Electrolytic transport through a synthetic nanometer-diameter pore

Abstract

We have produced single, synthetic nanometer-diameter pores by using a tightly focused, high-energy electron beam to sputter atoms in 10-nm-thick silicon nitride membranes. Subsequently, we measured the ionic conductance as a function of time, bath concentration, and pore diameter to infer the conductivity and ionic mobility through the pores. The pore conductivity is found to be much larger than the bulk conductivity for dilute bath concentrations, where the Debye length is larger than the pore radius, whereas it is comparable with or less than the bulk for high bath concentrations. We interpret these observations by using multiscale simulations of the ion transport through the pores. Molecular dynamics is used to estimate the ion mobility, and ion transport in the pore is described by the coupled Poisson-Nernst-Planck and the Stokes equations that are solved self-consistently for the ion concentration and velocity and electrical potential. We find that the measurements are consistent with the presence of fixed negative charge in the pore wall and a reduction of the ion mobility because of the fixed charge and the ion proximity to the pore wall.ion conduction ͉ nanopore ͉ nanostructured materials N anometer-diameter pores formed by proteins are prevalent in biology where they are used to regulate the flow of ions and molecules through the otherwise impermeable cell membrane. Even though the structure is known with atomic precision in some cases, there does not seem to be a simple relationship between the pore geometry and the conductivity (1). This difficulty may be due to the nonuniform, high concentration of charge in the pore (2).As a first step toward understanding the conductivity, we produced synthetic pores ranging in diameter from 1 to 3.2 nm in ultra-thin silicon nitride (Si 3 N 4 ) membranes and measured the ionic conductance as a function of time and electrolyte concentration to infer the conductivity and ionic mobility. This work measures the conductance through pores with radii comparable with the van der Waals radius of an ion (3-5). Similar claims by Siwy and Fuliński (6) that rely on the conductance through a single pore to estimate the pore diameter are unreliable, because conductance does not scale with the diameter. Like previous work in nanofiltration membranes that contain ensembles of pores with varying diameter (7), we find that the pore conductivity associated with a single pore is found to be much larger than the bulk conductivity for dilute electrolyte concentrations, where the Debye length is larger than the pore radius, whereas it is comparable with or less than the bulk for high concentrations. These observations are also consistent with a recent report by Stein et al. (8) of ion transport in silica channels Ͼ70 nm wide that is governed by surface charge. To interpret our observations, we use multiscale simulations of the ion transport through the pores. Molecular dynamics (MD) is used to estimate the ion mobility, and ion transport in the pore is described by the coupled Poisson-N...

Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor

“…5 shows the average density of the adenine nucleotides in the pore. Similar plots were obtained for (dC) 25 , (dG) 25 , and (dT) 25 (data not shown). The plots reveal equidistant peaks that pinpoint the locations where the nucleotides pause or stall.…”

“…2i, the motion of DNA nucleotides is not uniform, even under a constant bias. Although the 20 V bias used in our simulations is strong enough to force DNA through the pore at a high rate (up to 10 nucleotides per ns), a moderate reduction of the bias, for example to 10 V, leads to a dramatic reduction of the DNA translocation rate (by a factor of 40 for (dA) 25 , Fig. S5).…”

“…To demonstrate the feasibility of detecting a single nucleotide substitution using an alternating bias, we simulated two systems-(dC) 25 and d(C 15 AC 9 )-applying a voltage ramp of 16 V/ ns. In the second system, the mutated nucleotide was located just above the constriction, Fig.…”

“…The silicon layers are used as electrodes to measure the electrostatic potentials induced by DNA motion in the pore. 25 , (dG) 25 , and (dT) 25 are presented in Fig. S1 in the supporting information.…”

“…Reading a random sequence is more cumbersome but may still be possible because the duration of the pause separating the one-nucleotide displacements of the DNA strand depends mainly on the type of the nucleotide that is about to enter the pore. To demonstrate the feasibility of detecting a single nucleotide substitution using an alternating bias, we simulated two systems-(dC) 25 and d(C 15 AC 9 )-applying a voltage ramp of 16 V/ ns. In the second system, the mutated nucleotide was located just above the constriction, Fig.…”