Ion-beam sculpting at nanometre length scales

Analytical Model for Particle Capture in Nanopores Elucidates Competition among Electrophoresis, Electroosmosis, and Dielectrophoresis

The interaction between nanoparticles dispersed in a fluid and nanopores is governed by the interplay of hydrodynamical, electrical, and chemical effects. We developed a theory for particle capture in nanopores and derived analytical expressions for the capture rate under the concurrent action of electrical forces, fluid advection, and Brownian motion. Our approach naturally splits the average capture time in two terms, an approaching time due to the migration of particles from the bulk to the pore mouth and an entrance time associated with a free-energy barrier at the pore entrance. Within this theoretical framework, we described the standard experimental condition where a particle concentration is driven into the pore by an applied voltage, with specific focus on different capture mechanisms: under pure electrophoretic force, in the presence of a competition between electrophoresis and electroosmosis, and finally under dielectrophoretic reorientation of dipolar particles. Our theory predicts that dielectrophoresis is able to induce capture for both positive and negative voltages. We performed a dedicated experiment involving a biological nanopore (α-hemolysin) and a rigid dipolar dumbbell (realized with a β-hairpin peptide) that confirms the theoretically proposed capture mechanism.

High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System

Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing-an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores-could potentially improve single-molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate the potential utility of our double-nanopore system for DNA sequencing by simulating repeat back-and-forth motion-flossing-of a DNA strand through the double-nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.

Mechanisms of solid-state nanopore enlargement under electrical stress

We present a thorough exploration of nanopore growth under electrical stress in electrolyte solution, and demonstrate that despite their superficial similarities, nanopore formation by controlled breakdown (CBD) and nanopore growth under moderate voltage stress are fundamentally different processes. In particular, we demonstrate that unlike the CBD process, nanopore growth is primarily driven by the level of ionic current passing through the nanopore, rather than the strength of the electric field generating the current, and that enlargement has a much weaker pH dependence than does CBD pore formation. In combination with other works in the field, our results suggest that despite clear current-dependence, Joule heating is unlikely to be the main driver of pore growth during electrical stress, pointing instead toward electrochemical dissolution of membrane material along the pore walls. While the chemistry underlying the growth process remains unclear, the dependence of growth rate on current allows decoupling of the pore enlargement mechanism from the possibility of forming additional nanopores during the growth process, providing a practical method by which to rapidly enlarge a nanopore without risking opening a second nanopore.

Gas separation using graphene nanosheet: insights from theory and simulation

The investigation of porous graphene, especially experimental research, is a challenging issue in related academic and technology and has become a hot topic in recent years. It is well known that the preparation of porous graphene is a difficult problem in experimental techniques. To prepare nanoporous graphene, much attention must focus on the quality of nanoporous structures and throughput array pores. Therefore, a comprehensive summary as much as possible has been made to provide a better understanding of the progress. A summary of synthesis techniques, the properties of nanoporous graphene membranes from the synthesis point of view, and potential applications of porous graphene and graphene oxide for gas separation on the basis of theoretical studies were given attention in this paper. Gas separation, including carbon dioxide capture, gas storage, natural gas sweetening, and flue gas purification through porous graphene, is of great interest. Porous graphene with narrow pore distribution provides exciting opportunities in gas separation processes.

Electrophoretic Transport of Single-Stranded DNA through a Two Dimensional Nanopore Patterned on an In-Plane Heterostructure

Recent advances in nanotechnology have facilitated fabrication of various solid state nanopores as a versatile alternative to biological nanopores; however, effective transport of a single-stranded DNA (ssDNA) molecule through solid state nanopores for sequencing has remained a challenge. In particular, the nonspecific interactions between the ssDNA and the engineered nanopore surface are known to impose difficulties on both transport and interrogation. Here, we show that a two-dimensional (2D) nanopore patterned on an in-plane heterostructure comprising both graphene and hexagonal boron nitride (hBN) can be utilized to transport the ssDNA electrophoretically. Energetically, a ssDNA molecule prefers to stay on the hBN domain than the graphene one since the former has a stronger van der Waals attraction with the ssDNA, as demonstrated in both classic molecular dynamics (MD) simulations and density functional theory (DFT) based calculations, which leads to the confinement of the ssDNA in the 2D nanopore. Therefore, this nanopore enables the manipulation of the conformation of a highly flexible ssDNA molecule on a flat 2D heterostructure surface, making it possible for sensing ssDNA bases using the high resolution atomic force microscopy (AFM) or scanning tunneling microscopy (STM) in the third dimension (perpendicular to the 2D surface).

Spontaneous Translocation of Single-Stranded DNA in Graphene-MoS2 Heterostructure Nanopores: Shape Effect

The appropriate translocation speed of a single-stranded DNA (ssDNA) through a solid-state nanopore is crucial for DNA sequencing technologies. By studying the geometry effect of graphene-MoS₂ hetero-nanopores with molecular dynamics simulations, we have found that the shape of these nanopores (circular, square, or triangular, with similar size) may have a significant effect on the spontaneous translocation of ssDNA, with the triangular nanopore showing the slowest translocation and the circular one the fastest. Further analyses reveal that such differences in the spontaneous ssDNA translocation arise from different electrostatic attractions between the positively charged Mo atoms exposed in the pore and the negatively charged phosphate groups (PO₄^-) in nucleotides; the "sharpness" and the total number of the exposed Mo atoms of the nanopores are responsible for different electrostatic attractions between ssDNA and the nanopore. Our findings suggest that graphene-MoS₂ heterostructure nanopores with lower symmetries (i.e., having sharper corners) are capable of slowing down the ssDNA translocation, which might help better facilitate the nucleotide sensing and DNA sequencing. The conclusion from these findings might also extend to other solid-state nanopores in designing appropriate shapes for better controlling of the translocation speed.

Machine Learning to Improve the Sensing of Biomolecules by Conical Track-Etched Nanopore

Single nanopore is a powerful platform to detect, discriminate and identify biomacromolecules. Among the different devices, the conical nanopores obtained by the track-etched technique on a polymer film are stable and easy to functionalize. However, these advantages are hampered by their high aspect ratio that avoids the discrimination of similar samples. Using machine learning, we demonstrate an improved resolution so that it can identify short single- and double-stranded DNA (10- and 40-mers). We have characterized each current blockade event by the relative intensity, dwell time, surface area and both the right and left slope. We show an overlap of the relative current blockade amplitudes and dwell time distributions that prevents their identification. We define the different parameters that characterize the events as features and the type of DNA sample as the target. By applying support-vector machines to discriminate each sample, we show accuracy between 50% and 72% by using two features that distinctly classify the data points. Finally, we achieved an increased accuracy (up to 82%) when five features were implemented.

Confocal scanning photoluminescence for mapping electron and photon beam-induced microscopic changes in SiN x during nanopore fabrication

Focused electron and laser beams have shown the ability to form nanoscale pores in SiN _x membranes. During the fabrication process, areas beyond the final nanopore location will inevitably be exposed to the electron beams or the laser beams due to the need for localization, alignment and focus. It remains unclear how these unintended exposures affect the integrity of the membrane. In this work, we demonstrate the use of confocal scanning photoluminescence (PL) for mapping the microscopic changes in SiN _x nanopores when exposed to electron and laser beams. We developed and validated a model for the quantitative interpretation of the scanned PL result. The model shows that the scanning PL result is insensitive to the nanopore size. Instead, it is dominated by the product of two microscopic material factors: quantum yield profile (i.e. variations in electronic structure) and thickness profile (i.e. thinning of the membrane). We experimentally demonstrated that the electron and laser beams could alter the material electronic structures (i.e. quantum yield) even when no thinning of the membrane occurs. Our results suggest that minimizing the unintended e-beam or laser beam to the SiN _x during the fabrication is crucial if one desires the microscopic integrity of the membrane.

Deformation-Mediated Translocation of DNA Origami Nanoplates through a Narrow Solid-State Nanopore

With the development in DNA self-assembly technology, DNA origami nanostructures have been widely applied in biomedical research. Solid-state nanopores represent an emerging single-molecule sensing platform for studying nanostructures with arbitrary dimensions and physical characteristics, including DNA origami. Here, we employed relatively narrow silicon nitride nanopores to detect the deformation and translocation of DNA origami nanoplates with dimensions of approximately 60 × 54 nm. We performed translocation experiments using three nanopore diameters that are all smaller than the plat dimensions. Analysis of current blockade signals and the representative events reveals three types of translocation orientations for the nanoplates. Furthermore, by studying the electrical signal characteristics (current change and dwell time) for the different diameter pores, we obtained information about the translocation behaviors for the DNA nanoplates through different constrictions. Our investigation provides an approach to analyze the deformation and translocation of DNA origami structures.

Digital counting of nucleic acid targets using solid-state nanopores

Assays targeting biomarkers for the early diagnosis of disease demand a sensing platform with a high degree of specificity and sensitivity. In this work, we developed and characterized a solid-state nanopore-based sensing assay for the detection of short nucleic acid targets with readily customizable nanostructured DNA probe sets. We explored the electrical signatures of three DNA nanostructures to determine their performance as probe sets in a digital counting scheme to quantify the concentration of targets. With these probes, we demonstrate the specific, simultaneous detection of two different DNA targets in a 2-plex assay, and separately that of microRNA-155, a biomarker linked to various human cancers. In addition to specific target detection, our scheme demonstrated the ability to quantify at least six different microRNA concentrations. These results highlight the potential for solid-state nanopores as single-molecule counters for future digital diagnostic technologies.

Four Aspects about Solid-State Nanopores for Protein Sensing: Fabrication, Sensitivity, Selectivity, and Durability

Solid-state nanopores are a mimic of innate biological nanopores embedded on lipid membranes. They are fabricated on thin suspended layers of synthetic materials that provide superior thermal, mechanical, chemical stability, and geometry flexibility. As their counterpart biological nanopores reach the goal of DNA sequencing and become commercial, solid-state nanopores thrive in aspects of protein sensing and have become an important research component for clinical diagnostic technologies. This review focuses on resistive pulse sensing modes, which are versatile for low-cost, portable sensing devices and summarizes four main aspects toward commercially available resistive pulse-based protein sensing techniques using solid-state nanopores. In each aspect of fabrication, sensitivity, selectivity, and durability, brief fundamentals are introduced and the challenges and improvements are discussed. The rapid advance of a practical technique requires greater multidisciplinary cooperation. The review aims at clarifying existing obstacles in solid-state nanopore based protein sensing, intriguing readers with existing solutions and finally encouraging multidisciplinary researchers to advance the development of this promising protein sensing methodology.

Wafer-level fabrication of individual solid-state nanopores for sensing single DNAs

For biomolecule sensing purposes a solid-state nanopore platform based on silicon has certain advantages as compared to nanopores on other substrates such as graphene, silicon nitride, silicon oxide etc Capitalizing on the developed CMOS technology, nanopores on silicon are scalable without any requirement for additional processing, the devices are low cost and the process can be repeatable with a high yield. One of the essential requirements in biomolecule sensing is the ability of the nanopore to interact with the analyte. In this work, we present a method for processing high aspect ratio, single nanopores in the range of 10-30 nm in diameter and approximately 700 nm in length on a silicon-on-insulator (SOI) wafer. The presented method of manufacturing the high aspect ratio individual nanopores combines optical lithography and anisotropic KOH etching with a final electrochemical etching step to form the nanopores and is repeatable and can be processed in batches. We demonstrate electrical detection of dsDNA translocation, where the characteristic time of the process is in the millisecond range. We also analyse the translocation parameters and correlate the enhanced length of the nanopore to a longer translocation time as compared to other substrates.

The influence of electrolyte concentration on nanofractures fabricated in a 3D-printed microfluidic device by controlled dielectric breakdown

A three-dimensional-printed microfluidic device made of a thermoplastic material was used to study the creation of molecular filters by controlled dielectric breakdown. The device was made from acrylonitrile butadiene styrene by a fused deposition modeling three-dimensional printer and consisted of two V-shaped sample compartments separated by 750 µm of extruded plastic gap. Nanofractures were formed in the thin piece of acrylonitrile butadiene styrene by controlled dielectric breakdown by application voltage of 15-20 kV with the voltage terminated when reaching a defined current threshold. Variation of the size of the nanofractures was achieved by both variation of the current threshold and by variation of the ionic strength of the electrolyte used for breakdown. Electrophoretic transport of two proteins, R-phycoerythrin (RPE; <10 nm in size) and fluorescamine-labeled BSA (f-BSA; 2-4 nm), was used to monitor the size and transport properties of the nanofractures. Using 1 mM phosphate buffer, both RPE and f-BSA passed through the nanofractures when the current threshold was set to 25 µA. However, when the threshold was lowered to 10 µA or lower, RPE was restricted from moving through the nanofractures. When we increased the electrolyte concentration during breakdown from 1 to 10 mM phosphate buffer, BSA passed but RPE was blocked when the threshold was equal to, or lower than, 25 µA. This demonstrates that nanofracture size (pore area) is directly related to the breakdown current threshold but inversely related to the concentration of the electrolyte used for the breakdown process.

Sensing with Nanopores and Aptamers: A Way Forward

In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.

The Influence of Electric Field Intensity and Particle Length on the Electrokinetic Transport of Cylindrical Particles Passing through Nanopore

The electric transport of nanoparticles passing through nanopores leads to a change in the ion current, which is essential for the detection technology of DNA sequencing and protein determination. In order to further illustrate the electrokinetic transport mechanism of particles passing through nanopores, a fully coupled continuum model is constructed by using the arbitrary Lagrangian–Eulerian (ALE) method. The model consists of the electric field described by the Poisson equation, the concentration field described by Nernst–Planck equation, and the flow field described by the Navier–Stokes equation. Based on this model, the influence of imposed electric field and particle length on the electrokinetic transport of cylindrical particles is investigated. It is found firstly the translation velocities for the longer particles remain constant when they locate inside the nanopore. Both the ion current blockade effect and the ion current enhancement effect occur when cylindrical particles enter and exit the nanopore, respectively, for the experimental parameters employed in this research. Moreover, the particle translation velocity and current fluctuation amplitude are dominated by the electric field intensity, which can be used to adjust the particle transmission efficiency and the ion current detectability. In addition, the increase in particle length changes the particle position corresponding to the peak value of the ion current, which contributes to distinguishing particles with different lengths as well.

Recessed Ag/AgCl Microelectrode-Supported Lipid Bilayer for Nanopore Sensing

Biological nanopores reconstituted into supported lipid bilayer membranes are widely used as a platform for stochastic nanopore sensing with the ability to detect single molecules including, for example, single-stranded DNA (ssDNA) and miRNA. A main thrust in this area of research has been to improve overall bilayer stability and ease of measurements. These improvements are achieved through a variety of clever strategies including droplet-based techniques; however, they typically require specific microfabrication techniques to prepare devices or special manipulation techniques for microdroplets. Here, we describe a new method to prepare lipid bilayers using a recessed-in-glass Ag/AgCl microelectrode as a support structure. The lipid bilayer is formed at the tip of the microelectrode by immersing the microelectrode into a layered bath solution consisting of an oil/lipid mixture and an aqueous electrolyte solution. In this paper, we demonstrate this stable, supported lipid bilayer structure for channel current measurements of pore-forming toxins and single-molecule detection of ssDNA. This Ag/AgCl-supported lipid bilayer can potentially be widely adopted as a lipid membrane platform for nanopore sensing because of its simple and easy procedure needed to prepare lipid bilayers.

Crucial Role of Out-of-Pore Resistance on Temporal Response of Ionic Current in Nanopore Sensors

We investigated the temporal resolution of ionic current in solid-state nanopore sensors. Resistive pulses observed upon translocation of single-nanoparticles were found to become blunter as we imposed larger external resistance in series to the pore via the integrated microfluidic channels on the membrane. This was found to occur even when the out-of-pore resistance is more than an order of magnitude smaller than that at the nanopore, which can be understood as a predominant contribution of charging/discharging at the water-touching thin dielectrics to retard the response of the ionic current against ion blockage by a fast-moving object through the sensing zone. Most importantly, our results predict a time resolution of better than 12 ns, irrespective of the nanopore size, by optimizing the membrane capacitance and the external resistance that promises high-speed single-molecule sequencing by the ionic current at 10⁶ base/s.

Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements

Nanopores are promising for many applications including DNA sequencing and molecular filtration. Solid-state nanopores are preferable over their biological counterparts for applications requiring durability and operation under a wider range of external parameters, yet few studies have focused on optimizing their robustness. We report the lifetime and durability of pores and porous arrays in 10 to 100 nm-thick, low-stress silicon nitride (SiN_x) membranes. Pores are fabricated using a transmission electron microscope (TEM) and/or electron beam lithography (EBL) and reactive ion etching (RIE), with diameters from 2 to 80 nm. We store them in various electrolyte solutions (KCl, LiCl, MgCl₂) and record open pore conductance over months to quantify pore stability. Pore diameters increase with time, and diameter etch rate increases with electrolyte concentration from Δd/Δt ∼ 0.2 to ∼ 3 nm/day for 0.01 to 3 M KCl, respectively. TEM confirms the range of diameter etch rates from ionic measurements. Using electron energy loss spectroscopy (EELS), we observe a N-deficient region around the edges of TEM-drilled pores. Pore expansion is caused by etching of the Si/SiO₂ pore walls, which resembles the dissolution of silicon found in minerals such as silica (SiO₂) in salty ocean water. The etching process occurs where the membrane was exposed to the electron beam and can result in pore formation. However, coating pores with a conformal 1 nm-thick hafnium oxide layer prevents expansion in 1 M KCl, in stark contrast to bare SiN_x pores (∼ 1.7 nm/day). EELS data reveal the atomic composition of bare and HfO₂-coated pores.

Arrayed nanopore silver thin films for surface-enhanced Raman scattering

Active substrates are crucial for surface-enhanced Raman scattering (SERS). Among these substrates, large uniform area arrayed nanoporous silver thin films have been developed as active substrates. Arrayed nanoporous silver thin films with unique anisotropic morphologies and nanoporous structures can be fabricated onto the nanoporous anodic aluminum oxide (AAO) of controlled pore size and interspacing by precisely tuning the sputtering parameters. These thin films preserve locally enhanced electromagnetic fields by exciting the surface plasmon resonance, which is beneficial for SERS. In this study, nanoporous silver thin films were transferred into polymethylmethacrylate (PMMA) and polydimethylsiloxane (PDMS) substrates using our recently invented template-assisted sol-gel phase inverse-imprinting process to form two different nanopore thin films. The as-formed Ag nanoporous thin films on PMMA and PDMS exhibited intensively enhanced SERS signals using Rhodamine 6G (R6G) as the model molecule. The two nanopore thin films exhibited opposite pore size-dependent SERS tendencies, which were elucidated by the different enhancement tendencies of the electric field around pores of different diameters. In particular, the Ag nanoporous thin film on PMMA exhibited an R6G detection limit of as low as 10-6 mol L-1, and the SERS enhancement factor (EF) was more than 106. The low detection limit and large EF demonstrated the high sensitivity of the as-prepared SERS substrates for label-free detection of biomolecules. Compared with conventional smooth films, this nanopore structure can facilitate future application in biomolecular sensors, which allows the detection of single molecules via an electronic readout without requirement for amplification or labels.

Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS2 Nanopore

Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS₂ membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS₂ nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.

Surface modification of solid-state nanopore by plasma-polymerized chemical vapor deposition of poly(ethylene glycol) for stable device operation

Biopolymer adsorption onto a membrane is a significant issue in the reliability of solid-state nanopore devices, since it degrades the device performance or promotes device failure. In this work, a poly(ethylene glycol) (PEG) layer was coated on a silicon nitride (SiN_x) membrane by plasma-polymerized vapor deposition to inhibit biopolymer adsorption. From optical observations, the deposited PEG layer demonstrated increased hydrophilicity and anti-adsorption property compared to the SiN_x surface. Electrical properties of the PEG/SiN_x nanopore were characterized, showing Ohmic behavior and a 6.3 times higher flicker noise power due to the flexible conformation of PEG in water. Antifouling performance of each surface was analyzed by measuring the average time from voltage bias to the first adsorption during DNA translocation experiments, where the modified surface enabled two times prolonged device operation. The time to adsorption was dependent on the applied voltage, implying adsorption probability was dominated by the electrophoretic DNA approach to the nanopore. DNA translocation behaviors on each surface were identified from translocation signals, as the PEG layer promoted unfolded and fast movement of DNA through the nanopore. This work successfully analyzed the effect of the PEG layer on DNA adsorption and translocation in solid-state nanopore experiments.

Application of Solid-State Nanopore in Protein Detection

A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.

Controlling DNA Translocation Through Solid-state Nanopores

Compared with the status of bio-nanopores, there are still several challenges that need to be overcome before solid-state nanopores can be applied in commercial DNA sequencing. Low spatial and low temporal resolution are the two major challenges. Owing to restrictions on nanopore length and the solid-state nanopores' surface properties, there is still room for improving the spatial resolution. Meanwhile, DNA translocation is too fast under an electrical force, which results in the acquisition of few valid data points. The temporal resolution of solid-state nanopores could thus be enhanced if the DNA translocation speed is well controlled. In this mini-review, we briefly summarize the methods of improving spatial resolution and concentrate on controllable methods to promote the resolution of nanopore detection. In addition, we provide a perspective on the development of DNA sequencing by nanopores.

Fabrication of a Biomimetic Nanochannel Logic Platform and Its Applications in the Intelligent Detection of miRNA Related to Liver Cancer

Nanochannel-based analytical techniques have great potential applications for nucleic acid sequencing and high sensitivity detection of biological molecules. However, the sensitivity of conventional solid-state nanochannel sensors is hampered by a lack of effective signal amplification strategies, which has limited its utility in the field of analytical chemistry. Here we selected a solid-state nanochannnel modified with polyethylenimine and Zr⁴⁺ in combination with graphene oxide as the sensing platform. The high-performance sensor is based upon the change of the surface charge of the nanochannel, which is resulted from DNA cascade signal amplification in solution. The target miRNA (miR-122) can be indirectly quantitated with a detection limit of 97.2 aM with an excellent selectivity. Depending on the nucleic acid's hybridization and configuration transform, the designed nanochannel sensing systems can realize the intelligent detection of multiple liver cancer-related miRNA (miR-122 and miR Let-7a) integrating with cascaded INHIBIT-OR logic gate to provide theoretical guidance and technical support for clinical diagnosis and therapeutic evaluation of liver cancer.

Isolation and analysis methods of extracellular vesicles (EVs)

Extracellular vesicles (EVs) have been recognized as an evolving biomarker within the liquid biopsy family. While carrying both host cell proteins and different types of RNAs, EVs are also present in sufficient quantities in biological samples to be tested using many molecular analysis platforms to interrogate their content. However, because EVs in biological samples are comprised of both disease and non-disease related EVs, enrichment is often required to remove potential interferences from the downstream molecular assay. Most benchtop isolation/enrichment methods require > milliliter levels of sample and can cause varying degrees of damage to the EVs. In addition, some of the common EV benchtop isolation methods do not sort the diseased from the non-diseased related EVs. Simultaneously, the detection of the overall concentration and size distribution of the EVs is highly dependent on techniques such as electron microscopy and Nanoparticle Tracking Analysis, which can include unexpected variations and biases as well as complexity in the analysis. This review discusses the importance of EVs as a biomarker secured from a liquid biopsy and covers some of the traditional and non-traditional, including microfluidics and resistive pulse sensing, technologies for EV isolation and detection, respectively.

Ionic amplifying circuits inspired by electronics and biology

Integrated circuits are present in all electronic devices, and enable signal amplification, modulation, and relay. Nature uses another type of circuits composed of channels in a cell membrane, which regulate and amplify transport of ions, not electrons and holes as is done in electronic systems. Here we show an abiotic ionic circuit that is inspired by concepts from electronics and biology. The circuit amplifies small ionic signals into ionic outputs, and its operation mimics the electronic Darlington amplifier composed of transistors. The individual transistors are pores equipped with three terminals including a gate that is able to enrich or deplete ions in the pore. The circuits we report function at gate voltages < 1 V, respond to sub-nA gate currents, and offer ion current amplification with a gain up to ~300. Ionic amplifiers are a logical step toward improving chemical and biochemical sensing, separations and amplification, among others.

Durable, Stable, and Functional Nanopores Decorated by Self-Assembled Dipeptides

Nanopores have become an important tool for the detection and analysis of molecules at the single-molecule level. Surface modification of solid-state nanopores can improve their durability and efficiency. Peptides are ideal for surface modifications as they allow tailoring of multiple properties by a rational design of their sequence. Here, silicon nitride nanopores were coated by a dipeptide layer where a l-3,4-dihydroxyphenylalanine (DOPA) residue is the anchoring element and the other amino acid moiety is the functional element. DOPA binds tightly to many types of surfaces and allows a one-step functionalization of surfaces by simple immersion. As a result, the lifetime of coated nanopores increased from hours to months and the current-stability has significantly improved with respect to uncoated pores. This improvement is achieved by controlling the surface wettability and charge. Peptide-coated nanopores can be utilized as sensitive sensors that can be adjusted based on the choice of the functional moiety of the coated peptide. In addition, the coating slows down dsDNA translocation because of the DNA interaction with the pore coating.

Fabrication of Si Micropore and Graphene Nanohole Structures by Focused Ion Beam

A biosensor formed by a combination of silicon (Si) micropore and graphene nanohole technology is expected to act as a promising device structure to interrogate single molecule biopolymers, such as deoxyribonucleic acid (DNA). This paper reports a novel technique of using a focused ion beam (FIB) as a tool for direct fabrication of both conical-shaped micropore in Si₃N₄/Si and a nanohole in graphene to act as a fluidic channel and sensing membrane, respectively. The thinning of thick Si substrate down to 50 µm has been performed prior to a multi-step milling of the conical-shaped micropore with final pore size of 3 µm. A transfer of graphene onto the fabricated conical-shaped micropore with little or no defect was successfully achieved using a newly developed all-dry transfer method. A circular shape graphene nanohole with diameter of about 30 nm was successfully obtained at beam exposure time of 0.1 s. This study opens a breakthrough in fabricating an integrated graphene nanohole and conical-shaped Si micropore structure for biosensor applications.

Ion current rectification behavior of a nanochannel having nonuniform cross-section

Due to its versatile applications in biotechnology, ion current rectification (ICR), which arises from the asymmetric nature of the ion transport in a nanochannel, has drawn much attention, recently. Here, the ICR behavior of a pH-regulated nanochannel comprising two series connected cylindrical nanochannels of different radii is examined theoretically, focusing on the influences of the radii ratio, the length ratio, the bulk concentration, and the solution pH. The results of numerical simulation reveal that the rectification factor exhibits a local maximum with respect to both the radii ratio and the length ratio. The values of the radii ratio and the length ratio at which the local maximum in the rectification factor occur depend upon the level of the bulk salt concentration. The rectification factor also shows a local maximum as the solution pH varies. Among the factors examined, the solution pH influences the ICR behavior of the nanochannel most significantly.

Low-Noise Nanopore Enables In-Situ and Label-Free Tracking of a Trigger-Induced DNA Molecular Machine at the Single-Molecular Level

Solid-state nanopores have shown special high potential in a label-free molecular assay, structure identification, and target-index at the single-molecular level, even though frustrating electrical baseline noise is still one of the major factors that limit the spatial resolution and signaling reliability of solid-state nanopores, especially in small target detection. Here we develop a significant and easy-operating noise-reduction approach via mixing organic solvents with high dielectric constants into a traditional aqueous electrolyte. The strategy is generally effective for pores made of different materials, such as the most commonly used conical glass (CGN) or SiN_x. While the mechanism should be multisourced, MD simulations suggest the noise reduction may partially arise from the even ionic distribution caused by the addition of higher dielectric species. Among all solvents experimentally tested, the two with the highest dielectric constants, formamide and methylformamide, exhibit the best noise reduction effect for target detection of CGN. The power spectral density at the low-frequency limit is reduced by nearly 3 orders with the addition of 20% formamide. Our work qualifies the reliability of solid-state nanopores into much subtler scales of detection, such as dsDNAs under 100 bp. As a practical example, bare CGN is innovatively employed to perform in-situ tracking of trigger-responsive DNA machine forming oligomers.

Analysis Method of the Ion Current-Time Waveform Obtained from Low Aspect Ratio Solid-state Nanopores

Low aspect ratio nanopores are expected to be applied to the detection of viruses and bacteria because of their high spatial resolution. Multiphysics simulations have revealed that the ion current-time waveform obtained from low aspect ratio nanopores contains information on not only the volume of viruses and bacteria, but also the structure, surface charge, and flow dynamics. Analysis using machine learning extracts information about these analytes from the ion current-time waveform. The combination of low aspect ratio nanopores, multiphysics simulation, and machine learning has made it possible to distinguish different types of viruses and bacteria with high accuracy.

Stochastic electrochemistry at ultralow concentrations: the case for digital sensors

There is increasing demand, in particular from the medical field, for assays capable of detecting sub-pM macromolecular concentrations with high specificity. Methods for detecting single bio/macromolecules have already been developed based on a variety of transduction mechanisms, which represents the ultimate limit of mass sensitivity. Due to limitations imposed by mass transport and binding kinetics, however, achieving high concentration sensitivity additionally requires the massive parallelization of these single-molecule methods. This leads to a new sort of 'digital' assay based on large numbers of parallel, time-resolved measurements aimed at detecting, identifying and counting discrete macromolecular events instead of reading out an average response. In this Tutorial Review we first discuss the challenges inherent to trace-level detection and the motivations for developing digital assays. We then focus on the potential of recently developed single-entity impact electrochemistry methods for use in digital sensors. These have the inherent advantage of relying on purely electrical signals. They can thus in principle be implemented using integrated circuits to provide the parallelization, readout and analysis capabilities required for digital sensors.

Shape characterization and discrimination of single nanoparticles using solid-state nanopores

Resistive pulse sensing with nanopores is expected to enable identification and analysis of nanoscale objects in ionic solutions. However, there is currently no remarkable method to characterize the three-dimensional shape of charged biomolecules or nanoparticles with low-cost and high-throughput. Here we demonstrate the sensing capability of solid-state nanopores for shape characterization of single nanoparticles by monitoring the ionic current blockades during their electrophoretic translocation through nanopores. By using nanopores that are a bit larger than the particles, shape characterization of both spherical and cubic silver nanoparticles is successfully realized due to their rapid rotation with respect to the pore axis, which is further validated by our all-atom molecular dynamics simulations. The single-molecule approach based on nanopores will allow people to measure the dimension and to characterize the shape of single nanoparticles or proteins simultaneously in real time, which is significant for its potential application in investigation of structural biology and proteomics in the near future.

Designed Ionic Microchannels for Ultrasensitive Detection and Efficient Removal of Formaldehyde in an Aqueous Solution

Ultrasensitive and ultraprecise detection of toxic target molecules is highly desirable for monitoring water pollution and improving human safety. Herein, a novel formaldehyde (HCHO) responsive ionic microchannel was successfully fabricated through constructing ethylenediamine (EDA)-functionalized poly(ionic liquid)/polyacrylonitrile nanofibrous membrane (PIL/PAN NFM). By employing the reactivity of HCHO with EDA immobilized on the prepared ionic nanofibrous membrane, the resultant ionic current output can switch from low to high because of the electron affinity increase and zeta potential decrease of the microchannels when reacting with more HCHO. Meanwhile, benefiting from the poly(ionic liquid) backbones in the designed ionic microchannels, the ions in electrolyte were greatly enriched in the channels and facilitating more ion transport paths formed along with the ionic nanofibers, therefore amplifying the detected ionic current signals. On the basis of the ionic current amplification mechanism, it is further used to detect a trace of HCHO in an aqueous solution. Finally, the ionic microchannels exhibited high sensitivity for the determination of HCHO ranging from 360 ppm (3.6 × 10² mg/L) to 0.036 ppt (3.6 × 10^-8 mg/L) (R² = 0.93) through an established linear correlation between responsive ionic current and HCHO concentrations. Furthermore, the ionic microchannels can remove a large number of HCHO molecules from an aqueous solution due to the abundant amino grafted on the membrane. In a sum, this work paves a promising way toward the design of artificial microchannels for various harmful compounds' detection.

Self-supporting hybrid silica membranes with controlled porous architectures

Transferrable, self-supporting membranes with controlled and ordered pore architectures have been developed for potential applications in the fields of filtration, sensing, separation and catalysis.

Nanopore Fabrication and Application as Biosensors in Neurodegenerative Diseases

Since its conception as an applied biomedical technology nearly 30 years ago, nanopore is emerging as a promising, high-throughput, biomarker-targeted diagnostic tool for clinicians. The attraction of a nanopore-based detection system is its simple, inexpensive, robust, user-friendly, high-throughput blueprint with minimal sample preparation needed prior to analysis. The goal of clinical-based nanopore biosensing is to go from sample acquisition to a meaningful readout quickly. The most extensive work in nanopore applications has been targeted at DNA, RNA, and peptide identification. Although, biosensing of pathological biomarkers, which is covered in this review, is on the rise. This review is broken into two major sections: (i) the current state of existing biological, solid state, and hybrid nanopore systems and (ii) the applications of nanopore biosensors toward detecting neurodegenerative biomarkers.

Revealing the mechanism of DNA passing through graphene and boron nitride nanopores

Nanopores on 2D materials have great potential for DNA sequencing, which is attributed to their high sequencing speed and reduced cost. However, identifying DNA bases at such a high speed with nanometer precision has remained a big challenge. Here, we implemented theoretical calculations to show the translocation of single-stranded DNA (ssDNA) through solid-state nanopores on a 2D hexagonal boron nitride (h-BN) and graphene sheet. A base-specific ssDNA sequencing technique was devised, based on the individual differences in the ion current responses for the (polyA)₁₆, (polyG)₁₆, (polyC)₁₆, and (polyT)₁₆ bases of ssDNA. Our sequential procedure for sequencing is built on a comparative approach between the current signals obtained from the nanopores to achieve base-specific detection. Our results indicate that at higher voltages (1.0, 1.2, 1.4, 1.6, 1.8 and 2.0 V nm^-1), DNA translocation is tracked though the 1.5 and 2.0 nm nanopores, and at the 1.5 nm pore size, folded ssDNA close to the nanopore accounts for 93% and 81% of events for graphene and h-BN. Our calculations indicate charge transfer from the graphene to ssDNA, while the reverse happens in the case of the h-BN membrane. These results provide critical insights into our understanding of single molecule sequencing through solid-state nanopore research.

Fast and accurate quantification of insertion-site specific transgene levels from raw seed samples using solid-state nanopore technology

Many modern crop varieties contain patented biotechnology traits, and an increasing number of these crops have multiple (stacked) traits. Fast and accurate determination of transgene levels is advantageous for a variety of use cases across the food, feed and fuel value chain. With the growing number of new transgenic crops, any technology used to quantify them should have robust assays that are simple to design and optimize, thereby facilitating the addition of new traits to an assay. Here we describe a PCR-based method that is simple to design, starts from whole seeds, and can be run to end-point in less than 5 minutes. Subsequent relative quantification (trait vs. non-trait) using capillary electrophoresis performed in 5% increments across the 0-100% range showed a mean absolute error of 1.9% (s.d. = 1.1%). We also show that the PCR assay can be coupled to non-optical solid-state nanopore sensors to give seed-to-trait quantification results with a mean absolute error of 2.3% (s.d. = 1.6%). In concert, the fast PCR and nanopore sensing stages demonstrated here can be fully integrated to produce seed-to-trait quantification results in less than 10 minutes, with high accuracy across the full dynamic range.

Nanopipettes: a potential tool for DNA detection

As the information in DNA is of practical value for clinical diagnosis, it is important to develop efficient and rapid methods for DNA detection. In the past decades, nanopores have been extensively explored for DNA detection due to their low cost and high efficiency. As a sub-group of the solid-state nanopore, nanopipettes exhibit great potential for DNA detection which is ascribed to their stability, ease of fabrication and good compatibility with other technologies, compared with biological and traditional solid-state nanopores. Herein, the review systematically summarizes the recent progress in DNA detection with nanopipettes and highlights those studies dedicated to improve the performance of DNA detection using nanopipettes through different approaches, including reducing the rate of DNA translocation, improving the spatial resolution of sensing nanopipettes, and controlling DNA molecules through novel techniques. Besides, some new perspectives of the integration of nanopipettes with other technologies are reviewed.

Directed Irradiation Synthesis as an Advanced Plasma Technology for Surface Modification to Activate Porous and “as-received” Titanium Surfaces

For the design of smart titanium implants, it is essential to balance the surface properties without any detrimental effect on the bulk properties of the material. Therefore, in this study, an irradiation-driven surface modification called directed irradiation synthesis (DIS) has been developed to nanopattern porous and “as-received” c.p. Ti surfaces with the aim of improving cellular viability. Nanofeatures were developed using singly-charged argon ions at 0.5 and 1.0 keV energies, incident angles from 0° to 75° degrees, and fluences up to 5.0 × 1017 cm−2. Irradiated surfaces were evaluated by scanning electron microscopy, atomic force microscopy and contact angle, observing an increased hydrophilicity (a contact angle reduction of 73.4% and 49.3%) and a higher roughness on both surfaces except for higher incident angles, which showed the smoothest surface. In-vitro studies demonstrated the biocompatibility of directed irradiation synthesis (DIS) reaching 84% and 87% cell viability levels at 1 and 7 days respectively, and a lower percentage of damaged DNA in tail compared to the control c.p. Ti. All these results confirm the potential of the DIS technique to modify complex surfaces at the nanoscale level promoting their biological performance.