Solid-state nanopore: chemical modifications, interactions, and functionalities

Nanopore technology is a burgeoning detection technology for single-molecular sensing and ion rectification. Solid-state nanopores have attracted more and more attention because of their higher stability and tunability than biological nanopores. However, solid-state nanopores still suffer the drawbacks of low signal-to-noise ratio and low resolution, which hinders their practical applications. Thus, developing operatical and useful methods to overcome the shortages of solid-state nanopores is urgently needed. Here, we summarize the recent research on nanopore modification to achieve this goal. Modifying solid-state nanopores with different coating molecules can improve the selectivity, sensitivity, and stability of nanopores. The modified molecules can introduce different functions into the nanopores, greatly expanding the applications of this novel detection technology. We hope that this review of nanopore modification will provide new ideas for this field.

Methodology to Detect Biological Particles Using a Biosensing Surface Integrated in Resistive Pulse Sensing

Resistive pulse sensing (RPS) is an analytical method that can be used to individually count particles from a small sample. RPS simply monitors the physical characteristics of particles, such as size, shape, and charge density, and the integration of RPS with biosensing is an attractive theme to detect biological particles such as virus and bacteria. In this report, a methodology of biosensing on RPS was investigated. Polydopamine (PD), an adhesive component of mussels, was used as the base material to create a sensing surface. PD adheres to most materials, such as noble metals, metal oxides, semiconductors, and polymers; as a result, PD is a versatile intermediate layer for the fabrication of a biosensing surface. As an example of a biological particle, human influenza A virus (H1N1 subtype) was used to monitor translocation of particles through the pore membrane. When virus-specific ligands (6'-sialyllactose) were immobilized on the pore surface, the translocation time of the virus particles was considerably extended. The detailed translocation data suggest that the viral particles were trapped on the sensing surface by specific interactions. In addition, virus translocation processes on different pore surfaces were distinguished using machine learning. The result shows that the simple and versatile PD-based biosensor surface design was effective. This advanced RPS measurement system could be a promising analytical technique.

Gut Microbiota-Derived Small Extracellular Vesicles Endorse Memory-like Inflammatory Responses in Murine Neutrophils

Neutrophils are classically characterized as merely reactive innate effector cells. However, the microbiome is known to shape the education and maturation process of neutrophils, improving their function and immune-plasticity. Recent reports demonstrate that murine neutrophils possess the ability to exert adaptive responses after exposure to bacterial components such as LPS (Gram-negative bacteria) or LTA (Gram-positive bacteria). We now ask whether small extracellular vesicles (EVs) from the gut may directly mediate adaptive responses in neutrophils in vitro. Murine bone marrow-derived neutrophils were primed in vitro by small EVs of high purity collected from colon stool samples, followed by a second hit with LPS. We found that low-dose priming with gut microbiota-derived small EVs enhanced pro-inflammatory sensitivity as indicated by elevated levels of TNF-α, IL-6, ROS and MCP-1 and increased migratory and phagocytic activity. In contrast, high-dose priming resulted in a tolerant phenotype, marked by increased IL-10 and decreased transmigration and phagocytosis. Alterations in TLR2/MyD88 as well as TLR4/MyD88 signaling were correlated with the induction of adaptive cues in neutrophils in vitro. Taken together, our study shows that small EVs from stools can drive adaptive responses in neutrophils in vitro and may represent a missing link in the gut-immune axis.

A simple displacement aptamer assay on resistive pulse sensor for small molecule detection

A universal aptamer-based sensing strategy is proposed using DNA modified nanocarriers and Resistive Pulse Sensing (RPS) for the rapid (≤20 min) and label free detection of small molecules. The surface of a magnetic nanocarrier was first modified with a ssDNA (anchor) which is designed to be partially complimentary in sequence to the ssDNA aptamer. The aptamer and anchor form a stable dsDNA complex on the nanocarriers surface. Upon the addition of the target molecule, a conformational change takes place where the aptamer preferentially binds to the target over the anchor; causing the aptamer to be released into solution. The RPS measures the change in velocity of the nanocarrier as its surface changes from dsDNA to ssDNA, and its velocity is used as a proxy for the concentration of the target. The length of the aptamer and the ability to extract and preconcentrate the nanocarriers using a magnet, is shown to affect the sensitivity. We illustrate the versatility of the assay using the same anchor sequence and Aptamers to the antibiotic Moxifloxacin, and chemotherapeutics Imatinib and Irinotecan. In addition, the proposed assay can be easily extended to detect multiple analytes simultaneously, by utilizing nanocarriers with different diameters. Each sized particle is functionalised with a the same anchor but a unique aptamer. We illustrate this with the simultaneous detection of Imatinib and Moxifloxacin. The strategy could be easily adapted to a range of targets and unlike previous strategies that use aptamer modified nanocarriers, the signal is not dependent upon the tertiary structure of the aptamer-target interaction.

Characterization of positively charged polyplexes by tunable resistive pulse sensing

With the approval of the first siRNA-based drugs, non-viral siRNA delivery has gained special interest in industry and academia in the last two years. For non-viral delivery, positively charged lipid and polymer formulations play a central role in research and development. However, nanoparticle size characterization, particularly of polydisperse formulations, can be very challenging. Tunable resistive pulse sensing for particle by particle measurements of size, polydispersity, zeta potential and a direct concentration promises better assessment of nanoparticle formulations. However, the current application is not optimized for positively charged particles. A supplier-provided coating solution for difficult-to-measure samples does not allow for successful measurements of positively charged nanoparticles. This article describes a new coating solution based on choline-chloride. Coating is verified by current-voltage (I-V) recordings and ultimately tested on a positively charged nanoparticle formulation comprising of siRNA and PEG-PCL-PEI polymer. This coating allows successful size, polydispersity index (PDI) and concentration measurement by tunable resistive pulse sensing of positively charged PEI-based polyplexes. This article provides the foundation for further characterization of polyplexes as well as other positively charged nanoparticle formulations based on particle by particle measurements.

Sensing with Nanopores and Aptamers: A Way Forward

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

Rapid quantification of prion proteins using resistive pulse sensing

Prion diseases are a group of fatal transmissible neurological conditions caused by the change in conformation of intrinsic cellular prion protein (PrP^C). We present a rapid assay using aptamers and resistive pulse sensing, RPS, to extract and quantify PrP^C from complex sample matrices. We functionalise the surface of superparamagnetic beads, SPBs, with a DNA aptamer. First SPB's termed P-beads, are used to pre-concentrate the analyte from a large sample volume. The PrP^C protein is then eluted from the P-beads before aptamer modified sensing beads, S-beads, are added. The velocity of the S-beads through the nanopore reveals the concentration of the PrP^C protein. The process is done in under an hour and allows the detection of picomol's of protein.

Surface coatings for solid-state nanopores

Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.

Peptide Nanocarriers for Detection of Heavy Metal Ions Using Resistive Pulse Sensing

The use of nanocarriers within resistive pulse sensing facilitates the detection and quantification of analytes. To date the field has been dominated by polyionic carriers or nanomaterials. Together they combine the recognition elements of a ligand with a stable support, facilitating the sample handling, analysis times, and multiplex detection. Here we develop the use of peptide-functionalized superparamagnetic nanocarriers to extract and quantify metal ions in solution. The interaction between nickel and the peptide ligand is measured as a change in translocation velocity of the carrier. The magnitude of change is proportional to the concentration of the metal ions in solution. Unlike DNA aptamers where a change in the tertiary structure and the folding of the polyanionic backbone influences the carrier velocity, the peptides here had a lower net charge under the assay conditions. To try and enhance the signal we engineered charged groups within the peptide to explore the effects on the signal. In all cases the metal ion binding dominated the velocity of the carrier. The assay was shown to work across 3 orders of magnitude and can detect Ni²⁺ in the presence of some other heavy metal ions. We demonstrate this by quantifying Ni²⁺ in both tap and pond water. The work allows for future multiplexed sensing strategies using both peptides and DNA aptamers in resistive pulse sensors.

Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores

The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pulling forces and current blockades induced by the permeation of protein residues are found to be highly correlated with the type of amino acids, which makes the residues identifiable. It is also found that aside from the dimension, both the conformation and charge state of the residue can significantly influence the force and current signal during its permeation through the nanopore. In particular, due to the electro-osmotic flow effect, the blockade current for the double-protonated histidine is slightly smaller than that for single-protonated histidine, which makes it possible for discrimination of different protonation states of amino acids. The results reported here present a novel protein sequencing scheme using graphene nanopores combined with nanomanipulation technology.

Particle detection on microfluidic chips by differential resistive pulse sensing (RPS) method

The resistive pulse sensing (RPS) method has been widely used for characterization of particles, cells, and biomolecules due to its merits of high sensitivity and resolution. This paper investigates working parameters involved in detecting submicron and micron-sized particles by the differential RPS method on microfluidic chips. Effects of particle-to-sensor size ratio, ionic concentration and pH of the electrolyte solution, and applied electric field are studied systematically by using polystyrene particles with a size range from 140 nm to 5 µm. The results show that both the amplitude and the signal-to-noise ratio (SNR) of the RPS signals increase with the particle-to-sensor size ratio as well as the ionic concentration of the electrolyte media. The amplitude of the RPS signals also increases with increasing applied voltage, while the SNR experiences an upslope at low voltages and a decline under the condition of high voltages. pH has little effect on the background noise of the differential RPS signals but reduces the amplitude of the RPS signals at high pH. Grouping of RPS signals is considered to be caused by interactions between the sensor walls and the particles. Nanoparticle detection by the differential RPS method can be enhanced by optimizing these working parameters.

The Design and Characterization of Multifunctional Aptamer Nanopore Sensors

Aptamer-modified nanomaterials provide a simple, yet powerful sensing platform when combined with resistive pulse sensing technologies. Aptamers adopt a more stable tertiary structure in the presence of a target analyte, which results in a change in charge density and velocity of the carrier particle. In practice the tertiary structure is specific for each aptamer and target, and the strength of the signal varies with different applications and experimental conditions. Resistive pulse sensors (RPS) have single particle resolution, allowing for the detailed characterization of the sample. Measuring the velocity of aptamer-modified nanomaterials as they traverse the RPS provides information on their charge state and densities. To help understand how the aptamer structure and charge density effects the sensitivity of aptamer-RPS assays, here we study two metal binding aptamers. This creates a sensor for mercury and lead ions that is capable of being run in a range of electrolyte concentrations, equivalent to river to seawater conditions. The observed results are in excellent agreement with our proposed model. Building on this we combine two aptamers together in an attempt to form a dual sensing strand of DNA for the simultaneous detection of two metal ions. We show experimental and theoretical responses for the aptamer which creates layers of differing charge densities around the nanomaterial. The density and diameter of these zones effects both the viability and sensitivity of the assay. While this approach allows the interrogation of the DNA structure, the data also highlight the limitations and considerations for future assays.

Detection of Individual Molecules and Ions by Carbon Nanotube-Based Differential Resistive Pulse Sensor

This paper presents a new method of sensing single molecules and cations by a carbon nanotube (CNT)-based differential resistive pulse sensing (RPS) technique on a nanofluidic chip. A mathematical model for multichannel RPS systems is developed to evaluate the CNT-based RPS signals. Individual cations, rhodamine B dye molecules, and ssDNAs are detected successfully with high resolution and high signal-to-noise ratio. Differentiating ssDNAs with 15 and 30 nucleotides are achieved. The experimental results also show that translocation of negatively charged ssDNAs through a CNT decreases the electrical resistance of the CNT channel, while translocation of positively charged cations and rhodamine B molecules increases the electrical resistance of the CNT. The CNT-based nanofluidic device developed in this work provides a new avenue for single-molecule/ion detection and offers a potential strategy for DNA sequencing.

Rapid Assessment of Site Specific DNA Methylation through Resistive Pulse Sensing

Many diseases are defined by patterns of DNA methylation which result in aberrant gene expression. We present a rapid assay based upon resistive pulse sensing, RPS, to characterize sequence specific DNA methylation sites in genomic DNA. We modify the surface of superparamagnetic beads, SPBs, with DNA (capture probe). The particles are added to solution where they bind to and extract sequence specific DNA (target DNA). The target loaded SPBs are then incubated with antibodies which bind to the methylation sites, and the velocity of the SPBs through the nanopore reveals the number and location of the epigenetic markers within the target. The approach is capable of distinguishing between different methylation sites within a DNA promoter region. Crucially the approach is not dependent on accurate sequencing of assayed DNA, with genomic regions targeted through complementary probes. As such the number of stages and reagents costs are low and the assay is complete in under 60 min which includes the incubation and run times. The format also allows simultaneous quantification of number of copies of methylated DNA, and we illustrate this with a dose response curve.

Scanning ion conductance microscopy mapping of tunable nanopore membranes

We report on the use of scanning ion conductance microscopy (SICM) for in-situ topographical mapping of single tunable nanopores, which are used for tunable resistive pulse sensing. A customised SICM system was used to map the elastomeric pore membranes repeatedly, using pipettes with tip opening diameters of approximately 50 nm and 1000 nm. The effect of variations on current threshold, scanning step size, and stretching has been studied. Lowering the current threshold increased the sensitivity of the pipette while scanning, up to the point where the tip contacted the surface. An increase in the pore area was observed as the step size was decreased, and with increased stretching. SICM reveals details of the electric field near the pore entrance, which is important for understanding measurements of submicron particles using resistive pulse sensing.

A tunable nanopore sensor for the detection of metal ions using translocation velocity and biphasic pulses

A tunable resistive pulse sensor, utilising a polyurethane nanopore, has been used to characterise nanoparticles as they traverse the pore opening. Herein we demonstrate that the translocation speed, conductive and resistive pulse magnitude, can be used to infer the surface charge of a nanoparticle, and act as a specific transduction signal for the binding of metal ions to ligands on the particle surface. Surfaces of silica nanoparticles were modified with a ligand to demonstrate the concept, and used to extract copper(ii) ions (Cu²⁺) from solution. By tuning the pH and ionic strength of the solution, a biphasic pulse, a conductive followed by a resistive pulse is recorded. Biphasic pulses are becoming a powerful means to characterise materials, and provide insight into the translocation mechanism, and herein we present their first use to detect the presence of metal ions in solution. We demonstrate how combinations of translocation speed and/or biphasic pulse behaviour are used to detect Cu²⁺ with quantitative responses across a range of pH and ionic strengths. Using a generic ligand this assay allows a clear signal for Cu²⁺ as low as 1 ppm with a short 5-minute incubation time, and is capable of measuring 10 ppm Cu²⁺ in the presence of 5 other ions. The method has potential for monitoring heavy metals in biological and environmental samples.