Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping

Spatial Manipulation and Assembly of Nanoparticles by Atomic Force Microscopy Tip-Induced Dielectrophoresis

In this article, we present a novel method of spatial manipulation and assembly of nanoparticles via atomic force microscopy tip-induced dielectrophoresis (AFM-DEP). This method combines the high-accuracy positioning of AFM with the parallel manipulation of DEP. A spatially nonuniform electric field is induced by applying an alternating current (AC) voltage between the conductive AFM probe and an indium tin oxide glass substrate. The AFM probe acted as a movable DEP tweezer for nanomanipulation and assembly of nanoparticles. The mechanism of AFM-DEP was analyzed by numerical simulation. The effects of solution depth, gap distance, AC voltage, solution concentration, and duration time were experimentally studied and optimized. Arrays of 200 nm polystyrene nanoparticles were assembled into various nanostructures, including lines, ellipsoids, and arrays of dots. The sizes and shapes of the assembled structures were controllable. It was thus demonstrated that AFM-DEP is a flexible and powerful tool for nanomanipulation.

Substrate Dependent Ad-Atom Migration on Graphene and the Impact on Electron-Beam Sculpting Functional Nanopores

The use of atomically thin graphene for molecular sensing has attracted tremendous attention over the years and, in some instances, could displace the use of classical thin films. For nanopore sensing, graphene must be suspended over an aperture so that a single pore can be formed in the free-standing region. Nanopores are typically drilled using an electron beam (e-beam) which is tightly focused until a desired pore size is obtained. E-beam sculpting of graphene however is not just dependent on the ability to displace atoms but also the ability to hinder the migration of ad-atoms on the surface of graphene. Using relatively lower e-beam fluxes from a thermionic electron source, the C-atom knockout rate seems to be comparable to the rate of carbon ad-atom attraction and accumulation at the e-beam/graphene interface (i.e., R_knockout ≈ R_accumulation). Working at this unique regime has allowed the study of carbon ad-atom migration as well as the influence of various substrate materials on e-beam sculpting of graphene. We also show that this information was pivotal to fabricating functional graphene nanopores for studying DNA with increased spatial resolution which is attributed to atomically thin membranes.

Selective single molecule nanopore sensing of proteins using DNA aptamer-functionalised gold nanoparticles

Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor. We show that this approach offers numerous advantages including: high levels of selectivity, efficient capture from a complex mixture, enhanced signal, minimized analyte-sensor surface interactions, and finally can be used to enhance the event detection rate. This is demonstrated by incorporating a lysozyme binding aptamer to a 5 nm AuNP carrier to selectively probe lysozyme within a cocktail of proteins. We show that nanopores can reveal sub-complex molecular information, by discriminating the AuNP from the protein analyte, indicating the potential use of this technology for single molecule analysis of different molecular analytes specifically bound to AuNP.

Mechanistic Challenges and Advantages of Biosensor Miniaturization into the Nanoscale

Over the past few decades, there has been tremendous interest in developing biosensing systems that combine high sensitivity and specificity with rapid sample-to-answer times, portability, low-cost operation, and ease-of-use. Miniaturizing the biosensor dimensions into the nanoscale has been identified as a strategy for addressing the functional requirements of point-of-care and wearable biosensors. However, it is important to consider that decreasing the critical dimensions of biosensing elements impacts the two most important performance metrics of biosensors: limit-of-detection and response time. Miniaturization into the nanoscale enhances signal-to-noise-ratio by increasing the signal density (signal/geometric surface area) and reducing background signals. However, there is a trade-off between the enhanced signal transduction efficiency and the longer time it takes to collect target analytes on sensor surfaces due to the increase in mass transport times. By carefully considering the signal transduction mechanisms and reaction-transport kinetics governing different classes of biosensors, it is possible to develop structure-level and device-level strategies for leveraging miniaturization toward creating biosensors that combine low limit-of-detection with rapid response times.

Resistive-pulse and rectification sensing with glass and carbon nanopipettes

Along with more prevalent solid-state nanopores, glass or quartz nanopipettes have found applications in resistive-pulse and rectification sensing. Their advantages include the ease of fabrication, small physical size and needle-like geometry, rendering them useful for local measurements in small spaces and delivery of nanoparticles/biomolecules. Carbon nanopipettes fabricated by depositing a thin carbon layer on the inner wall of a quartz pipette provide additional means for detecting electroactive species and fine-tuning the current rectification properties. In this paper, we discuss the fundamentals of resistive-pulse sensing with nanopipettes and our recent studies of current rectification in carbon pipettes.

Photonic and Plasmonic Nanotweezing of Nano- and Microscale Particles

The ability to manipulate and sense biological molecules is important in many life science domains, such as single-molecule biophysics, the development of new drugs and cancer detection. Although the manipulation of biological matter at the nanoscale continues to be a challenge, several types of nanotweezers based on different technologies have recently been demonstrated to address this challenge. In particular, photonic and plasmonic nanotweezers are attracting a strong research effort especially because they are efficient and stable, they offer fast response time, and avoid any direct physical contact with the target object to be trapped, thus preventing its disruption or damage. In this paper, we critically review photonic and plasmonic resonant technologies for biomolecule trapping, manipulation, and sensing at the nanoscale, with a special emphasis on hybrid photonic/plasmonic nanodevices allowing a very strong light-matter interaction. The state-of-the-art of competing technologies, e.g., electronic, magnetic, acoustic and carbon nanotube-based nanotweezers, and a description of their applications are also included.

Interference-Free Detection of Genetic Biomarkers Using Synthetic Dipole-Facilitated Nanopore Dielectrophoresis

The motion of polarizable particles in a nonuniform electric field (i.e., dielectrophoresis) has been extensively used for concentration, separation, sorting, and transport of biological particles from cancer cells and viruses to biomolecules such as DNAs and proteins. However, current approaches to dielectrophoretic manipulation are not sensitive enough to selectively target individual molecular species. Here, we describe the application of the dielectrophoretic principle for selective detection of DNA and RNA molecules using an engineered biological nanopore. The key element of our approach is a synthetic polycationic nanocarrier that selectively binds to the target biomolecules, dramatically increasing their dielectrophoretic response to the electric field gradient generated by the nanopore. The dielectrophoretic capture of the nanocarrier-target complexes is detected as a transient blockade of the nanopore ionic current, while any nontarget nucleic acids are repelled from the nanopore by electrophoresis and thus do not interfere with the signal produced by the target's capture. Strikingly, we show that even modestly charged nanocarriers can be used to capture DNA or RNA molecules of any length or secondary structure and simultaneously detect several molecular targets. Such selective, multiplex molecular detection technology would be highly desirable for real-time analysis of complex clinical samples.

Simultaneous Ionic Current and Potential Detection of Nanoparticles by a Multifunctional Nanopipette

Nanopore sensing-based technologies have made significant progress for single molecule and single nanoparticle detection and analysis. In recent years, multimode sensing by multifunctional nanopores shows the potential to greatly improve the sensitivity and selectivity of traditional resistive-pulse sensing methods. In this paper, we showed that two label-free electric sensing modes could work cooperatively to detect the motion of 40 nm diameter spherical gold nanoparticles (GNPs) in solution by a multifunctional nanopipette. The multifunctional nanopipettes containing both nanopore and nanoelectrode (pyrolytic carbon) at the tip were fabricated quickly and cheaply. We demonstrated that the ionic current and local electrical potential changes could be detected simultaneously during the translocation of individual GNPs. We also showed that the nanopore/CNE tip geometry enabled the CNE not only to detect the translocation of single GNP but also to collectively detect several GNPs outside the nanopore entrance. The dynamic accumulation of GNPs near the nanopore entrance resulted in no detectable current changes, but was detected by the potential changes at the CNE. We revealed the motions of GNPs both outside and inside the nanopore, individually and collectively, with the combination of ionic current and potential measurements.

Ultralow-Power Electronic Trapping of Nanoparticles with Sub-10 nm Gold Nanogap Electrodes

We demonstrate nanogap electrodes for rapid, parallel, and ultralow-power trapping of nanoparticles. Our device pushes the limit of dielectrophoresis by shrinking the separation between gold electrodes to sub-10 nm, thereby creating strong trapping forces at biases as low as the 100 mV ranges. Using high-throughput atomic layer lithography, we manufacture sub-10 nm gaps between 0.8 mm long gold electrodes and pattern them into individually addressable parallel electronic traps. Unlike pointlike junctions made by electron-beam lithography or larger micron-gap electrodes that are used for conventional dielectrophoresis, our sub-10 nm gold nanogap electrodes provide strong trapping forces over a mm-scale trapping zone. Importantly, our technology solves the key challenges associated with traditional dielectrophoresis experiments, such as high voltages that cause heat generation, bubble formation, and unwanted electrochemical reactions. The strongly enhanced fields around the nanogap induce particle-transport speed exceeding 10 μm/s and enable the trapping of 30 nm polystyrene nanoparticles using an ultralow bias of 200 mV. We also demonstrate rapid electronic trapping of quantum dots and nanodiamond particles on arrays of parallel traps. Our sub-10 nm gold nanogap electrodes can be combined with plasmonic sensors or nanophotonic circuitry, and their low-power electronic operation can potentially enable high-density integration on a chip as well as portable biosensing.

Engineered transmembrane pores

Today, hundreds of researchers are working on nanopores, making an impact in both basic science and biotechnology. Proteins remain the most versatile sources of nanopores, based on our ability to engineer them with sub-nanometer precision. Recent work aimed at the construction and discovery of novel pores has included unnatural amino acid mutagenesis and the application of selection techniques. The diversity of structures has now been increased through the development of helix-based pores as well as the better-known β barrels. New developments also include truncated pores, which pierce bilayers through lipid rearrangement, and hybrid pores, which do away with bilayers altogether. Pore dimers, which span two lipid bilayers, have been constructed and pores based on DNA nanostructures are gaining in importance. While nanopore DNA sequencing has received enthusiastic attention, protein pores have a wider range of potential applications, requiring specifications that will require engineering efforts to continue for years to come.

Tailoring particle translocation via dielectrophoresis in pore channels

Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification.

Biomimetic Solid-State Nanochannels: From Fundamental Research to Practical Applications

In recent years, solid-state smart nanopores/nanochannels for intelligent control of the transportation of ions and molecules as organisms have been extensively studied, because they hold great potential applications in molecular sieves, nanofluidics, energy conversion, and biosensors. To keep up with the fast development of this field, it is necessary to summarize the construction, characterization, and application of biomimetic smart nanopores/nanochannels. These can be classified into four sections: the fabrication of solid-state nanopores/nanochannels, the functionalization methods and materials, the mechanism explanation about the ion rectification, and the practical applications. A brief conclusion and outlook for the biomimetic nanochannels is provided, highlighting those that could be developed and integrated into devices for use in tackling current and the future problems including resources, energy, environment, and health.

Template-Stripped Multifunctional Wedge and Pyramid Arrays for Magnetic Nanofocusing and Optical Sensing

We present large-scale reproducible fabrication of multifunctional ultrasharp metallic structures on planar substrates with capabilities including magnetic field nanofocusing and plasmonic sensing. Objects with sharp tips such as wedges and pyramids made with noble metals have been extensively used for enhancing local electric fields via the lightning-rod effect or plasmonic nanofocusing. However, analogous nanofocusing of magnetic fields using sharp tips made with magnetic materials has not been widely realized. Reproducible fabrication of sharp tips with magnetic as well as noble metal layers on planar substrates can enable straightforward application of their material and shape-derived functionalities. We use a template-stripping method to produce plasmonic-shell-coated nickel wedge and pyramid arrays at the wafer-scale with tip radius of curvature close to 10 nm. We further explore the magnetic nanofocusing capabilities of these ultrasharp substrates, deriving analytical formulas and comparing the results with computer simulations. These structures exhibit nanoscale spatial control over the trapping of magnetic microbeads and nanoparticles in solution. Additionally, enhanced optical sensing of analytes by these plasmonic-shell-coated substrates is demonstrated using surface-enhanced Raman spectroscopy. These methods can guide the design and fabrication of novel devices with applications including nanoparticle manipulation, biosensing, and magnetoplasmonics.

Sensitive Detection of Small Particles in Fluids Using Optical Fiber Tip with Dielectrophoresis

This work presents using a tapered fiber tip coated with thin metallic film to detect small particles in water with high sensitivity. When an AC voltage applied to the Ti/Al coated fiber tip and indium tin oxide (ITO) substrate, a gradient electric field at the fiber tip induced attractive/repulsive force to suspended small particles due to the frequency-dependent dielectrophoresis (DEP) effect. Such DEP force greatly enhanced the concentration of the small particles near the tip. The increase of the local concentration also increased the scattering of surface plasmon wave near the fiber tip. Combined both DEP effect and scattering optical near-field, we show the detection limit of the concentration for 1.36 μm polystyrene beads can be down to 1 particle/mL. The detection limit of the Escherichia coli (E. coli) bacteria was 20 CFU/mL. The fiber tip sensor takes advantages of ultrasmall volume, label-free and simple detection system.