDNA molecule increases the current, transiently, in region D.

Figure 3

(a) Scatter plot of 86 10-kb dsDNA events at 600 mV in 100 mM KCl. Seventeen of the 86 events show a decrease in the ionic current before translocation (top trace). The remaining events exhibit only the typical translocation induced increase in the ionic current (bottom trace). (b) 285 10-kb dsDNA translocation events through the same nanopore as in panel a, at 500 mV in 1 M KCl. Current traces show representative events from different areas of the scatter plot.

Figure 4

Profile of the nanopore geometry used in the finite element calculations along with potential contours at 600-mV applied bias.

Figure 5

Translocation experimental data (gray circles) and simulation prediction (gray solid line). Trapping experimental data (black squares) and simulation prediction (black lines). The dashed and solid lines represent 2.8 nm and 2.2 nm diameter dsDNA trapping models, respectively.