The design and characterization of multifunctional aptamer nanopore sensors

Aptamer-modified nanomaterials provide a simple, yet powerful sensing platform when combined with resistive pulse sensing technologies. Aptamers adopt a more stable tertiary structure in the presence of a target analyte, which results in a change in charge density and velocity of the carrier particle. In practice the tertiary structure is specific for each aptamer and target, and the strength of the signal varies with different applications and experimental conditions. Resistive pulse sensors (RPS) have single particle resolution, allowing for the detailed characterization of the sample. Measuring the velocity of aptamer-modified nanomaterials as they traverse the RPS provides information on their charge state and densities. To help understand how the aptamer structure and charge density effects the sensitivity of aptamer-RPS assays, here we study two metal binding aptamers. This creates a sensor for mercury and lead ions that is capable of being run in a range of electrolyte concentrations, equivalent to river to seawater conditions. The observed results are in excellent agreement with our proposed model. Building on this we combine two aptamers together in an attempt to form a dual sensing strand of DNA for the simultaneous detection of two metal ions. We show experimental and theoretical responses for the aptamer which creates layers of differing charge densities around the nanomaterial. The density and diameter of these zones effects both the viability and sensitivity of the assay. While this approach allows the interrogation of the DNA structure, the data also highlight the limitations and considerations for future assays

Gating with Charge Inversion to Control Ionic Transport in Nanopores

Multivalent ions modify the properties of the solid/liquid interfaces, and in some cases, they can even invert the polarity of surface charge, having large consequences for separation processes based on charge. The so-called charge inversion is observed as a switch from negative surface charge in monovalent salts, e.g., KCl, to effective positive surface charge in multivalent salts that is possible through a strong accumulation and correlation of the multivalent ions at the surface. It is not known yet, however, whether the density of the positive charge induced by charge inversion depends on the pore opening diameter, especially in extreme nanoconfinement. Here, we probe how the effective surface charge induced by charge inversion is influenced by the pore opening diameter using a series of nanopores with an opening between 4 and 25 nm placed in contact with trivalent chromium ions in tris(ethylenediamine)chromium(III) sulfate at different concentrations. Our results suggest that the effective positive charge density can indeed be modified by nanoconfinement to the extent that is dependent on the pore diameter, salt concentration, and applied voltage. In addition, the correlated ions can increase the transmembrane current in nanopores with an opening diameter down to 10 nm and cause a significant blockage of the current for narrower pores. The results provide guidelines to control ionic transport at the nanoscale with multivalent ions and demonstrate that in the same experimental conditions, differently sized pores in the same porous material can feature different surface charge density and possibly ion selectivity

Ionic Current Rectification in a pH-Tunable Polyelectrolyte Brushes Functionalized Conical Nanopore: Effect of Salt Gradient

The behavior of ionic current rectification (ICR) in a conical nanopore with its surface modified by pH-tunable polyelectrolyte (PE) brushes connecting two large reservoirs subject to an applied electric field and a salt gradient is investigated. Parameters including the solution pH, types of ionic species, strength of applied salt gradient, and applied potential bias are examined for their influences on the ionic current and rectification factor, and the mechanisms involved are investigated comprehensively. The ICR behavior depends highly on the charged conditions of the PE layer, the level of pH, the geometry of nanopore, and the thickness of the double layer. In particular, the distribution of ionic species and the local electric field near the nanopore openings play a key role, yielding profound and interesting results that are informative to device design as well as experimental data interpretation

Influences of Cone Angle and Surface Charge Density on the Ion Current Rectification Behavior of a Conical Nanopore

Due to its potential applications in biotechnology, ion current rectification (ICR) arising from the asymmetric nature of ion transport in a nanochannel has drawn the attention of researchers in various fields. Previous studies usually neglect the effects of osmotic and electroosmotic flows. In this study, a more general model taking account of these effects is adopted to describe the ICR behavior of a conical nanopore. The influences of the cone angle, surface charge density, and bulk salt concentration on this behavior are investigated, and mechanisms proposed to explain the results are obtained. We show that if the cone angle is enlarged by fixing the nanopore tip radius and raising its base radius, the ICR ratio has a local maximum. This behavior may not present if the cone angle is enlarged by fixing the nanopore base radius and raising its tip radius. The local maximum in the ICR ratio does not exist if the bulk salt concentration is sufficiently low or sufficiently high. This ratio also has a local maximum as the surface charge density varies, and the larger the cone angle, the higher the surface charge density at which the local maximum in the ICR ratio occurs

Charge Inversion and Calcium Gating in Mixtures of Ions in Nanopores

Calcium ions play important roles in many physiological processes, yet their concentration is much lower than the concentrations of potassium and sodium ions. The selectivity of calcium channels is often probed in mixtures of calcium and a monovalent salt, e.g., KCl or NaCl, prepared such that the concentration of cations is kept constant with the mole fraction of calcium varying from 0 and 1. In biological channels, even sub-mM concentration of calcium can modulate the channels’ transport characteristics; this effect is often explained via the existence of high affinity Ca2+ binding sites on the channel walls. Inspired by properties of biological calcium-selective channels, we prepared a set of nanopores with tunable opening diameters that exhibited a similar response to the presence of calcium ions as biochannels. Nanopores in 15 nm thick silicon nitride films were drilled using focused ion beam and e-beam in a transmission electron microscope and subsequently rendered negatively charged through silanization. We found that nanopores with diameters smaller than 20 nm were blocked by calcium ions such that the ion currents in mixtures of KCl and CaCl2 and in CaCl2 were even ten times smaller than the ion currents in KCl solution. The ion current blockage was explained by the effect of local charge inversion where accumulated calcium ions switch the effective surface charge from negative to positive. The modulation of surface charge with calcium leads to concentration and voltage dependent local charge density and ion current. The combined experimental and modeling results provide a link between calcium ion-induced changes in surface charge properties and resulting ionic transport

Ionic Current Rectification in a Conical Nanopore: Influences of Electroosmotic Flow and Type of Salt

The influence of electroosmotic flow (EOF) on the behavior of the ionic current rectification (ICR) in a conical nanopore connecting two large identical reservoirs is investigated. In particular, the effect of the type of salt is examined by considering LiCl, NaCl, and KCl. We show that neglecting EOF is capable of influencing ICR both quantitatively and qualitatively. If EOF is neglected, the rectification factor at each level of the applied electric potential bias across the two reservoirs for the case of LiCl (KCl) is always the largest (smallest). However, if EOF is taken into account, the relative magnitude of the rectification factors for various salts depends upon the level of the applied electric potential bias. This behavior is consistent with the experimental observation in the literature and can be explained by the degree of ion enrichment/depletion in a nanopore

Electrophoresis of Deformable Polyelectrolytes in a Nanofluidic Channel

The influence of the shape of a polyelectrolyte (PE) on its electrophoretic behavior in a nanofluidic channel is investigated by considering the translocation of a deformable ellipsoidal PE along the axis of a cylindrical nanochannel. A continuum model comprising a Poisson equation for the electric potential, Nernst–Planck equations for the ionic concentrations, and modified Stokes equations for the flow field is adopted. The effects of the PE shape, boundary, bulk ionic concentration, counterion condensation, electroosmotic retardation flow, and electroosmotic flow (EOF) on the PE mobility are discussed. Several interesting behaviors are observed. For example, if the nanochannel is uncharged and the double layer is thick, then the PE mobility increases (decreases) with increasing double-layer thickness for a smaller (larger) boundary, which has not been reported previously. If the nanochannel is negatively charged and the double layer is thick, then a negatively charged PE moves in the direction of the applied electric field. The results gathered provide necessary information for both the interpretation of experimental data and the design of nanochannel-based sensing devices

Ion Current Rectification Behavior of Bioinspired Nanopores Having a pH-Tunable Zwitterionic Surface

The ion current rectification behavior of bioinspired nanopores is modeled by adopting a bullet-shaped nanopore having a pH-tunable zwitterionic surface, focusing on discussing the underlying mechanisms. We show that with its specific geometry, such nanopore is capable of exhibiting several interesting behaviors, including ion concentration polarization and ion current rectification. The influences of the nanopore shape, solution pH, and bulk salt concentration on the associated ion current rectification behavior are examined. We found that if pH exceeds the isoelectric point, the rectification factor has a local maximum as the curvature of the nanopore surface varies, and if it is lower than the isoelectric point, that factor increases (rectification effect decreases) monotonically with increasing surface curvature. In addition to capable of interpreting relevant electrokinetic phenomena, the results gathered also provide necessary information for a sophisticated design of relevant devices