Nanopore/electrode structures for single-molecule biosensing

Chemically Functionalizing Controlled Dielectric Breakdown Silicon Nitride Nanopores by Direct Photohydrosilylation

Nanopores are a prominent enabling tool for single-molecule applications such as DNA sequencing, protein profiling, and glycomics, and the construction of ionic circuit elements. Silicon nitride (SiN_x) is a leading scaffold for these <100 nm-diameter nanofluidic ion-conducting channels, but frequently challenging surface chemistry remains an obstacle to their use. We functionalized more than 100 SiN_x nanopores with different surface terminations-acidic (Si-R-OH, Si-R-CO₂H), basic (Si-R-NH₂), and nonionizable (Si-R-C₆H₃(CF₃)₂)-to chemically tune the nanopore size, surface charge polarity, and subsequent chemical reactivity and to change their conductance by changes of solution pH. The initial one-reaction-step covalent chemical film formation was by hydrosilylation and could be followed by straightforward condensation and click reactions. The hydrosilylation reaction step used neat reagents with no special precautions such as guarding against water content. A key feature of the approach was to combine controlled dielectric breakdown (CDB) with hydrosilylation to create and functionalize SiN_x nanopores. CDB thus replaced the detrimental but conventionally necessary surface pretreatment with hydrofluoric acid. Proof-of-principle detection of the canonical test molecule, λ-DNA, yielded signals that showed that the functionalized pores were not obstructed by chemical treatments but could translocate the biopolymer. The characteristics were tuned by the surface coating character. This robust and flexible surface coating method, freed by CDB from HF etching, portends the development of nanopores with surface chemistry tuned to match the application, extending even to the creation of biomimetic nanopores.

Silicon Nitride Thin Films for Nanofluidic Device Fabrication

Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.

Real-Time Profiling of Solid-State Nanopores During Solution-Phase Nanofabrication

We describe a method for simply characterizing the size and shape of a nanopore during solution-based fabrication and surface modification, using only low-overhead approaches native to conventional nanopore measurements. Solution-based nanopore fabrication methods are democratizing nanopore science by supplanting the traditional use of charged-particle microscopes for fabrication, but nanopore profiling has customarily depended on microscopic examination. Our approach exploits the dependence of nanopore conductance in solution on nanopore size, shape, and surface chemistry in order to characterize nanopores. Measurements of the changing nanopore conductance during formation by etching or deposition can be analyzed using our method to characterize the nascent nanopore size and shape, beyond the typical cylindrical approximation, in real-time. Our approach thus accords with ongoing efforts to broaden the accessibility of nanopore science from fabrication through use: it is compatible with conventional instrumentation and offers straightforward nanoscale characterization of the core tool of the field.

Characterization of Lactate Sensors Based on Lactate Oxidase and Palladium Benzoporphyrin Immobilized in Hydrogels

An optical biosensor for lactate detection is described. By encapsulating enzyme-phosphor sensing molecules within permeable hydrogel materials, lactate-sensitive emission lifetimes were achieved. The relative amount of monomer was varied to compare three homo- and co-polymer materials: poly(2-hydroxyethyl methacrylate) (pHEMA) and two copolymers of pHEMA and poly(acrylamide) (pAam). Diffusion analysis demonstrated the ability to control lactate transport by varying the hydrogel composition, while having a minimal effect on oxygen diffusion. Sensors displayed the desired dose-variable response to lactate challenges, highlighting the tunable, diffusion-controlled nature of the sensing platform. Short-term repeated exposure tests revealed enhanced stability for sensors comprising hydrogels with acrylamide additives; after an initial "break-in" period, signal retention was 100% for 15 repeated cycles. Finally, because this study describes the modification of a previously developed glucose sensor for lactate analysis, it demonstrates the potential for mix-and-match enzyme-phosphor-hydrogel sensing for use in future multi-analyte sensors.

Precise attoliter temperature control of nanopore sensors using a nanoplasmonic bullseye

Targeted temperature control in nanopores is greatly important in further understanding biological molecules. Such control would extend the range of examinable molecules and facilitate advanced analysis, including the characterization of temperature-dependent molecule conformations. The work presented within details well-defined plasmonic gold bullseye and silicon nitride nanopore membranes. The bullseye nanoantennae are designed and optimized using simulations and theoretical calculations for interaction with 632.8 nm laser light. Laser heating was monitored experimentally through nanopore conductance measurements. The precise heating of nanopores is demonstrated while minimizing the accumulation of heat in the surrounding membrane material.

SSB binding to single-stranded DNA probed using solid-state nanopore sensors

Single-stranded DNA (ssDNA) binding protein plays an important role in the DNA replication process in a wide range of organisms. It binds to ssDNA to prevent premature reannealing and to protect it from degradation. Current understanding of SSB/ssDNA interaction points to a complex mechanism, including SSB motion along the DNA strand. We report on the first characterization of this interaction at the single-molecule level using solid-state nanopore sensors, namely without any labeling or surface immobilization. Our results show that the presence of SSB on the ssDNA can control the speed of nanopore translocation, presumably due to strong interactions between SSB and the nanopore surface. This enables nanopore-based detection of ssDNA fragments as short as 37 nt, which is normally very difficult with solid-state nanopore sensors, due to constraints in noise and bandwidth. Notably, this fragment is considerably shorter than the 65 nt binding motif, typically required for SSB binding at high salt concentrations. The nonspecificity of SSB binding to ssDNA further suggests that this approach could be used for fragment sizing of short ssDNA.

Nanopore surface coating delivers nanopore size and shape through conductance-based sizing

The performance of nanopore single-molecule sensing elements depends intimately on their physical dimensions and surface chemical properties. These factors underpin the dependence of the nanopore ionic conductance on electrolyte concentration, yet the measured, or modeled, dependence only partially illuminates the details of geometry and surface chemistry. Using the electrolyte-dependent conductance data before and after selective surface functionalization of solid-state nanopores, however, introduces more degrees of freedom and improves the performance of conductance-based nanopore characterizations. Sets of representative nanopore profiles were used to generate conductance data, and the nanopore shape and exact dimensions were identified, through conductance alone, by orders-of-magnitude reductions in the geometry optimization metrics. The optimization framework could similarly be used to evaluate the nanopore surface coating thickness.

Single-molecule studies of intrinsically disordered proteins using solid-state nanopores

Partially or fully disordered proteins are instrumental for signal-transduction pathways; however, many mechanistic aspects of these proteins are not well-understood. For example, the number and nature of intermediate states along the binding pathway is still a topic of intense debate. To shed light on the conformational heterogeneity of disordered protein domains and their complexes, we performed single-molecule experiments by translocating disordered proteins through a nanopore embedded within a thin dielectric membrane. This platform allows for single-molecule statistics to be generated without the need of fluorescent labels or other modification groups. These studies were performed on two different intrinsically disordered protein domains, a binding domain from activator of thyroid hormone and retinoid receptors (ACTR) and the nuclear coactivator binding domain of CREB-binding protein (NCBD), along with their bimolecular complex. Our results demonstrate that both ACTR and NCBD populate distinct conformations upon translocation through the nanopore. The folded complex of the two disordered domains, on the other hand, translocated as one conformation. Somewhat surprisingly, we found that NCBD undergoes a charge reversal under high salt concentrations. This was verified by both translocation statistics as well as by measuring the ζ-potential. Electrostatic interactions have been previously suggested to play a key role in the association of intrinsically disordered proteins, and the observed behavior adds further complexity to their binding reactions.

Mapping the ion current distribution in nanopore/electrode devices

Solid-state nanopores with integrated electrodes have interesting prospects in next-generation single-molecule biosensing and sequencing. These include "gated" nanopores with a single electrode integrated into the membrane, as well as two-electrode designs, such as a transversal tunneling junction. Here we report the first comprehensive analysis of current flow in a three-electrode device as a model for this class of sensors. As a new feature, we observe apparent rectification in the pore current that is rooted in the current distribution of the cell, rather than the geometry or electrostatics of the pore. We benchmark our results against a recently developed theoretical model and define operational parameters for nanopore/electrode structures. Our findings thus facilitate the rational design of such sensor devices.

Conductance-Based Determination of Solid-State Nanopore Size and Shape: An Exploration of Performance Limits

Knowledge of nanopore size and shape is critical for many implementations of these single-molecule sensing elements. Geometry determination by fitting the electrolyte-concentration-dependence of the conductance of surface-charged, solid-state nanopores has been proposed to replace demanding electron microscope-based methods. The functional form of the conductance poses challenges for this method by restricting the number of free parameters used to characterize the nanopore. We calculated the electrolyte-dependent conductance of nanopores with an exponential-cylindrical radial profile using three free geometric parameters; this profile, itself, could not be uniquely geometry-optimized by the conductance. Several different structurally simplified models, however, generated quantitative agreement with the conductance, but with errors exceeding 40% for estimates of key geometrical parameters. A tractable conical-cylindrical model afforded a good characterization of the nanopore size and shape, with errors of less than 1% for the limiting radius. Understanding these performance limits provides a basis for using and extending analytical nanopore conductance models.

Solid-state nanopores for biosensing with submolecular resolution

Biological cell membranes contain various types of ion channels and transmembrane pores in the 1–100 nm range, which are vital for cellular function. Individual channels can be probed electrically, as demonstrated by Neher and Sakmann in 1976 using the patch-clamp technique [Neher and Sakmann (1976) Nature 260, 799–802]. Since the 1990s, this work has inspired the use of protein or solid-state nanopores as inexpensive and ultrafast sensors for the detection of biomolecules, including DNA, RNA and proteins, but with particular focus on DNA sequencing. Solid-state nanopores in particular have the advantage that the pore size can be tailored to the analyte in question and that they can be modified using semi-conductor processing technology. This establishes solid-state nanopores as a new class of single-molecule biosensor devices, in some cases with submolecular resolution. In the present review, we discuss a few of the most important recent developments in this field and how they might be applied to studying protein–protein and protein–DNA interactions or in the context of ultra-fast DNA sequencing.

Electrochemical tunnelling sensors and their potential applications

The quantum-mechanical tunnelling effect allows charge transport across nanometre-scale gaps between conducting electrodes. Application of a voltage between these electrodes leads to a measurable tunnelling current, which is highly sensitive to the gap size, the voltage applied and the medium in the gap. Applied to liquid environments, this offers interesting prospects of using tunnelling currents as a sensitive tool to study fundamental interfacial processes, to probe chemical reactions at the single-molecule level and to analyse the composition of biopolymers such as DNA, RNA or proteins. This offers the possibility of a new class of sensor devices with unique capabilities.

Resizing metal-coated nanopores using a scanning electron microscope

Electron beam-induced shrinkage provides a convenient way of resizing solid-state nanopores in Si(3) N(4) membranes. Here, a scanning electron microscope (SEM) has been used to resize a range of different focussed ion beam-milled nanopores in Al-coated Si(3) N(4) membranes. Energy-dispersive X-ray spectra and SEM images acquired during resizing highlight that a time-variant carbon deposition process is the dominant mechanism of pore shrinkage, although granular structures on the membrane surface in the vicinity of the pores suggest that competing processes may occur. Shrinkage is observed on the Al side of the pore as well as on the Si(3) N(4) side, while the shrinkage rate is observed to be dependent on a variety of factors.

How to understand and interpret current flow in nanopore/electrode devices

Nanopore-based single-molecule sensors have become an important class of analytical devices that have in some cases already reached the market place. Traditionally operated in a two-electrode configuration, devices with three or more electrodes have emerged recently, for example with a view on switching the transport properties of the nanopore or even tunneling-based detection of analytes with the ultimate goal of inexpensive and ultrafast DNA sequencing. How do these additional electrodes affect the current distribution in the cell and hence the sensor performance? This is significantly less clear and thus in focus here. We use impedance modeling of a prototypical three-electrode nanopore sensor and show that, depending on the conditions, standard experimental device characterization is severely affected by the presence of the third electrode. On the other hand, the simulations also provide guidelines on how to avoid such complications, identify "safe" operating conditions, and design criteria for optimized nanopore sensors.

DNA tunneling detector embedded in a nanopore

We report on the fabrication and characterization of a DNA nanopore detector with integrated tunneling electrodes. Functional tunneling devices were identified by tunneling spectroscopy in different solvents and then used in proof-of-principle experiments demonstrating, for the first time, concurrent tunneling detection and ionic current detection of DNA molecules in a nanopore platform. This is an important step toward ultrafast DNA sequencing by tunneling.

Investigative Study of Nucleic Acid-Gold Nanoparticle Interactions Using Laser-based Techniques, Electron Microscopy, and Resistive Pulse Sensing with a Nanopore

In this study, we employ a range of analytical tools to study the interactions between a mixed base peptide nucleic acid (PNA, 22-mer) probe and gold nanoparticles (AuNP). The binding of charge neutral PNA to citrate capped AuNP (50 nm) causes the particles to change size and/or aggregation/dispersion status in a PNA concentration-dependent manner. Under a UV-vis spectrophotometer, AuNP aggregation can be detected at PNA concentrations as high as 400 nm. Using dynamic light scattering measurement, the changing of particle sizes can be detected at a relatively low PNA concentration of 50 nm. Using a resistive pulse sensor, i.e. nanopore-based sensing platform, a particle-by-particle measurement technique, subtle changes of the AuNP size induced by PNA at very low concentrations of 5 nm can be identified. Transmission electron microscopy measurement confirmed that at very low PNA concentration, a small population of particles form a nano-assembly of NP clusters. Based on the fact that hybridization of PNA probe with target DNA is able to retard particle aggregation, we can quantify specific DNA sequences with a limit of detection ranging from 10 nm to 1 nm, depending on the characterization tools used. With this study, we show that as a complementary technique, the resistive pulse nanopore-based sensing platform provides significant resolution advantages for metal nanoparticle measurement as compared with light-based techniques.

Precise electrochemical fabrication of sub-20 nm solid-state nanopores for single-molecule biosensing

It has recently been shown that solid-state nanometer-scale pores ('nanopores') can be used as highly sensitive single-molecule sensors. For example, electrophoretic translocation of DNA, RNA and proteins through such nanopores has enabled both detection and structural analysis of these complex biomolecules. Control over the nanopore size is critical as the pore must be comparable in size to the analyte molecule in question. The most widely used fabrication methods are based on focused electron or ion beams and thus require (scanning) transmission electron microscopy and focused ion beam (FIB) instrumentation. Even though very small pores have been made using these approaches, several issues remain. These include the requirement of being restricted to rather thin, mechanically less stable membranes, particularly for pore diameters in the single-digit nanometer range, lack of control of the surface properties at and inside the nanopore, and finally, the fabrication cost. In the proof-of-concept study, we report on a novel and simple route for fabricating metal nanopores with apparent diameters below 20 nm using electrodeposition and real-time ionic current feedback in solution. This fabrication approach inserts considerable flexibility into the kinds of platforms that can be used and the nanopore membrane material. Starting from much larger pores, which are straightforward to make using FIB or other semiconductor fabrication methods, we electrodeposit Pt at the nanopore interface while monitoring its ionic conductance at the same time in a bi-potentiostatic setup. Due to the deposition of Pt, the nanopore decreases in size, resulting in a decrease of the pore conductance. Once a desired pore conductance has been reached, the electrodeposition process is stopped by switching the potential of the membrane electrode and the fabrication process is complete. Furthermore, we demonstrate that these pores can be used for single-biomolecule analysis, such as that of λ-DNA, which we use in a proof-of-concept study. Importantly, our approach is applicable to single nanopores as well as nanopore arrays, and can easily be extended to deposits of metal other than Pt.