Bioinspired Protein Channel-Based Scanning Ion Conductance Microscopy (Bio-SICM) for Simultaneous Conductance and Specific Molecular Imaging

The combination of DNA nanostructures and materials for highly sensitive electrochemical detection

Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.

Tuning the Probe-Bilayer Architecture of Silver Nanoneedle-based Ion Channel Probes

Ion channel probes, as one of the ion channel platforms, provide an appealing opportunity to perform localized detection with a high precision level. These probes come basically in two classes: glass and metal. While the glass-based probes showed the potential to be employed for molecular sensing and chemical imaging, these probes still suffer from limited resolution and lack of control over protein insertion. On the other hand, metal-based nanoneedle probes (gold and silver) have been recently developed to allow reducing probe dimensions to the nanoscale geometry. More specifically, silver probes are preferable owing to their ability to mitigate the channel current decay observed with gold probes and provide a stable DC channel current. However, there are still some challenges related to the probe design and bilayer curvature that render such probes insensitive to small changes in the tip-substrate distance. Herein, we introduce two main pathways to control the probe-bilayer architecture; the first is by altering the probe shape and geometry during the fabrication process of silver probes. The second pathway is by altering the surface characteristics of the silver probe via an electrophoretic deposition process. Our findings reveal that varying the electrochemical etching parameters results in different probe geometries and producing sharper tips with a 2-fold diameter reduction. In addition, the electrophoretic deposition of a cathodic paint on the silver nanoneedle surface led to a miniaturized exposed silver tip that enables the formation of a confined bilayer. We further investigated the characteristics of bilayers supported on both the sharper nanoneedles and the HSR-coated silver probes produced by controlling the etching conditions and electrodeposition process, respectively. We believe this work paves the way to rationally design silver nanoneedle ion channel probes, which are well suited for localized molecular sensing and chemical imaging.

Operando Scanning Electrochemical Probe Microscopy during Electrocatalysis

Scanning electrochemical probe microscopy (SEPM) techniques can disclose the local electrochemical reactivity of interfaces in single-entity and sub-entity studies. Operando SEPM measurements consist of using a SEPM tip to investigate the performance of electrocatalysts, while the reactivity of the interface is simultaneously modulated. This powerful combination can correlate electrochemical activity with changes in surface properties, e.g., topography and structure, as well as provide insight into reaction mechanisms. The focus of this review is to reveal the recent progress in local SEPM measurements of the catalytic activity of a surface toward the reduction and evolution of O₂ and H₂ and electrochemical conversion of CO₂. The capabilities of SEPMs are showcased, and the possibility of coupling other techniques to SEPMs is presented. Emphasis is given to scanning electrochemical microscopy (SECM), scanning ion conductance microscopy (SICM), electrochemical scanning tunneling microscopy (EC-STM), and scanning electrochemical cell microscopy (SECCM).

Maintaining Single-Channel Recordings on a Silver Nanoneedle through Probe Design and Feedback Tip Positioning Control

Ion channel proteins showed great promise in the field of nanopore sensing and molecular flux imaging applications due to the atomic-level precision of the pore size and a high signal-to-noise ratio. More specifically, ion channel probes, where the protein channels are integrated at the end of a solid probe, can achieve highly localized detection. Metal probe materials such as gold and silver have been developed to support lipid bilayers and enable the use of smaller probes, or nanoneedles, compared to more traditional glass micropipette ion channel probes. Silver probes are preferable because they support sustained DC stable channel current due to the AgCl layer formed around the tip during the fabrication process. However, one of the current challenges in ion channel measurements is maintaining a single-channel recording. Multiple protein insertions complicate data analysis and destabilize the bilayer. Herein, we combine the promising probe material (Ag/AgCl) with an approach based on current feedback-controlled tip positioning to maintain long-term single-channel recordings for up to 3 h. We develop a hybrid positioning control system, where the channel current is used as feedback to control the vertical movement of the silver tip and, subsequently, control the number of protein channels inserted in the lipid membrane. Our findings reveal that the area of the lipid bilayer decreases with moving the silver tip up (i.e., decreasing the displacement in the z-direction). By reducing the bilayer area around the fine silver tip, we minimize the probability of multiple insertions and remove unwanted proteins. In addition, we characterize the effect of lipid properties such as fluidity on the lipid membrane area. We believe that the use of silver nanoneedles, which enables DC stable channel current, coupled with the developed tip displacement mechanism will offer more opportunities to employ these probes for chemical imaging and mapping different surfaces.

Scanning Ion Conductance Microscopy

Scanning ion conductance microscopy (SICM) has emerged as a versatile tool for studies of interfaces in biology and materials science with notable utility in biophysical and electrochemical measurements. The heart of the SICM is a nanometer-scale electrolyte filled glass pipette that serves as a scanning probe. In the initial conception, manipulations of ion currents through the tip of the pipette and appropriate positioning hardware provided a route to recording micro- and nanoscopic mapping of the topography of surfaces. Subsequent advances in instrumentation, probe design, and methods significantly increased opportunities for SICM beyond recording topography. Hybridization of SICM with coincident characterization techniques such as optical microscopy and faradaic electrodes have brought SICM to the forefront as a tool for nanoscale chemical measurement for a wide range of applications. Modern approaches to SICM realize an important tool in analytical, bioanalytical, biophysical, and materials measurements, where significant opportunities remain for further exploration. In this review, we chronicle the development of SICM from the perspective of both the development of instrumentation and methods and the breadth of measurements performed.

Silver Nanoneedle Probes Enable Sustained DC Current, Single-Channel Resistive Pulse Nanopore Sensing

Resistive pulse sensing using ion channel proteins (biological nanopores) has been evolving as a single-molecule approach to detect small biomolecules owing to atomically precise pore size reproducibility, high signal-to-noise ratio, and molecular selectivity. The incorporation of biological nanopores in sensing platforms requires a stable lipid membrane that can be formed by a variety of methods such as the painting method and droplet-based techniques. However, these methods are limited by the fragility of the unsupported bilayer or the need for specific microdevices. Electrode-supported bilayers, in which a metal electrode is used as a support structure, have been recently developed using a fine gold nanoneedle. We previously described the utility of the gold nanoneedle-supported ion channel probe to detect small molecules with high spatial resolution; however, it exhibited a channel current decay over time, which affected the binding frequency of the target molecule to the protein pore as well. Here, we introduce a silver nanoneedle probe to support the lipid bilayer formation and ion channel measurements. The silver nanoneedle mitigates the current decay observed on gold electrodes and produces stable DC channel currents. Our findings propose the formation of a AgCl layer creating a nonpolarizable electrode. The new nanoneedle is successfully applied for single-molecule detection of sulfonated β-cyclodextrin (S₇βCD) using αHL as a test bed protein. We believe that this new silver nanoneedle platform has great potential given the relative ease of lipid bilayer formation and stable open channel currents.

Micropipet-Based Navigation in a Microvascular Model for Imaging Endothelial Cell Topography Using Scanning Ion Conductance Microscopy

Scanning ion conductance microscopy (SICM) has enabled cell surface topography at a high resolution with low invasiveness. However, SICM has not been applied to the observation of cell surfaces in hydrogels, which can serve as scaffolds for three-dimensional cell culture. In this study, we applied SICM for imaging a cell surface in a microvascular lumen reconstructed in a hydrogel. To achieve this goal, we developed a micropipet navigation technique using ionic current to detect the position of a microvascular lumen. Combining this navigation technique with SICM, endothelial cells in a microvascular model and blebs were visualized successfully at the single-cell level. To the best of our knowledge, this is the first report on visualizing cell surfaces in hydrogels using a SICM. This technique will be useful for furthering our understanding of the mechanism of intravascular diseases.

Analysis and improvement of positioning reliability and accuracy of theta pipette configuration for scanning ion conductance microscopy

Scanning ion conductance microscopy (SICM) as an emerging non-contact scanning probe microscopy technique and featuring its strong in-situ detectability for soft and viscous samples, is increasingly used in biomedical and materials related studies. In SICM measurements, employing theta pipette as SICM probe to scan sample is an effective method to extend the applications of SICM for multi-parameter measurement. There are two crucial but still unclear issues that influence the reliability and accuracy of the usage of theta pipette in the SICM measurements, which are the safe feedback threshold and the horizontal measurement offset. In this work, aiming at the theta pipette configuration of SICM, we systematically investigated the two issues of the theta pipette by both finite element method (FEM) simulation and SICM experiments. The FEM analysis results show that the safe feedback threshold of the one side barrel of the theta pipette is above 99.5%, and the horizontal measurement offset is ~0.53 times of the inner radius of the probe tip. Based on this, we proposed an improved scanning method used by the theta pipette to solve the reliability and accuracy problems caused by the feedback threshold too close to the reference current (100%) and the measurement offset error at the tip radius level. Then through testing the polydimethylsiloxane (PDMS) samples with different embossed patterns with the improved method of SICM, we can conclude that the improved method can enhance the scanning reliability by adding the double barrels approaching process and increase the positioning accuracy by compensating an offset distance. The theoretical analysis and the improved scanning method in this work demonstrate more property and usage details of the theta pipette, and further improve the reliability and accuracy of the diversified multifunctional applications of the theta pipette for SICM to meet the increasingly complex and precise research needs.

Wireless nanopore electrodes for analysis of single entities

Measurements of a single entity underpin knowledge of the heterogeneity and stochastics in the behavior of molecules, nanoparticles, and cells. Electrochemistry provides a direct and fast method to analyze single entities as it probes electron/charge-transfer processes. However, a highly reproducible electrochemical-sensing nanointerface is often hard to fabricate because of a lack of control of the fabrication processes at the nanoscale. In comparison with conventional micro/nanoelectrodes with a metal wire inside, we present a general and easily implemented protocol that describes how to fabricate and use a wireless nanopore electrode (WNE). Nanoscale metal deposition occurs at the tip of the nanopipette, providing an electroactive sensing interface. The WNEs utilize a dynamic ionic flow instead of a metal wire to sense the interfacial redox process. WNEs provide a highly controllable interface with a 30- to 200-nm diameter. This protocol presents the construction and characterization of two types of WNEs-the open-type WNE and closed-type WNE-which can be used to achieve reproducible electrochemical measurements of single entities. Combined with the related signal amplification mechanisms, we also describe how WNEs can be used to detect single redox molecules/ions, analyze the metabolism of single cells, and discriminate single nanoparticles in a mixture. This protocol is broadly applicable to studies of living cells, nanomaterials, and sensors at the single-entity level. The total time required to complete the protocol is ~10-18 h. Each WNE costs ~$1-$3.

Spatially Resolved Chemical Detection with a Nanoneedle-Probe-Supported Biological Nanopore

In this article, we describe the quantitative characterization of a gold nanoneedle ion channel probe and demonstrate the utility of this probe for spatially resolved detection of a small molecule using ion channel activity. Our report builds on recent reports of Ide and co-workers, who reported the use of an etched gold wire modified with a poly(ethylene) glycol monolayer as a support for a lipid bilayer and subsequent single ion channel recordings. Although this nanoneedle electrode approach was reported previously, in our report, we investigate the effects of several operational parameters on the performance of the ion channel measurement and electrochemical phenomenon that occur in the nanoconfined space between the supported bilayer and the gold electrode. More specifically, we address the effects of length of the supporting monolayer and the composition of the electrolyte baths on channel current measurements and provide a quantitative description of what carries current at the working electrode (double-layer charging). In addition, we demonstrate the ability to control the direction of protein insertion (tip side vs bath side) with freely diffusing protein, which has not been previously reported, with the former method (tip side) enabling single-molecule detection of β-cyclodextrin (βCD) using a reconstituted α-hemolysin channel. Finally, anticipating future use of a nanoneedle-based biological nanopore probe in a scanned-probe microscopy, we demonstrate the ability to quantify and spatially resolve the concentration of βCD molecules in a microfluidic channel. We believe, in the long term, the described nanoneedle-based biological nanopore probe can be employed in, for example, scanning ion conductance microscopy using ion channels.

Membrane patches as ion channel probes for scanning ion conductance microscopy

We describe dual-barrel ion channel probes (ICPs), which consist of an open barrel and a barrel with a membrane patch directly excised from a donor cell. When incorporated with scanning ion conductance microscopy (SICM), the open barrel (SICM barrel) serves to measure the distance-dependent ion current for non-invasive imaging and positioning of the probe in the same fashion of traditional SICM. The second barrel with the membrane patch supports ion channels of interest and was used to investigate ion channel activities. To demonstrate robust probe control with the dual-barrel ICP-SICM probe and verify that the two barrels are independently addressable, current-distance characteristics (approach curves) were obtained with the SICM barrel and simultaneous, current-time (I-T) traces were recorded with the ICP barrel. To study the influence that the distance between ligand-gated ion channels (i.e., large conductance Ca²⁺-activated K⁺ channels/BK channels) and the ligand source (i.e., Ca²⁺ source) has on channel activations, ion channel activities were recorded at two fixed probe-substrate distances (D_ps) with the ICP barrel. The two fixed positions were determined from approach curves acquired with the SICM barrel. One position was defined as the "In-control" position, where the probe was in close proximity to the ligand source; the second position was defined as the "Far" position, where the probe was retracted far away from the ligand source. Our results confirm that channel activities increased dramatically with respect to both open channel probability and single channel current when the probe was near the ligand source, as opposed to when the probe was far away from the ligand source.

Characterization of Membrane Patch-Ion Channel Probes for Scanning Ion Conductance Microscopy

Integration of dual-barrel membrane patch-ion channel probes (MP-ICPs) to scanning ion conductance microscopy (SICM) holds promise of providing a revolutionized approach of spatially resolved chemical sensing. A series of experiments are performed to further the understanding of the system and to answer some fundamental questions, in preparation for future developments of this approach. First, MP-ICPs are constructed that contain different types of ion channels including transient receptor potential vanilloid 1 and large conductance Ca2⁺ -activated K⁺ channels to establish the generalizability of the methods. Next, the capability of the MP-ICP platforms in single ion channel activity measurements is proved. In addition, the interplay between the SICM barrel and the ICP barrel is studied. For ion channels gated by uncharged ligands, channel activity at the ICP barrel is unaffected by the SICM barrel potential; whereas for ion channels that are gated by charged ligands, enhanced channel activity can be obtained by biasing the SICM barrel at potentials with opposite polarity to the charge of the ligand molecules. Finally, a proof-of-principle experiment is performed and site-specific molecular/ionic flux sensing is demonstrated at single-ion-channel level, which show that the MP-ICP platform can be used to quantify local molecular/ionic concentrations.

Quantitative Framework for Stochastic Nanopore Sensors Using Multiple Channels

Membrane protein channels employed as stochastic sensors offer large signal-to-noise ratios and high specificity in single molecule binding measurements. Stochastic events in a single ion channel system can be measured using current-time traces, which are straightforward to analyze. Signals arising from measurement using multiple ion channels are more complicated to interpret. We show that multiple independent ion channels offer improved detection sensitivity compared to single channel measurements and that increased signal complexity can be accounted for using binding event frequency. More specifically, the leading edge of binding events follows a Poisson point process, which means signals from multiple channels can be superimposed and the association times (between each binding event leading edge), allow for sensitive and quantitative measurements. We expand our calibration to high ligand concentrations and high numbers of ion channels to demonstrate that there is an upper limit of quantification, defined by the time resolution of the measurement. The upper limit is a combination of the instrumental time resolution and the dissociation time of a ligand and protein which limits the number of detectable events. This upper limit also allows us to predict, in general, the measurement requirements needed to observe any process as a Poisson point process. The nanopore-based sensing analysis has wide implications for stochastic sensing platforms that operate using multiple simultaneous superimposable signals.

Scanning ion conductance microscopy mapping of tunable nanopore membranes

We report on the use of scanning ion conductance microscopy (SICM) for in-situ topographical mapping of single tunable nanopores, which are used for tunable resistive pulse sensing. A customised SICM system was used to map the elastomeric pore membranes repeatedly, using pipettes with tip opening diameters of approximately 50 nm and 1000 nm. The effect of variations on current threshold, scanning step size, and stretching has been studied. Lowering the current threshold increased the sensitivity of the pipette while scanning, up to the point where the tip contacted the surface. An increase in the pore area was observed as the step size was decreased, and with increased stretching. SICM reveals details of the electric field near the pore entrance, which is important for understanding measurements of submicron particles using resistive pulse sensing.