Direction- and Salt-Dependent Ionic Current Signatures for DNA Sensing with Asymmetric Nanopores

Abstract

Solid-state nanopores are promising tools for single-molecule detection of both DNA and proteins. In this study, we investigated the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of conically shaped pores across a wide range of salt conditions. We studied how the geometry of a nanopore affects the detected ionic current signal of a translocating DNA molecule over a wide range of salt concentration. The blockade level in the ionic current depends on the translocation direction at a high salt concentration, and at lower salt concentrations we find a nonintuitive ionic current decrease and increase within each single event for the DNA translocations exiting from confinement. We use a recently developed method for synthesizing DNA molecules with multiple position markers, which provides further experimental characterization by matching the position of the DNA in the pore with the observed ionic current signal. Finally, we employ finite element calculations to explain the shapes of the signals observed at all salt concentrations and show that the unexpected current decrease and increase are due to the competing effects of ion concentration polarization and geometric exclusion of ions. Our analysis shows that over a wide range of geometries, voltages, and salt concentrations, we are able to understand the ionic current signals of DNA in asymmetric nanopores, enabling signal optimization in molecular sensing applications.

Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore

“…Figure 1a shows a scanning electron microscope image of a conically shaped nanopore fabricated by laser-assisted capillary pulling. Such conical pores have previously been used to study the transport of ions 30 , 31 and macromolecules 32 – 34 in confinement. The diameter of the nanopores used here was estimated as 14 ± 3 nm (mean ± s.d.)…”

Analysis of 2D DNA Origami with Nanopipettes

“…A voltage of À350 mV was applied between the electrode inside the nanopipette and the electrode in the surrounding electrolyte to translocate the origami through the apex of the nanopore. [32] The ion current was sampled at a rate of 100 kHz and low-pass-filtered at 20 kHz. Also, the increase in absolute ion current observed for our DNA origami is in good 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 agreement with previous DNA translocation studies at salt concentrations similar to the one used here.…”

Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores

“… 13 , 29 Four molar LiCl solution was used as the electrolyte as it is known to slow the DNA translocation relative to other commonly used salts such as NaCl and KCl. 13 , 30 , 31 A voltage of 600 mV was chosen to strike a balance between the requirements for high capture rate and slow translocation velocity. 32 When entering the nanopore, DNA molecules cause a lowering of the current and passage of streptavidin bound to the DNA creates additional current drops.…”