Nanopore blockade sensors for ultrasensitive detection of proteins in complex biological samples

DNA origami in the quest for membrane piercing

The tool kit for label-free single-molecule sensing, nucleic acid sequencing (DNA, RNA and protein) and other biotechnological applications has been significantly broadened due to the wide range of available nanopore-based technologies. Currently, various sources of nanopores, including biological, fabricated solid-state, hybrid and recently de novo chemically synthesized ion-like channels have put in use for rapid single-molecule sensing of biomolecules and other diagnostic applications. At length scales of hundreds of nanometers, DNA nanotechnology, particularly DNA origami-based devices, enables the assembly of complex and dynamic 3-dimensional nanostructures, including nanopores with precise control over the size/shape. DNA origami technology has enabled to construct nanopores by DNA alone or hybrid architects with solid-state nanopore devices or nanocapillaries. In this review, we briefly discuss the nanopore technique that uses DNA nanotechnology to construct such individual pores in lipid-based systems or coupled with other solid-state devices, nanocapillaries for enhanced biosensing function. We summarize various DNA-based design nanopores and explore the sensing properties of such DNA channels. Apart from DNA origami channels we also pointed the design principles of RNA nanopores for peptide sensing applications.

Application of nanopore sensors for biomolecular interactions and drug discovery

Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.

Probing the Hepatitis B Virus E-Antigen with a Nanopore Sensor Based on Collisional Events Analysis

Real-time monitoring, simple operation, and cheaper methods for detecting immunological proteins hold the potential for a solid influence on proteomics and human biology, as they can promote the onset of timely diagnoses and adequate treatment protocols. In this work we present an exploratory study suggesting the applicability of resistive-pulse sensing technology in conjunction with the α-hemolysin (α-HL) protein nanopore, for the detection of the chronic hepatitis B virus (HBV) e-antigen (HBeAg). In this approach, the recognition between HBeAg and a purified monoclonal hepatitis B e antibody (Ab(HBeAg)) was detected via transient ionic current spikes generated by partial occlusions of the α-HL nanopore by protein aggregates electrophoretically driven toward the nanopore’s vestibule entrance. Despite the steric hindrance precluding antigen, antibody, or antigen–antibody complex capture inside the nanopore, their stochastic bumping with the nanopore generated clear transient blockade events. The subsequent analysis suggested the detection of protein subpopulations in solution, rendering the approach a potentially valuable label-free platform for the sensitive, submicromolar-scale screening of HBeAg targets.

Understanding and modelling the magnitude of the change in current of nanopore sensors

Nanopores are promising sensing devices that can be used for the detection of analytes at the single molecule level. It is of importance to understand and model the current response of a nanopore sensor for improving the sensitivity of the sensor, a better interpretation of the behaviours of different analytes in confined nanoscale spaces, and quantitative analysis of the properties of the targets. The current response of a nanopore sensor, usually called a resistive pulse, results from the change in nanopore resistance when an analyte translocates through the nanopore. This article reviews the theoretical models used for the calculation of the resistance of the nanopore, and the corresponding change in nanopore resistance due to a translocation event. Models focus on the resistance of the pore cavity region and the access region of the nanopore. The influence of the sizes, shapes and surface charges of the translocating species and the nanopore, as well as the trajectory that the analyte follows are also discussed. This review aims to give a general guidance to the audience for understanding the current response of a nanopore sensor and the application of this class of sensor to a broad range of species with the theoretical models.

Dynamic Chemistry Interactions: Controlled Single-Entity Electrochemistry

Single-entity electrochemistry (SEE) provides powerful means to measure single cells, single particles, and even single molecules at the nanoscale by diverse well-defined interfaces. The nanoconfined electrode interface has significantly enhanced structural, electrical, and compositional characteristics that have great effects on the assay limitation and selectivity of single-entity measurement. In this Perspective, after introducing the dynamic chemistry interactions of the target and electrode interface, we present a fundamental understanding of how these dynamic interactions control the features of the electrode interface and thus the stochastic and discrete electrochemical responses of single entities under nanoconfinement. Both stochastic single-entity collision electrochemistry and nanopore electrochemistry as examples in this Perspective explore how these interactions alter the transient charge transfer and mass transport. Finally, we discuss the further challenges and opportunities in SEE, from the design of sensing interfaces to hybrid spectro-electrochemical methods, theoretical models, and advanced data processing.

The application of single molecule nanopore sensing for quantitative analysis

Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.

Effects of off-axis translocation through nanopores on the determination of shape and volume estimates for individual particles

Resistive pulses generated by nanoparticles that translocate through a nanopore contain multi-parametric information about the physical properties of those particles. For example, non-spherical particles sample several different orientations during translocation, producing fluctuations in blockade current that relate to their shape. Due to the heterogenous distribution of electric field from the center to the wall of a nanopore while a particle travels through the pore, its radial position influences the blockade current, thereby affecting the quantification of parameters related to the particle's characteristics. Here, we investigate the influence of these off-axis effects on parameters estimated by performing finite element simulations of dielectric particles transiting a cylindrical nanopore. We varied the size, ellipsoidal shape, and radial position of individual particles, as well as the size of the nanopore. As expected, nanoparticles translocating near the nanopore wall produce increase current blockades, resulting in overestimates of particle volume. We demonstrated that off-axis effects also influence estimates of shape determined from resistive pulse analyses, sometimes producing a multiple-fold deviation in ellipsoidal length-to-diameter ratio between estimates and reference values. By using a nanopore with the minimum possible diameter that still allows the particle to rotate while translocating, off-axis effects on the determination of both volume and shape can be minimized. In addition, tethering the nanoparticles to a fluid coating on the nanopore wall makes it possible to determine an accurate particle shape with an overestimated volume. This work provides a framework to select optimal ratios of nanopore to nanoparticle size for experiments targeting free translocations.

Spiers Memorial Lecture. Next generation nanoelectrochemistry: the fundamental advances needed for applications

Nanoelectrochemistry, where electrochemical processes are controlled and investigated with nanoscale resolution, is gaining more and more attention because of the many potential applications in energy and sensing and the fact that there is much to learn about fundamental electrochemical processes when we explore them at the nanoscale. The development of instrumental methods that can explore the heterogeneity of electrochemistry occurring across an electrode surface, monitoring single molecules or many single nanoparticles on a surface simultaneously, have been pivotal in giving us new insights into nanoscale electrochemistry. Equally important has been the ability to synthesise or fabricate nanoscale entities with a high degree of control that allows us to develop nanoscale devices. Central to the latter has been the incredible advances in nanomaterial synthesis where electrode materials with atomic control over electrochemically active sites can be achieved. After introducing nanoelectrochemistry, this paper focuses on recent developments in two major application areas of nanoelectrochemistry; electrocatalysis and using single entities in sensing. Discussion of the developments in these two application fields highlights some of the advances in the fundamental understanding of nanoelectrochemical systems really driving these applications forward. Looking into our nanocrystal ball, this paper then highlights: the need to understand the impact of nanoconfinement on electrochemical processes, the need to measure many single entities, the need to develop more sophisticated ways of treating the potentially large data sets from measuring such many single entities, the need for more new methods for characterising nanoelectrochemical systems as they operate and the need for material synthesis to become more reproducible as well as possess more nanoscale control.

Nanopore Current Enhancements Lack Protein Charge Dependence and Elucidate Maximum Unfolding at Protein's Isoelectric Point

Protein sequencing, as well as protein fingerprinting, has gained tremendous attention in the electrical sensing realm of solid-state nanopores and is challenging due to fast translocations and the use of high molar electrolytes. Despite providing an appreciable signal-to-noise ratio, high electrolyte concentrations can have adverse effects on the native protein structure. Herein, we present a thorough investigation of low electrolyte sensing conditions across a broad pH and voltage range generating conductive pulses (CPs) irrespective of protein net charge. We used Cas9 as the model protein and demonstrated that unfolding is noncooperative, represented by the gradual elongation or stretching of the protein, and sensitive to both the applied voltage and pH (i.e., charge state). The magnitude of unfolding and the isoelectric point (pI) of Cas9 was found to be correlated and a critical factor in our experiments. Electroosmotic flow (EOF) was always aligned with the transit direction, whereas electrophoretic force (EPF) was either reinforcing (pH < pI) or opposing (pH > pI) the protein's movement, which led to slower translocations at higher pH values. Further exploration of higher pH values led to slowing down of protein with > 30% of the population being slower than 0.5 ms. Our results would be critical for protein sensing at very low electrolytes and to retard their translocation speed without resorting to high-bandwidth equipment.

Optical Nanopore Sensors for Quantitative Analysis

Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.

Crystal-reconstructed BiVO4 semiconductor photoelectrochemical sensor for ultra-sensitive tumor biomarker detection

In this study, we developed a crystal-reconstructed-BiVO₄ aptamer photoelectrochemical (PEC) biosensor by a high-energy laser treatment technique. This biosensor achieves a limit of detection (LOD) (0.82 ag mL^-1), linear detection range (1 ag mL^-1 to 2 ng mL^-1), and resolution ratio (∼18 molecules per mL) for prostate-specific antigen (PSA) tumor biomarker detection. Furthermore, reconstructed surface microstructure and oxygen vacancy doping energy formation after crystal reconstruction induce the stereo-hindrance effect and photogenerated hole energy is reduced during PSA target detection. In this case, a photocurrent inhibition phenomenon for PSA detection is noticed. Based on this photocurrent inversion phenomenon, some dysoxidizable nucleonic acid tumor (miRNA-21) and virus biomarkers (RdRp-COVID) can be detected with a LOD level of ∼10^-16 M by linking the corresponding base paring probe on the surface of the crystal-reconstructed photoanode. In addition to high sensitivity, this PEC biosensor presents high detection specificity, stability, and accuracy in clinical verification. Thus, this crystal-reconstructed PEC biosensor shows application potential in the fields of multi-tumor or viral biomarker detection.

Recent advances in nanomaterials for prostate cancer detection and diagnosis

Despite the significant progress in the discovery of biomarkers and the exploitation of technologies for prostate cancer (PCa) detection and diagnosis, the initial screening of these PCa-related biomarkers using current...

Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing

Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.

Responsive Sensors of Upconversion Nanoparticles

Upconversion nanoparticles are a class of luminescent materials that convert longer-wavelength near-infrared photons into visible and ultraviolet emissions. They can respond to various external stimuli, which underpins many opportunities for developing the next generation of sensing technologies. In this perspective, the unique stimuli-responsive properties of upconverting nanoparticles are introduced, and their recent implementations in sensing are summarized. Promising material development strategies for enhancing the key sensing merits, including intrinsic sensitivity, biocompatibility and modality, are identified and discussed. The outlooks on future technological developments, novel sensing concepts, and applications of nanoscale upconversion sensors are provided.

Optical trapping assisted label-free and amplification-free detection of SARS-CoV-2 RNAs with an optofluidic nanopore sensor

Ultrasensitive, versatile sensors for molecular biomarkers are a critical component of disease diagnostics and personalized medicine as the COVID-19 pandemic has revealed in dramatic fashion. Integrated electrical nanopore sensors can fill this need via label-free, direct detection of individual biomolecules, but a fully functional device for clinical sample analysis has yet to be developed. Here, we report amplification-free detection of SARS-CoV-2 RNAs with single molecule sensitivity from clinical nasopharyngeal swab samples on an electro-optofluidic chip. The device relies on optically assisted delivery of target carrying microbeads to the nanopore for single RNA detection after release. A sensing rate enhancement of over 2,000x with favorable scaling towards lower concentrations is demonstrated. The combination of target specificity, chip-scale integration and rapid detection ensures the practicality of this approach for COVID-19 diagnosis over the entire clinically relevant concentration range from 10⁴-10⁹ copies/mL.

COVID-19 challenges: From SARS-CoV-2 infection to effective point-of-care diagnosis by electrochemical biosensing platforms

In January 2020, the World Health Organization (WHO) identified a new zoonotic virus, SARS-CoV-2, responsible for causing the COVID-19 (coronavirus disease 2019). Since then, there has been a collaborative trend between the scientific community and industry. Multidisciplinary research networks try to understand the whole SARS-CoV-2 pathophysiology and its relationship with the different grades of severity presented by COVID-19. The scientific community has gathered all the data in the quickly developed vaccines that offer a protective effect for all variants of the virus and promote new diagnostic alternatives able to have a high standard of efficiency, added to shorter response analysis time and portability. The industry enters in the context of accelerating the path taken by science until obtaining the final product. In this review, we show the principal diagnostic methods developed during the COVID-19 pandemic. However, when we observe the diagnostic tools section of an efficient infection outbreak containment report and the features required for such tools, we could observe a highlight of electrochemical biosensing platforms. Such devices present a high standard of analytical performance, are low-cost tools, easy to handle and interpret, and can be used in the most remote and low-resource regions. Therefore, probably, they are the ideal point-of-care diagnostic tools for pandemic scenarios.

Key Parameters That Determine the Magnitude of the Decrease in Current in Nanopore Blockade Sensors

Nanopore blockade sensors were developed to address the challenges of sensitivity and selectivity for conventional nanopore sensors. To date, the parameters affecting the current of the sensor have not been elucidated. Herein, the impacts of nanopore size and charge and the shape, size, surface charge, and aggregation state of magnetic nanoparticles were assessed. The sensor was tolerant to all parameters contrary to predictions from electronic or geometric arguments on the current change. Theoretical models showed the greater importance of the polymers around nanoparticles and the access resistance of nanopores to the current, when compared with translocation-based nanopore sensors. The signal magnitude was dominated by the change in access resistance of ∼4.25 MΩ for all parameters, resulting in a robust system. The findings provide understandings of changes in current when nanopores are blocked, like in RNA trapping or nanopore blockade sensors, and are important for designing sensors based on nanopore blockades.

Nanoconfinement Effect for Signal Amplification in Electrochemical Analysis and Sensing

Owing to the urgent need for electrochemical analysis and sensing of trace target molecules in various fields such as medical diagnosis, agriculture and food safety, and environmental monitoring, signal amplification is key to promoting analysis and sensing performance. The nanoconfinement effect, derived from nanoconfined spaces and interfaces with sizes approaching those of target molecules, has witnessed rapid development for ultra-sensitive analyzing and sensing. In this review, the two main types of nanoconfinement systems - confined nanochannels and planes - are assessed and recent progress is highlighted. The merits of each nanoconfinement system, the nanoconfinement effect mechanisms, and applications for electrochemical analysis and sensing are summarized and discussed. This review aims to help deepen the understanding of nanoconfinement devices and their effects in order to develop new analysis and sensing applications for researchers in various fields.

Digital immunoassay for biomarker concentration quantification using solid-state nanopores

Single-molecule counting is the most accurate and precise method for determining the concentration of a biomarker in solution and is leading to the emergence of digital diagnostic platforms enabling precision medicine. In principle, solid-state nanopores—fully electronic sensors with single-molecule sensitivity—are well suited to the task. Here we present a digital immunoassay scheme capable of reliably quantifying the concentration of a target protein in complex biofluids that overcomes specificity, sensitivity, and consistency challenges associated with the use of solid-state nanopores for protein sensing. This is achieved by employing easily-identifiable DNA nanostructures as proxies for the presence (“1”) or absence (“0”) of the target protein captured via a magnetic bead-based sandwich immunoassay. As a proof-of-concept, we demonstrate quantification of the concentration of thyroid-stimulating hormone from human serum samples down to the high femtomolar range. Further optimization to the method will push sensitivity and dynamic range, allowing for development of precision diagnostic tools compatible with point-of-care format.

The concentration of a biomarker in solution can be determined by counting single molecules. Here the authors report a digital immunoassay scheme with solid-state nanopore readout to quantify a target protein and use this to measure thyroid-stimulating hormone from human serum.

Understanding Electrical Conduction and Nanopore Formation During Controlled Breakdown

Controlled breakdown has recently emerged as a highly appealing technique to fabricate solid-state nanopores for a wide range of biosensing applications. This technique relies on applying an electric field of approximately 0.4-1 V nm-1 across the membrane to induce a current, and eventually, breakdown of the dielectric. Although previous studies have performed controlled breakdown under a range of different conditions, the mechanism of conduction and breakdown has not been fully explored. Here, electrical conduction and nanopore formation in SiNx membranes during controlled breakdown is studied. It is demonstrated that for Si-rich SiNx , oxidation reactions that occur at the membrane-electrolyte interface limit conduction across the dielectric. However, for stoichiometric Si3 N4 the effect of oxidation reactions becomes relatively small and conduction is predominately limited by charge transport across the dielectric. Several important implications resulting from understanding this process are provided which will aid in further developing controlled breakdown in the coming years, particularly for extending this technique to integrate nanopores with on-chip nanostructures.

Metal-organic framework-based micropipette is a metal ion responsive nanochannel after adsorbing H2S

Glass micropipettes are easy to fabricate, have excellent flexibility and stable properties. HKUST-1 and MIL-68(In) are in situ grown in the tip of a micropipette to construct porous nanochannels. After absorbing H2S, the MIL-68(In)-based nanochannel shows effective metal ion responsiveness for Hg2+-detection.

Recent advances in integrated solid-state nanopore sensors

The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.

Nanopore Technology for the Application of Protein Detection

Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.

Dynamic Behavior of Charged Particles at the Nanopipette Orifice

Understanding the dynamic behavior of charged particles driven by flow and electric field in nanochannels/pores is highly important for both fundamental study and practical applications. While a great breakthrough has been made in understanding the translocation dynamics of charged particles within the nanochannels/pores, studies on the dynamics of particles at the orifice of nanochannels/pores are scarcely reported. Here, we study particle motion at a smaller-sized orifice of a nanopipette by combining experimentally observed current transients with simulated force conditions. The theoretical force analysis reveals that dielectrophoretic force plays an equally important role as electrophoretic force and electroosmotic force, although it has often been neglected in understanding the particle translocation dynamics within the nanopipette. Under the combined action of these forces, it thus becomes difficult for particles to physically collide with the orifice of the nanopipette, resulting in a relatively low decrease in the current transients, which coincides with experimental results. We then regulate the dynamic behavior by altering experimental conditions (i.e., bias potential, nanopipette surface charge, and particle size), and the results further validate the presence and influence of forces being considered. This study improves the understanding of the relationship between particle properties and observed current transients, providing more possibilities for accurate single-particle analysis and single-entity regulation.

Nanodiagnostics: A review of the medical capabilities of nanopores

Modern diagnostics strive to be accurate, fast, and inexpensive in addition to properly identifying the presence of a disease, infection, or illness. Early diagnosis is key; catching a disease in its early stages can be the difference between fatality and treatment. The challenge with many diseases is that detectability of the disease scales with disease progression. Since single molecule sensors, e.g., nanopores, can sense biomolecules at low concentrations, they have the potential to become clinically relevant in many of today's medical settings. With nanopore-based sensing, lower volumes and concentrations are required for detection, enabling it to be clinically beneficial. Other advantages to using nanopores include that they are tunable to an enormous variety of molecules and boast low costs, and fabrication is scalable for manufacturing. We discuss previous reports and the potential for incorporating nanopores into the medical field for early diagnostics, therapeutic monitoring, and identifying relapse/recurrence.

Inverted Ion Current Rectification-Based Chemical Delivery Probes for Stimulation of Neurons

Ion current rectification (ICR), diodelike behavior in surface-charged nanopores, shows promise in the design of delivery probes for manipulation of neural networks as it can solve diffusive leakages that might be critical in clinical and research applications. However, it has not been achieved because ICR has restrictions in nanosized dimension and low electrolyte concentration, and rectification direction is inappropriate for delivery. Herein, we present a polyelectrolyte gel-filled (PGF) micropipette harnessing inverted ICR as a delivery probe, which quantitatively transports glutamate to stimulate primary cultured neurons with high efficiency while minimizing leakages. Since the gel works as an ensemble of numerous surface-charged nanopores, the current is rectified in the micro-opening and physiological environment. By extending the charge-selective region using the gel, inverted ICR is generated, which drives outward deliveries of major charge carriers. This study will help in exploring new aspects of ICR and broaden its applications for advanced chemical delivery.

A sequentially bioconjugated optofluidic laser for wash-out-free and rapid biomolecular detection

Microstructures can improve both sensitivity and assay time in heterogeneous assays (such as ELISA) for biochemical analysis; however, it remains a challenge to perform the essential wash process in those microstructure-based heterogeneous assays. Here, we propose a sequential bioconjugation protocol to solve this problem and demonstrate a new type of fiber optofluidic laser for biosensing. Except for acting as an optical microresonator and a microstructured substrate, the miniaturized hollow optical fiber (HOF) is used as a microfluidic channel for storing and transferring reagents thanks to its capability in length extension. Through the capillary action, different reagents were sequentially withdrawn into the fiber for specific binding and washing purposes. By using the sequentially bioconjugated FOFL, avidin molecules are detected based on competitive binding with a limit of detection of 9.5 pM, ranging from 10 pM to 100 nM. It is demonstrated that a short incubation time of 10 min is good enough to allow the biomolecules to conjugate on the inner surface of the HOF. Owing to its miniaturized size, only 589 nL of liquid is required for incubation, which reduces the sample consumption and cost for each test. This work provides a tool to exploit the potential of microstructured optical fibers in high-performance biosensing.

Synchronized resistive-pulse analysis with flow visualization for single micro- and nanoscale objects driven by optical vortex in double orifice

Resistive-pulse analysis is a powerful tool for identifying micro- and nanoscale objects. For low-concentration specimens, the pulse responses are rare, and it is difficult to obtain a sufficient number of electrical waveforms to clearly characterize the targets and reduce noise. In this study, we conducted a periodic resistive-pulse analysis using an optical vortex and a double orifice, which repetitively senses a single micro- or nanoscale target particle with a diameter ranging from 700 nm to 2 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mu$$\end{document}μm. The periodic motion results in the accumulation of a sufficient number of waveforms within a short period. Acquired pulses show periodic ionic-current drops associated with the translocation events through each orifice. Furthermore, a transparent fluidic device allows us to synchronously average the waveforms by the microscopic observation of the translocation events and improve the signal-to-noise ratio. By this method, we succeed in distinguishing single particle diameters. Additionally, the results of measured signals and the simultaneous high-speed observations are used to quantitatively and systematically discuss the effect of the complex fluid flow in the orifices on the amplitude of the resistive pulse. The synchronized resistive-pulse analysis by the optical vortex with the flow visualization improves the pulse-acquisition rate for a single specific particle and accuracy of the analysis, refining the micro- and nanoscale object identification.

In situ solid-state nanopore fabrication

Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.

Quantitative Measurements of Protein Volume and Concentration using Hydrogel-Backed Nanopores

Accurate identification and quantification of proteins in solution using nanopores is technically challenging in part because of the large fraction of missed translocation events due to short event times and limitations of conventional current amplifiers. Previously, we have shown that a nanopore interfaced with a poly(ethylene glycol)-dimethacrylate hydrogel with an average mesh size of 3.1 nm significantly enhances the protein residence time within the pore, reducing the number of missed events. We used hydrogel-backed nanopores to sense unlabeled proteins as small as 5.5 kDa in size and 10 fM in concentration. We show that the frequency of protein translocation events linearly scales with bulk concentration over a wide range of concentrations and that unknown protein concentrations can be determined from an interpolation of the frequency-concentration curve with less than 10% error. Further, we show an iterative method to determine a protein volume accurately from measurement data for proteins with a diameter comparable to a nanopore diameter. Our measurements and analysis also suggest several competing mechanisms for the detection enhancement enabled by the presence of the hydrogel.

Ultrasensitive detection of programmed death-ligand 1 (PD-L1) in whole blood using dispersible electrodes

The direct quantification of programmed death-ligand 1 (PD-L1) as a biomarker for cancer diagnosis, prognosis and treatment efficacy is an unmet clinical need. Herein, we demonstrate the first report of rapid, ultrasensitive and selective electrochemical detection of PD-L1 directly in undiluted whole blood using modified gold-coated magnetic nanoparticles as "dispersible electrodes" with an ultralow detection limit of 15 attomolar and a response time of only 15 minutes.

High optical enhancement in Au/Ag alloys and porous Au using Surface-Enhanced Raman spectroscopy technique

We report high optical enhancement in Ag/Au alloys and porous gold nanostructures using Surface Enhanced Raman Spectroscopy (SERS) technique. Scanning electron microscopy investigation shows the formation of Ag/Au alloys particles during irradiation of Ag-Au bilayer deposited on FTO (SnO2:F) substrate by laser fluency equal to 0.5 J/cm2 or 1.0 J/cm2 with 12 ns laser pulse duration. The dealloying process of these Au-Ag alloy particles leads to the formation of Au nanoporous particles. The obtained nanostructures were studied with SERS and revealed a promising enhancement factor in porous Au nanostructure and tunability of localized surface plasmon resonance. The highly dense strong hot spots and large specific area in porous structure of gold nanostructures is the origin of the highly enhancement factor observed experimentally and theoretically. A very good agreement between simulation and experimental results was found confirming the potential of Au/Ag alloys and particularly porous gold nanostructure in SERS application.

Magnetic nanoparticles in developing electrochemical sensors for pharmaceutical and biomedical applications

A revolutionary impact on the pharmaceutical and biomedical applications has been arisen in the few years to come as a result of the advances made in magnetic nanoparticles (MNPs) research. The use of MNPs opens wide opportunities in diagnostics, drug and gene delivery, in vivo imaging, magnetic separation, and hyperthermia therapy, etc. Besides, their possible integration in sensors makes them an ideal essential element of innovative pharmaceutical and biomedical applications. Nowadays, MNPs-based electrochemical sensors have attracted great attention to pharmaceutical and biomedical applications owing to their high sensitivity, stability. Selectivity towards the target as well as their simplicity of manufacture. Therefore, this review focus on recent advances with cutting-edge approaches dealing with the synthesis, design, and advantageous analytical performance of MNPs in the electrochemical sensors utilized for pharmaceutical and biomedical applications between 2015 and 2020. The challenges existing in this research area and some potential strategies/future perspectives for the rational design of electrochemical sensors are also outlined.

Electrokinetic behavior of bullet-shaped nanopores modified by functional groups: Influence of finite thickness of modified layer

We examined theoretically the electrokinetic behavior of a bullet-shaped nanopore modified by a functional layer, focusing on the influence of its thickness. The nanopore contains both fixed surface charge coming from the original bare surface, and space fixed charge from the modified layer. The results of numerical simulation reveal that the presence of this layer is crucial to the electrokinetic behavior of the nanopore. In particular, its softness is capable of influencing ionic profiles through electroosmotic flow (EOF). Unlike a conical nanopore where its surface normal vector is constant, that of the present bullet-shaped nanopore varies along the pore axis, thereby affecting the degree of EOF, which in turn, can make the ionic profile inside the modified layer more uniform. This is crucial to the applications of the nanopore, for example, in mimicking biological membranes and sensing metal ions.

Effect of single nanoparticle-nanopore interaction strength on ionic current modulation

Solid-state nanopores are rapidly emerging as promising platforms for developing various single molecule sensing applications. The modulation of ionic current through the pore due to translocation of the target molecule has been the dominant measurement modality in nanopore sensors. Here, we focus on the dwell time, which is the duration taken by the target molecule or particle to traverse the pore and study its dependence on the strength of interaction of the target with the pore using single gold nanoparticles (NPs) as targets interacting with a silicon nitride (SiN) nanopore. The strength of interaction, which in our case is electrostatic in nature, can be controlled by coating the nanoparticles with charged polymers. We report on an operating regime of this nanopore sensor, characterized by attractive interactions between the nanoparticle and the pore, where the dwell time is exponentially sensitive to the target-pore interaction. We used negatively and positively charged gold nanoparticles to control the strength of their interaction with the Silicon Nitride pore which is negatively charged. Our experiments revealed how this modulation of the electrostatic force greatly affects the dwell time. Positively charged NPs with strong attractive interactions with the pore resulted in increase of dwell times by 2-3 orders of magnitude, from 0.4 ms to 75.3 ms. This extreme sensitivity of the dwell time on the strength of interaction between a target and nanopore can be exploited in emerging nanopore sensor applications.

Dynamics of DNA Clogging in Hafnium Oxide Nanopores

Interfacing solid-state nanopores with biological systems has been exploited as a versatile analytical platform for analysis of individual biomolecules. Although clogging of solid-state nanopores due to nonspecific interactions between analytes and pore walls poses a persistent challenge in attaining the anticipated sensing efficacy, insufficient studies focus on elucidating the clogging dynamics. Herein, we investigate the DNA clogging behavior by passing double-stranded (ds) DNA molecules of different lengths through hafnium oxide(HfO₂)-coated silicon (Si) nanopore arrays, at different bias voltages and electrolyte pH values. Employing stable and photoluminescent-free HfO₂/Si nanopore arrays permits a parallelized visualization of DNA clogging with confocal fluorescence microscopy. We find that the probability of pore clogging increases with both DNA length and bias voltage. Two types of clogging are discerned: persistent and temporary. In the time-resolved analysis, temporary clogging events exhibit a shorter lifetime at higher bias voltage. Furthermore, we show that the surface charge density has a prominent effect on the clogging probability because of electrostatic attraction between the dsDNA and the HfO₂ pore walls. An analytical model based on examining the energy landscape along the DNA translocation trajectory is developed to qualitatively evaluate the DNA–pore interaction. Both experimental and theoretical results indicate that the occurrence of clogging is strongly dependent on the configuration of translocating DNA molecules and the electrostatic interaction between DNA and charged pore surface. These findings provide a detailed account of the DNA clogging phenomenon and are of practical interest for DNA sensing based on solid-state nanopores.

Nanoparticle enhanced optical biosensing technologies for Prostate Specific Antigen biomarker detection

Prostate Cancer (PCa) is one of the deadliest forms of Cancer among men. Early screening process for PCa is primarily conducted with the help of a FDA approved biomarker known as Prostate Specific Antigen (PSA). The PSA-based screening is challenged with the inability to differentiate between the cancerous PSA and Benign Prostatic Hyperplasia (BPH), resulting in high rates of false-positives. Optical techniques such as optical absorbance, scattering, surface plasmon resonance (SPR), and fluorescence have been extensively employed for Cancer diagnostic applications. One of the most important diagnostic applications involves utilization of nanoparticles (NPs) for highly specific, sensitive, rapid, multiplexed, and high performance Cancer detection and quantification. The incorporation of NPs with these optical biosensing techniques allow realization of low cost, point-of-care, highly sensitive, and specific early cancer detection technologies, especially for PCa. In this work, the current state-of-the-art, challenges, and efforts made by the researchers for realization of low cost, point-of-care (POC), highly sensitive, and specific NP enhanced optical biosensing technologies for PCa detection using PSA biomarker are discussed and analyzed.

Selectively detecting attomolar concentrations of proteins using gold lined nanopores in a nanopore blockade sensor

Disease diagnosis at earlier stages requires the development of ultrasensitive biosensors for detecting low-abundance biomarkers in complex biological fluids within a reasonable time frame. Here, we demonstrate the development of an ultrasensitive nanopore blockade biosensor that can rapidly diagnose a model protein biomarker, prostate-specific antigen (PSA) with high selectivity. The solid-state nanopores have gold located only along the length of the nanopore whilst the rest of the membrane is silicon nitride. The orthogonal use of materials allows nanopore arrays with a different surface chemistry inside the nanopore relative to the rest of the membrane to be fabricated. The importance of this differential surface chemistry is it can improve the detection limit of nanopore blockade sensors in quantitative analysis. Based on such functionalized nanopore devices, nanopore blockade sensors lower the limit of detection by an order of magnitude and enable ultrasensitive detection of PSA as low as 80 aM. The findings from this study open new opportunities for nanopore sensors in further developments including optical detection and ultralow detection limit biosensing at complex biological fluids.

Reduction chemistry-assisted nanopore determination method for immunoglobulin isotypes

Immunoglobulins can bind to an unlimited array of foreign antigens presented to the immune system. Among those isotypes, IgG and IgM play crucial roles in initial immune defense associated with innate immunity factors. Hence, the determination of IgG and IgM deficiencies or varying concentrations is widely used as a diagnostic indicator for immune deficiency disorders. Herein, we report a reduction chemistry-assisted nanopore method for IgG and IgM determination. TCEP (tris(2-carboxyethyl)phosphine) was used to cleave Ig proteins in fragments by means of disulfide bond reduction under different experimental conditions. This strategy enabled the observation of distinguishable current signals afforded by separated polypeptide fragments in an αHL nanopore. Together with molecular dynamics (MD) simulation results, highly effective electrostatic potentials and H-bonds, the dominant factors for these current signals, facilitated the capture of Ig fragments in an α-HL nanopore. More importantly, the signature signals were applicable for differentiating between IgG and IgM in blood serum without any problems of protein adsorption and clogging in the nanopore sensing. Furthermore, with comparative sensing sensitivity and selectivity, it is concluded that our method is a label-free single-molecule approach to measuring disease states that present as a result of the absence or over presence of immunoglobulin isotypes.

Analysis with biological nanopore: On-pore, off-pore strategies and application in biological fluids

Inspired from ion channels in biology, nanopores have been developed as promising analytical tools. In principle, nanopores provide crucial information from the observation and analysis of ionic current modulations caused by the interaction between target analytes and fluidic pores. In this respect, the biological, chemical and physical parameters of the nanopore regime need to be well-understood and regulated for intermolecular interaction. Because of well-defined molecular structures, biological nanopores consequently are of a focal point, allowing precise interaction analysis at single-molecule level. In this overview, two analytical strategies are summarized and discussed accordingly, upon the challenges arising in case-dependent analysis using biological nanopores. One kind of strategies relies on modification, functionalization and engineering on nanopore confined interface to improve molecular recognition sites (on-pore strategies); The other kind of highlighted strategies concerns to measurement of various chemistry/biochemistry based interactions triggered by employed molecular agents or probes (off-pore strategies). In particularly, a few recent paradigms using these strategies for practical application of accurate analysis of biomarkers in biological fluids are illustrated. To end, the challenging and future outlook of using analytical tools by means of biological nanopores are depicted.

Single particle detection of protein molecules using dark-field microscopy to avoid signals from nonspecific adsorption

A massively parallel single particle sensing method based on core-satellite formation of Au nanoparticles was introduced for the detection of interleukin 6 (IL-6). This method exploits the fact that the localized plasmon resonance (LSPR) of the plasmonic nanoparticles will change as a result of core-satellite formation, resulting in a change in the observed color. In this method, the hue (color) value of thousands of 67 nm Au nanoparticles immobilized on a glass coverslip surface is analyzed by a Matlab code before and after the addition of reporter nanoparticles containing IL-6 as target protein. The average hue shift as the result of core-satellite formation is used as the basis to detect small amount of proteins. This method enjoys two major advantages. First it is able to analyze the hue values of thousands of nanoparticles in parallel in less than a minute. Secondly the method is able to circumvent the effect of non-specific adsorption, a major issue in the field of biosensing.

Critical Review: digital resolution biomolecular sensing for diagnostics and life science research

One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.

Two Orders of Magnitude Boost in the Detection Limit of Droplet-Based Micro-Magnetofluidics with Planar Hall Effect Sensors

Magnetofluidics is a dynamic research field, which requires novel sensor solutions to boost the detection limit of tiny quantities of magnetized objects. Here, we present a sensing strategy relying on planar Hall effect sensors in droplet-based micro-magnetofluidics for the detection of a multiphase liquid flow, i.e., superparamagnetic aqueous droplets in an oil carrier phase. The high resolution of the sensor allows the detection of nanoliter-sized superparamagnetic droplets with a concentration of 0.58 mg/cm³, even when they are biased in a geomagnetic field only. The limit of detection can be boosted another order of magnitude, reaching 0.04 mg/cm³ (1.4 million particles in a single 100 nL droplet) when a magnetic field of 5 mT is applied to bias the droplets. With this performance, our sensing platform outperforms the state-of-the-art solutions in droplet-based micro-magnetofluidics by a factor of 100. This allows us to detect ferrofluid droplets in clinically and biologically relevant concentrations and even below without the need of externally applied magnetic fields. These results open the route for new strategies of the utilization of ferrofluids in microfluidic geometries in, e.g., bio(-chemical) or medical applications.