Detection of local protein structures along DNA using solid-state nanopores

Immunological assay using a solid-state pore with a low limit of detection

Emerging infectious diseases, cancer, and other diseases are quickly tested mainly via immune reactions based on specific molecular recognition between antigens and antibodies. By changing the diameter of solid-state pores, biomolecules of various sizes can be rapidly detected at the single-molecule level. The combination of immunoreactions and solid-state pores paves the way for an efficient testing method with high specificity and sensitivity. The challenge in developing this method is achieving quantitative analysis using solid-state pores. Here, we demonstrate a method with a low limit of detection for testing tumor markers using a combination of immunoreactions and solid-state pore technology. Quantitative analysis of the mixing ratio of two and three beads with different diameters was achieved with an error rate of up to 4.7%. The hybrid solid-state pore and immunoreaction methods with prostate-specific antigen (PSA) and anti-PSA antibody-modified beads achieved a detection limit of 24.9 fM PSA in 30 min. The hybrid solid-state pore and immunoreaction enabled the rapid development of easy-to-use tests with lower limit of detection and greater throughput than commercially available immunoassay for point-of-care testing.

Single-Digit Nanobubble Sensing via Nanopore Technology

Nanobubbles play an important role in diverse fields, including engineering, medicine, and agriculture. Understanding the characteristics of individual nanobubbles is essential for comprehending fluid dynamics behaviors and advancing nanoscale science across various fields. Here, we report a strategy based on nanopore sensors for characterizing single-digit nanobubbles. We investigated the sizes and diffusion coefficients of nanobubbles at different voltages. Additionally, the finite element simulation and molecular dynamics simulation were introduced to account for counterion concentration variation around nanobubbles in the nanopore. In particular, the differences in stability and surface charge density of nanobubbles under various solution environments have been studied by the ion-stabilized model and the DLVO theory. Additionally, a straightforward method to mitigate nanobubble generation in the bulk for reducing current noise in nanopore sensing was suggested. The results hold significant implications for enhancing the understanding of individual nanobubble characterizations, especially in the nanofluid field.

Pulley Effect in the Capture of DNA Translocation through Solid-State Nanopores

Nanopores are powerful single-molecule sensors for analyzing biomolecules such as DNA and proteins. Understanding the dynamics of DNA capture and translocation through nanopores is essential for optimizing their performance. In this study, we examine the effects of applied voltage and pore diameter on current blockage, translocation time, collision, and capture location by translocating λ-DNA through 5.7 and 16 nm solid-state nanopores. Ionic current changes are used to infer DNA conformations during translocation. We find that translocation time increases with pore diameter, which can be attributed to the decrease of the stall force. Linear and exponential decreases of collision frequency with voltage are observed in the 16 and 5.7 nm pores, respectively, indicating a free energy barrier in the small pore. Moreover, the results reveal a voltage-dependent bias in the capture location toward the DNA ends, which is explained by a "pulley effect" deforming the DNA as it approaches the pore. This study provides insights into the physics governing DNA capture and translocation, which can be useful for promoting single-file translocation to enhance nanopore sensing.

Single-Molecule Analysis of SARS-CoV-2 Double-Stranded Polynucleotides Using Solid-State Nanopore with AI-Assisted Detection and Classification: Implications for Understanding Disease Severity

This study utilized solid-state nanopores, combined with artificial intelligence (AI), to analyze the double-stranded polynucleotides encoding angiotensin-converting enzyme 2, receptor-binding domain, and N protein, important parts of SARS-CoV-2 infection. By examining ionic current signals during DNA translocation, we revealed the dynamic interactions and structural characteristics of these nucleotide sequences and also quantified their abundance. Nanopores of sizes 3 and 10 nm were efficiently fabricated and characterized, ensuring an optimal experimental approach. Our results showed a clear relationship between DNA capture rates and concentration, proving our method's effectiveness. Notably, longer DNA sequences had higher capture rates, suggesting their importance for potential disease marker analysis. The 3 nm nanopore demonstrated superior performance in our DNA analysis. Using dwell time measurements and excluded currents, we were able to distinguish the longer DNA fragments, paving the way for a DNA length-based analysis. Overall, our research underscores the potential of nanopore technology, enhanced with AI, in analyzing COVID-19-related DNA and its implications for understanding disease severity. This provides insight into innovative diagnostic and treatment strategies.

Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability

The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability.

DNA Barcodes Using a Dual Nanopore Device

We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.

Multiplexed Digital Characterization of Misfolded Protein Oligomers via Solid-State Nanopores

Misfolded protein oligomers are of central importance in both the diagnosis and treatment of Alzheimer's and Parkinson's diseases. However, accurate high-throughput methods to detect and quantify oligomer populations are still needed. We present here a single-molecule approach for the detection and quantification of oligomeric species. The approach is based on the use of solid-state nanopores and multiplexed DNA barcoding to identify and characterize oligomers from multiple samples. We study α-synuclein oligomers in the presence of several small-molecule inhibitors of α-synuclein aggregation as an illustration of the potential applicability of this method to the development of diagnostic and therapeutic methods for Parkinson's disease.

Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing

Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.

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.

Customized low-cost high-throughput amplifier for electro-fluidic detection of cell volume changes in point-of-care applications

Physical parameters of the pathogenic cells, like its volume, shape, and stiffness, are important biomarkers for diseases, chemical changes within the cell, and overall cell health. The response of pathogenic bacteria and viruses to different chemical disinfectants is studied widely. Some of the routinely employed techniques to measure these changes require elaborate and expensive equipment which limits any study to a non-mobile research lab facility. Recently, we showed a micropore-based electro-fluidic technique to have great promise in measuring subtle changes in cell volumes at high throughput and resolution. This method, however, requires commercial amplifiers, which makes this technique expensive and incompatible for in-field use. In this paper, we develop a home-built amplifier to make this technique in-field compatible and apply it to measure changes in bacterial volumes upon exposure to alcohol. First, we introduce our low-cost and portable transimpedance amplifier and characterize the maximum range, absolute error percentage, and RMS noise of the amplifier in the measured current signal, along with the amplifier's bandwidth, and compared these characteristics with the commercial amplifiers. Using our home-built amplifier, we demonstrate a high throughput detection of ~1300 cells/second and resolve cell diameter changes down to 1 μm. Finally, we demonstrate measurement of cell volume changes in E. coli bacteria when exposed to ethanol (5% v/v), which is otherwise difficult to measure via imaging techniques. Our low-cost amplifier (~100-fold lower than commercial alternatives) is battery-run, completely portable for point-of-care applications, and the electro-fluidic devices are currently being tested for in-field applications.

Protein-enabled detection of ibuprofen and sulfamethoxazole using solid-state nanopores

Enabled by proteins, we present an all-electrical method for rapid detection of small pharmaceuticals (ibuprofen and sulfamethoxazole [SMZ]) in aqueous media using silicon nitride pores. Specifically, we use carrier proteins, bovine serum albumin (BSA), and take advantage of their interactions with two small drug molecules to form BSA-drug complexes which can be detected by nm-diameter pores, thereby confirming the presence of small pharmaceuticals. We demonstrate detection of ibuprofen and SMZ at concentrations down to 100 nM (∼21 μg/L) and 48.5 nM (12 μg/L), respectively. We observe changes in electrical signal characteristics (reflected in event durations, rates, current magnitudes, and estimated particle diameters) of BSA-drug complexes compared to BSA-only, and differences between these two small pharmaceuticals, possibly paving a path toward developing selective sensors by identifying "electrical fingerprints" of these molecules in the future. These distinct electrical signals are likely a combined result of diffusion, electrophoretic and electroosmotic effects, interactions between the pore and particles, which depend on pore diameters, pH, and the resulting surface charges. The use of single-molecule-counting nanopores allows sensing of small pharmaceuticals, studies of protein conformational changes, and may aid in efforts to evaluate the impact of small drug molecules on aquatic and human life.

Solid-state nanopore analysis on the conformation change of DNA polymerase I induced by a DNA substrate

We studied the conformational changes between a Klenow fragment and its monomer complex with a DNA substrate using a SiN nanopore and found that the monomer complex has a tighter structure and transports slower.

Solid-state and polymer nanopores for protein sensing: A review

In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.

Tailoring Thermoplastic In-Plane Nanopore Size by Thermal Fusion Bonding for the Analysis of Single Molecules

We report a simple method for tailoring the size of in-plane nanopores fabricated in thermoplastics for single-molecule sensing. The in-plane pores were fabricated via nanoimprint lithography (NIL) from resin stamps, which were generated from Si masters. We could reduce the size of the in-plane nanopores from 30 to ∼10 nm during the thermal fusion bonding (TFB) step, which places a cover plate over the imprinted polymer substrate under a controlled pressure and temperature to form the relevant nanofluidic devices. Increased pressures during TFB caused the cross-sectional area of the in-plane pore to be reduced. The in-plane nanopores prepared with different TFB pressures were utilized to detect single-λ-DNA molecules via resistive pulse sensing, which showed a higher current amplitude in devices bonded at higher pressures. Using this method, we also show the ability to tune the pore size to detect single-stranded (ss) RNA molecules and single ribonucleotide adenosine monophosphate (rAMP). However, due to the small size of the pores required for detection of the ssRNA and rAMPs, the surface charge arising from carboxylate groups generated during O2 plasma oxidation of the surfaces of the nanopores to make them wettable had to be reduced to allow translocation of coions. This was accomplished using EDC/NHS coupling chemistry and ethanolamine. This simple modification chemistry increased the event frequency from ∼1 s-1 to >136 s-1 for an ssRNA concentration of 100 nM.

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

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

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.

Detection and Characterization of Single Cisplatin Adducts on DNA by Nanopore Sequencing

Detection and characterization of an individual cisplatin adduct on a single DNA molecule is a demanding task. We explore the characteristic features of cisplatin adducts in the nanopore sequencing signal in aspects of dwell time, genome anchored current trace, and basecalling accuracy. The offset between the motor protein and the nanopore constriction region is revealed by dwell time analysis to be about 14 bases in the nanopore device as we examined. Characteristic distortions due to cisplatin adducts are illustrated in genome anchored current trace analysis, constituting the fingerprint for identification of cisplatin adduct. The sharp increase in odds ratio at the location of adducting sites provides additional feature in the detection of the adduct. By these combined methods, single cisplatin adducts can be detected with high fidelity on a single read of the DNA sequence. The study demonstrates an effective method in the detection and characterization of single cisplatin adducts on DNA at the single-molecule level and with single nucleotide spatial resolution.

Structure-flexible DNA origami translocation through a solid-state nanopore

Nanopore detection is a label-free detection method designed to analyze single molecules by comparing specific translocation events with high signal-to-noise ratios. However, it is still challenging to understand the influences of structural flexibility of 100 nm DNA origami on nanopore translocations. Here, we used solid-state nanopores to characterize the translocation of “nunchaku” origami structures, the flexibility of which can be regulated by introducing specific DNA strands and streptavidin protein. The structural changes can result in significant variations in the translocation signals and distributions. It is anticipated that such a method of the flexible DNA origami translocation through a solid-state nanopore will find further applications in molecular detection as well as biosensing.

Using a solid-state nanopore to characterize the translocation of “nunchaku” origami with tunable-structures.

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.

Intrinsic fractional noise in nanopores: The effect of reservoirs

Fluctuations affect nanoporous transport in complex and intricate ways, making optimization of the signal-to-noise ratio in artificial designs challenging. Here, we focus on the simplest nanopore system, where non-interacting particles diffuse through a pore separating reservoirs. We find that the concentration difference between both sides (akin to the osmotic pressure drop) exhibits fractional noise in time t with mean square average that grows as t^1/2. This originates from the diffusive exchange of particles from one region to another. We fully rationalize this effect, with particle simulations and analytic solutions. We further infer the parameters (pore radius and pore thickness) that control this exotic behavior. As a consequence, we show that the number of particles within the pore also exhibits fractional noise. Such fractional noise is responsible for noise spectral density scaling as 1/f^3/2 with frequency f, and we quantify its amplitude. Our theoretical approach is applicable to more complex nanoporous systems (for example, with adsorption within the pore) and drastically simplifies both particle simulations and analytic calculus.

Translocation of a looped polymer threading through a nanopore

Recent experiments reported that the complicated translocation dynamics of a looped DNA chain through a nanopore can be detected by ionic current blockade profiles. Inspired by the experimental results, we systematically study the translocation dynamics of a looped polymer, formed by three building blocks of a loop in the middle and two tails of the same length connected with the loop, by using Langevin dynamics simulations. Based on two entering modes (tail-leading and loop-leading) and three translocation orders (loop-tail-tail, tail-loop-tail, and tail-tail-loop), the translocation of the looped polymer is classified into six translocation pathways, corresponding to different current blockade profiles. The probabilities of the six translocation pathways are dependent on the loop length, polymer length, and pore radius. Moreover, the translocation times of the entire polymer and the loop are investigated. We find that the two translocation times show different dependencies on the translocation pathways and on the lengths of the loop and the entire polymer.

Quantification of low affinity binding interactions between natural killer cell inhibitory receptors and targeting ligands with a self-induced back-action actuated nanopore electrophoresis (SANE) sensor

A plasmonic nanopore sensor enabling detection of bimodal optical and electrical molecular signatures was fabricated and tested for its ability to characterize low affinity ligand-receptor interactions. This plasmonic nanosensor uses self-induced back-action (SIBA) for optical trapping to enable SIBA-actuated nanopore electrophoresis (SANE) through a nanopore located immediately below the optical trap volume. A natural killer (NK) cell inhibitory receptor heterodimer molecule CD94/NKG2A was synthesized to target a specific peptide-presenting Qa-1^b Qdm ligand as a simplified model of low-affinity interactions between immune cells and peptide-presenting cancer cells that occurs during cancer immunotherapy. A cancer-irrelevant Qa-1^b GroEL ligand was also targeted by the same receptor as a control experiment to test for non-specific binding. The analysis of different pairs of bimodal SANE sensor signatures enabled discrimination of ligand, receptor and their complexes and enabled differentiating between specific and non-specific ligand interactions. We were able to detect ligand-receptor complex binding at concentrations over 500 times lower than the free solution equilibrium binding constant (K _D ). Additionally, SANE sensor measurements enabled estimation of the fast dissociation rate (k _off) for this low-affinity specific ligand-receptor system, previously shown to be challenging to quantify with commercial technologies. The k _off value of targeted peptide-presenting ligands is known to correlate with the subsequent activation of immune cells in vivo, suggesting the potential utility of the SANE senor as a screening tool in cancer immunotherapy.

Characterization of deep sub-wavelength nanowells by imaging the photon state scattering spectra

Optical-matter interactions and photon scattering in a sub-wavelength space are of great interest in many applications, such as nanopore-based gene sequencing and molecule characterization. Previous studies show that spatial distribution features of the scattering photon states are highly sensitive to the dielectric and structural properties of the nanopore array and matter contained on or within them, as a result of the complex optical-matter interaction in a confined system. In this paper, we report a method for shape characterization of subwavelength nanowells using photon state spatial distribution spectra in the scattering near field. Far-field parametric images of the near-field optical scattering from sub-wavelength nanowell arrays on a SiN substrate were obtained experimentally. Finite-difference time-domain simulations were used to interpret the experimental results. The rich features of the parametric images originating from the interaction of the photons and the nanowells were analyzed to recover the size of the nanowells. Experiments on nanoholes modified with Shp2 proteins were also performed. Results show that the scattering distribution of modified nanoholes exhibits significant differences compared to empty nanoholes. This work highlights the potential of utilizing the photon status scattering of nanowells for molecular characterization or other virus detection applications.

Measurement of Alcohol-Dependent Physiological Changes in Red Blood Cells Using Resistive Pulse Sensing

Alcohol exposure has been postulated to adversely affect the physiology and function of the red blood cells (RBCs). The global pervasiveness of alcohol abuse, causing health issues and social problems, makes it imperative to resolve the physiological effects of alcohol on RBC physiology. Alcohol consumed recreationally or otherwise almost immediately alters cell physiology in ways that is subtle and still unresolved. In this paper, we introduce a high-resolution device for quantitative electrofluidic measurement of changes in RBC volume upon alcohol exposure. We present an exhaustive calibration of our device using model cells to measure and resolve volume changes down to 0.6 fL. We find an RBC shrinkage of 5.3% at 0.125% ethanol (the legal limit in the United States) and a shrinkage of 18.5% at 0.5% ethanol (the lethal limit) exposure. Further, we also measure the time dependence of cell volume shrinkage (upon alcohol exposure) and then recovery (upon alcohol removal) to quantify shrinkage and recovery of RBC volumes. This work presents the first direct quantification of temporal and concentration-dependent changes in red blood cell volume upon ethanol exposure. Our device presents a universally applicable high-resolution and high-throughput platform to measure changes in cell physiology under native and diseased conditions.

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.

Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores

As a type of biological macromolecule, the conformation of proteins dynamically changes in a solution, which often results in a change in their function. However, traditional biological assays have significant drawbacks in detecting the conformation properties of proteins. Alternatively, nanopores have potential advantages in this area, which can detect protein in high throughput and without labelling. Herein, we investigated the translocation of calmodulins through silicon nitride nanopores using molecular dynamics (MD) simulation. Initially, the calmodulins were fixed in the nanopore. Distinguished blocked ionic currents were obtained between the two forms of calmodulin. Next, in the translocation simulations, a prominent difference in time resolution was easily found between the two states of calmodulin by using the appropriate voltage and comparable size of pore to protein, r_p/r_g→ 1, 4.5 nm (where r_p is the protein radius and r_g is the gyration radius). These simulations on the nanoscale are helpful for developing Ca²⁺-sensitive ion channels and nanodevices.

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.

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.

Capture of rod-like molecules by a nanopore: Defining an "orientational capture radius"

Both the translational diffusion coefficient D and the electrophoretic mobility μ of a short rod-like molecule (such as dsDNA) that is being pulled toward a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous electric field, D and μ will change as the molecule approaches the nanopore, and this will impact the capture process. We present a simplified study of this problem using theoretical arguments and Langevin dynamics simulations. In particular, we introduce a new orientational capture radius, which we compare to the capture radius for the equivalent point-like particle, and we discuss the different physical regimes of orientation during capture and the impact of initial orientations on the capture time.

Detection of single analyte and environmental samples with silicon nitride nanopores: Antarctic dirt particulates and DNA in artificial seawater

Nanopore sensing is a powerful tool for the detection of biomolecules. Solid-state nanopores act as single-molecule sensors that can function in harsh conditions. Their resilient nature makes them attractive candidates for taking this technology into the field to measure environmental samples for life detection in space and water quality monitoring. Here, we discuss the fabrication of silicon nitride pores from ∼1.6 to 20 nm in diameter in 20-nm-thick silicon nitride membranes suspended on glass chips and their performance. We detect pure laboratory samples containing a single analyte including DNA, BSA, microRNA, TAT, and poly-D-lys-hydrobromide. We also measured an environmental (mixed-analyte) sample, containing Antarctic dirt provided by NASA Ames. For DNA measurements, in addition to using KCl and NaCl solutions, we used the artificial (synthetic) seawater, which is a mixture of different salts mimicking the composition of natural seawater. These samples were spiked with double-stranded DNA (dsDNA) fragments at different concentrations to establish the limits of nanopore sensitivity in candidate environment conditions. Nanopore chips were cleaned and reused for successive measurements. A stand-alone, 1-MHz-bandwidth Chimera amplifier was used to determine the DNA concentration in artificial seawater that we can detect in a practical time scale of a few minutes. We also designed and developed a new compact nanopore reader, a portable read-out device with miniaturized fluidic cells, which can obtain translocation data at bandwidths up to 100 kHz. Using this new instrument, we record translocations of 400 bp, 1000 bp, and 15000 bp dsDNA fragments and show discrimination by analysis of current amplitude and event duration histograms.

Improved Measurement of Proteins Using a Solid-State Nanopore Coupled with a Hydrogel

Although resistive pulse sensing using solid-state nanopores is capable of single-molecule sensitivity, previous work has shown that nanoparticles, such as proteins, pass through nanopores too quickly for accurate detection with typical measurement apparatus. As a result, nanopore measurements of these particles significantly deviate from theoretically estimated current amplitudes and detection rates. Here, we show that a hydrogel placed on the distal side of a nanopore can increase the residence time of nanoparticles within the nanopore, significantly increasing the detection rate and allowing improved resolution of blockage currents. The method is simple and inexpensive to implement while being label-free and applicable to a wide range of nanoparticle targets. Using hydrogel-backed nanopores, we detected the protein IgG with event frequencies several orders of magnitude higher than those in the absence of the hydrogel and with larger measured currents that agree well with theoretical models. We also show that the improved measurement also enables discrimination of IgG and bovine serum albumin in a mixed solution. Finally, we show that measurements of IgG with the hydrogel-backed nanopores can also yield current amplitude distributions that can be analyzed to infer its approximate shape.

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.

On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA

Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.

Transverse Detection of DNA Using a MoS2 Nanopore

Classical nanopore sensing relies on the measurement of the ion current passing through a nanopore. Whenever a molecule electrophoretically translocates through the narrow constriction, it modulates the ion current. Although this approach allows one to measure single molecules, the access resistance limits the spatial resolution. This physical limitation could potentially be overcome by an alternative sensing scheme taking advantage of the current across the membrane material itself. Such an electronic readout would also allow better temporal resolution than the ionic current. In this work, we present the fabrication of an electrically contacted molybdenum disulfide (MoS₂) nanoribbon integrated with a nanopore. DNA molecules are sensed by correlated signals from the ionic current through the nanopore and the transverse current through the nanoribbon. The resulting signal suggests a field-effect sensing scheme where the charge of the molecule is directly sensed by the nanoribbon. We discuss different sensing schemes such as local potential sensing and direct charge sensing. Furthermore, we show that the fabrication of freestanding MoS₂ ribbons with metal contacts is reliable and discuss the challenges that arise in the fabrication and usage of these devices.

Detection of specific antibody-ligand interactions with a self-induced back-action actuated nanopore electrophoresis sensor

Recent advances in plasmonic nanopore technologies have enabled the use of concurrently acquired bimodal optical-electrical data for improved quantification of molecular interactions. This work presents the use of a new plasmonic nanosensor employing self-induced back-action (SIBA) for optical trapping to enable SIBA-actuated nanopore electrophoresis (SANE) for quantifying antibody-ligand interactions. T-cell receptor-like antibodies (TCRmAbs) engineered to target peptide-presenting major histocompatibility complex (pMHC) ligands, representing a model of target ligands presented on the surface of cancer cells, were used to test the SANE sensor's ability to identify specific antibody-ligand binding. Cancer-irrelevant TCRmAbs targeting the same pMHCs were also tested as a control. It was found that the sensor could provide bimodal molecular signatures that could differentiate between antibody, ligand and the complexes that they formed, as well as distinguish between specific and non-specific interactions. Furthermore, the results suggested an interesting phenomenon of increased antibody-ligand complex bound fraction detected by the SANE sensor compared to that expected for corresponding bulk solution concentrations. A possible physical mechanism and potential advantages for the sensor's ability to augment complex formation near its active sensing volume at concentrations lower than the free solution equilibrium binding constant (K D ) are discussed.

Adsorption Kinetics in Open Nanopores as a Source of Low-Frequency Noise

Ionic current measurements through solid-state nanopores consistently show a power spectral density that scales as 1/f ^α at low frequency f, with an exponent α ∼ 0.5-1.5, but strikingly, the physical origin of this behavior remains elusive. Here, we perform simulations of particles reversibly adsorbing at the surface of a nanopore and show that the fluctuations in the number of adsorbed particles exhibit low-frequency pink noise. We furthermore propose theoretical modeling for the time-dependent adsorption of particles on the nanopore surface for various geometries, which predicts a frequency spectrum in very good agreement with the simulation results. Altogether, our results highlight that the low-frequency noise takes its origin in the reversible adsorption of ions at the pore surface combined with the long-lasting excursions of the ions in the reservoirs. The scaling regime of the power spectrum extends down to a cutoff frequency which is far smaller than simple diffusion estimates. Using realistic values for the pore dimensions and the adsorption-desorption kinetics, this predicts the observation of pink noise for frequencies down to the hertz for a typical solid-state nanopore, in good agreement with experiments.

Colloidal lithography double-nanohole optical trapping of nanoparticles and proteins

Double-nanoholes fabricated by colloidal lithography were used for trapping single colloidal particles and single proteins. A gap separation of 60 nm between the cusps of the double-nanohole was achieved in a gold film of 70 nm thickness sputter coated onglass. The cusp separation was reduced steadily down to 10 nm by plasma etching the colloidal particles prior to sputter coating. Scanning electron microscopy was used to locate a particular double-nanohole and it was registered for later microscopy experiments. 30 nm polystyrene particles, the rubisco protein and bovine serum albumin were trapped using a laser focused through the aperture. Compared to other methods that require top-down nanofabrication, this approach is inexpensive and produces high-quality samples.

Channel from bacterial virus T7 DNA packaging motor for the differentiation of peptides composed of a mixture of acidic and basic amino acids

Protein mutations can result in dysfunctional cell signaling pathways; therefore it is of significance to develop a robust platform for the detection of protein mutations. Here, we report that the channel of bacterial virus T7 DNA packaging motor is able to discriminate peptides containing a mixture of acidic (negatively charged) and basic (positively charged) amino acids. Peptides were differentiated based on their current signatures created by their unique charge compositions. In combination with protease digestion, peptides with the locational differences of single amino acid were also identified. The results suggest that the T7 motor channel has the potential for peptide differentiation, mutation verification, and analysis of protein sequence.

DNA translocation through a nanopore in an ultrathin self-assembled peptide membrane

Here, we explore the possibility of using peptide-based materials as a membrane in solid-state nanopore devices in an effort to develop a sequence-specific, programmable biological membrane platform. We use a recently developed tyrosine-mediated self-assembly peptide sheet. At the air/water interface, the 5mer peptide YFCFY self-assembles into a uniform and robust two-dimensional (2D) structure, and the peptide sheet is easily transferred to a low-noise glass substrate. The thickness of the peptide membrane can be adjusted to approximately 5 nm (or even to 2 nm) by an etching process, and the diameters of the peptide nanopores can be precisely controlled using a focused electron beam with an attuned spot size. The ionic current noise of the peptide nanopore is comparable to those of typical silicon nitride nanopores or multilayer 2D materials. Using this membrane, we successfully observe translocation of 1000 bp double-stranded DNA with a sufficient signal-to-noise ratio of ∼30 and an elongated translocation speed of ∼1 bp μs^-1. Our results suggest that the self-assembled peptide film can be used as a sensitive nanopore membrane and employed as a platform for applying biological functionalities to solid-state substrates.

Fabrication and Applications of Solid-State Nanopores

Nanopores fabricated from synthetic materials (solid-state nanopores), platforms for characterizing biological molecules, have been widely studied among researchers. Compared with biological nanopores, solid-state nanopores are mechanically robust and durable with a tunable pore size and geometry. Solid-state nanopores with sizes as small as 1.3 nm have been fabricated in various films using engraving techniques, such as focused ion beam (FIB) and focused electron beam (FEB) drilling methods. With the demand of massively parallel sensing, many scalable fabrication strategies have been proposed. In this review, typical fabrication technologies for solid-state nanopores reported to date are summarized, with the advantages and limitations of each technology discussed in detail. Advanced shrinking strategies to prepare nanopores with desired shapes and sizes down to sub-1 nm are concluded. Finally, applications of solid-state nanopores in DNA sequencing, single molecule detection, ion-selective transport, and nanopatterning are outlined.

Translocation of tetrahedral DNA nanostructures through a solid-state nanopore

Tetrahedral DNA nanostructures (TDNs) are programmable DNA nanostructures that have great potential in bio-sensing, cell imaging and therapeutic applications. In this study, we investigate the translocation behavior of individual TDNs through solid-state nanopores. Pronounced translocation signals for TDNs are observed that are sensitive to the size of the nanostructures. TDNs bound to linear DNA molecules produce an extra signal in the ionic current traces. Statistical analysis of its relative temporal position reveals distinct features between TDNs bound to the end and those bound to the middle of the linear DNA molecules. A featured current trace for two TDNs bound to the same linear DNA molecule has also been observed. Our study demonstrates the potential of using TDNs as sensitive bio-sensors to detect specific segments of a single DNA molecule in real time, based on solid-state nanopore devices.

Discrimination of single-stranded DNA homopolymers by sieving out G-quadruplex using tiny solid-state nanopores

Nanopore sensor has been developed as a promising technology for DNA sequencing at the single-base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G-quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20-nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105-nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore-based DNA sequencing at single-base level.

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

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

Differentiation of selectively labeled peptides using solid-state nanopores

Determination of the amino acid sequence of a protein is critical for understanding various biological processes. Mass spectrometry has mainly been used for protein identification; however, there are limitations to its sensitivity when detecting low abundance proteins. In this study, we attempted to distinguish between three similar peptide sequences (∼40 amino acids, ∼5 kDa) that differed only by the location or number of cysteine residues with solid-state nanopores. The cysteine residues are located at one end, one at the center, and at both ends for each of the three peptides. We found that differentiation of the three types of peptides by nanopore signals was difficult. However, when the cysteine residue was labeled with a negatively charged molecule, Flamma® 496, the labeled peptides showed distinct signals for each peptide. Comparing the relative current blockades of labeled peptides with applied voltages, we found that the label was able to change peptide conformations and the resulting ionic current signals from the three labeled peptides were distinguished based on the relative current blockade, full width at half-maximum of the current blockade distribution, and single-molecule level peak shape analysis. Our results suggest that solid-state nanopores combined with a targeted labeling strategy could be used to obtain characteristic peptide signatures that could ultimately be used for protein identification.