Detection of target-probe oligonucleotide hybridization using synthetic nanopore resistive pulse sensing

Solid-State Glass Nanopipettes: Functionalization and Applications

Solid-state glass nanopipettes provide a promising confined space that offers several advantages such as controllable size, simple preparation, low cost, good mechanical stability, and good thermal stability. These advantages make them an ideal choice for various applications such as biosensors, DNA sequencing, and drug delivery. In this review, we first delve into the functionalized nanopipettes for sensing various analytes and the methods used to develop detection means with them. Next, we provide an in-depth overview of the advanced functionalization methodologies of nanopipettes based on diversified chemical kinetics. After that, we present the latest state-of-the-art achievements and potential applications in detecting a wide range of targets, including ions, molecules, biological macromolecules, and single cells. We examine the various challenges that arise when working with these targets, as well as the innovative solutions developed to overcome them. The final section offers an in-depth overview of the current development status, newest trends, and application prospects of sensors. Overall, this review provides a comprehensive and detailed analysis of the current state-of-the-art functionalized nanopipette perception sensing and development of detection means and offers valuable insights into the prospects for this exciting field.

Detection and Separation of DNA and Silver Nanoparticles Using a Solid-State Nanopore

Nanopore sensors, a new generation of single-molecule sensors, are increasingly used to detect and analyze various analytes and have great potential for rapid gene sequencing. However, there are still some problems in the preparation of small diameter nanopores, such as imprecise pore size and porous defects, while the detection accuracy of large-diameter nanopores is relatively low. Therefore, how to achieve more precise detection of large diameter nanopore sensors is an urgent problem to be studied. Here, SiN nanopore sensors were used to detect DNA molecules and silver nanoparticles (NPs) separately and in combination. The experimental results show that large-size solid-state nanopore sensors can identify and discriminate between DNA molecules, NPs, and NP-bound DNA molecules clearly according to resistive pulses. In addition, the detection mechanism of using NPs to assist in identifying target DNA molecules in this study is different from previous reports. We find that silver NPs can simultaneously bind to multiple probes and target DNA molecules and generate a larger blocking current than free DNA molecules when passing through the nanopore. In conclusion, our research indicates that large-sized nanopores can distinguish the translocation events, thereby identifying the presence of the target DNA molecules in the sample. This nanopore-sensing platform can produce rapid and accurate nucleic acid detection. Its application in medical diagnosis, gene therapy, virus identification, and many other fields is highly significant.

In-plane Extended Nano-coulter Counter (XnCC) for the Label-free Electrical Detection of Biological Particles

We report an in-plane extended nanopore Coulter counter (XnCC) chip fabricated in a thermoplastic via imprinting. The fabrication of the sensor utilized both photolithography and focused ion beam milling to make the microfluidic network and the in-plane pore sensor, respectively, in Si from which UV resin stamps were generated followed by thermal imprinting to produce the final device in the appropriate plastic (cyclic olefin polymer, COP). As an example of the utility of this in-plane extended nanopore sensor, we enumerated SARS-CoV-2 viral particles (VPs) affinity-selected from saliva and extracellular vesicles (EVs) affinity-selected from plasma samples secured from mouse models exposed to different ionizing radiation doses.

Sequence-Specific Detection of DNA Strands Using a Solid-State Nanopore Assisted by Microbeads

Simple, rapid, and low-cost detection of DNA with specific sequence is crucial for molecular diagnosis and therapy applications. In this research, the target DNA molecules are bonded to the streptavidin-coated microbeads, after hybridizing with biotinylated probes. A nanopore with a diameter significantly smaller than the microbeads is used to detect DNA molecules through the ionic pulse signals. Because the DNA molecules attached on the microbead should dissociate from the beads before completely passing through the pore, the signal duration time for the target DNA is two orders of magnitude longer than free DNA. Moreover, the high local concentration of target DNA molecules on the surface of microbeads leads to multiple DNA molecules translocating through the pore simultaneously, which generates pulse signals with amplitude much larger than single free DNA translocation events. Therefore, the DNA molecules with specific sequence can be easily identified by a nanopore sensor assisted by microbeads according to the ionic pulse signals.

A Microfluidic Sensor for Continuous, in Situ Surface Charge Measurement of Single Cells

Cell surface charge has been recognized as an important cellular property. We developed a microfluidic sensor based on resistive pulse sensing to assess surface charge and sizes of single cells suspended in a continuous flow. The device consists of two consecutive resistive pulse sensors (RPSs) with identical dimensions. Opposite electric fields were applied on the two RPSs. A charged cell in the RPSs was accelerated or decelerated by the electric fields and thus exhibited different transit times passing through the two RPSs. The cell surface charge is measured with zeta potential that can be quantified with the transit time difference. The transit time of each cell can be accurately detected with the width of pulses generated by the RPS, while the cell size can be calculated with the pulse magnitude at the same time. This device has the ability to detect surface charges and sizes of individual cells with high tolerance in cell types and testing solutions compared with traditional electrophoretic light scattering methods. Three different types of cells including HeLa cancer cells, human dermal fibroblast cells, and human umbilical vein endothelial cells (HUVECs) were tested with the sensor. Results showed a significant difference of zeta potentials between HeLa cells and fibroblasts or HUVECs. In addition, when HeLa cells were treated with various concentrations of glutamine, the effects on cancer cell surface charge were detected. Our results demonstrated the great potential of using our sensor for cell type sorting, cancer cell detection, and cell status analysis.

Simultaneous electric production and sizing of emulsion droplets in microfluidics

Microscale emulsions are widely used in fundamental and applied sciences. To expand their utilization, various methods have been developed for manipulating and measuring the physical properties of fabricated emulsions inside microchannels. Herein, we present an electric emulsification platform that can produce emulsions and simultaneously detect their physical properties (size and production speed). The characterization of the emulsion properties during the fabrication process will broaden the application fields for microscale emulsions because it can avoid time-consuming post image processing and simplify the emulsification platform. To accomplish this, a "bottleneck" channel is implanted between two reservoirs of immiscible fluids (continuous and dispersion phases). This channel can not only confine one fluid within the other when the electric field is on, resulting in emulsification via electrohydrodynamically induced Rayleigh instability, but also act as a resistive pulse sensor (RPS). The fluctuation of the liquid/liquid interface during emulsification induces the fluctuation of the electric resistance in the bottleneck channel, as the two fluid phases have different electrical conductivities. With this simple but dual-functional channel, the emulsion size (radius of 5-10 μm) and production speed (7-12 Hz) can be controlled by adjusting the electric field and the channel-neck geometry. Additionally, the properties can be measured using the RPS; the data obtained through the RPS exhibit high correlations with the validated data obtained using a high-speed camera and microscopy (>95%). The proposed buffer-less electric emulsification with the embedded RPS is a simple and cost-effective emulsion production method that allows real-time emulsion characterization with a limited sample volume.

Probing the conformational switch of I-motif DNA using tunable resistive pulse sensing

I-motif DNA, which can fold and unfold reversibly in various environments, plays a significant role in DNA nanotechnology and biological functions. Thus, it is of fundamental importance to identify the different conformations of i-motif DNA. Here, we demonstrate that distinct structures of i-motif DNA conjugated to polystyrene spheres can be distinguished through tunable resistive pulse sensing technique. When dispersed in acidic buffer, i-motif DNA coating on polystyrene spheres would fold into quadruplex structure and subsequently induce an apparent increase in the translocation duration time upon passing through a nanopore due to the shielding effect of the surface charge of the nanospheres. However, if the DNA strands don't have conformational changes in acidic buffer, little shift can be observed in the translocation duration time of the DNA functionalized polystyrene spheres. A before-and-after assay was also performed to illustrate the fast speed of i-motif DNA folding using this technique. The successful implementation of tunable resistive pulse sensing to monitor the conformational transition of i-motif DNA provides a potential tool to detect the structural changes of DNA and an alternative approach to study the function of DNA structures.

Microfluidic and Nanofluidic Resistive Pulse Sensing: A Review

The resistive pulse sensing (RPS) method based on the Coulter principle is a powerful method for particle counting and sizing in electrolyte solutions. With the advancement of micro- and nano-fabrication technologies, microfluidic and nanofluidic resistive pulse sensing technologies and devices have been developed. Due to the unique advantages of microfluidics and nanofluidics, RPS sensors are enabled with more functions with greatly improved sensitivity and throughput and thus have wide applications in fields of biomedical research, clinical diagnosis, and so on. Firstly, this paper reviews some basic theories of particle sizing and counting. Emphasis is then given to the latest development of microfuidic and nanofluidic RPS technologies within the last 6 years, ranging from some new phenomena, methods of improving the sensitivity and throughput, and their applications, to some popular nanopore or nanochannel fabrication techniques. The future research directions and challenges on microfluidic and nanofluidic RPS are also outlined.

Magnetic particles for in vitro molecular diagnosis: From sample preparation to integration into microsystems

Colloidal magnetic particles (MPs) have been developed in association with molecular diagnosis for several decades. MPs have the great advantage of easy manipulation using a magnet. In nucleic acid detection, these particles can act as a capture support for rapid and simple biomolecule separation. The surfaces of MPs can be modified by coating with various polymer materials to provide functionalization for different applications. The use of MPs enhances the sensitivity and specificity of detection due to the specific activity on the surface of the particles. Practical applications of MPs demonstrate greater efficiency than conventional methods. Beyond traditional detection, MPs have been successfully adopted as a smart carrier in microfluidic and lab-on-a-chip biosensors. The versatility of MPs has enabled their integration into small single detection units. MPs-based biosensors can facilitate rapid and highly sensitive detection of very small amounts of a sample. In this review, the application of MPs to the detection of nucleic acids, from sample preparation to analytical readout systems, is described. State-of-the-art integrated microsystems containing microfluidic and lab-on-a-chip biosensors for the nucleic acid detection are also addressed.

Determination of Zeta Potential via Nanoparticle Translocation Velocities through a Tunable Nanopore: Using DNA-modified Particles as an Example

Nanopore technologies, known collectively as Resistive Pulse Sensors (RPS), are being used to detect, quantify and characterize proteins, molecules and nanoparticles. Tunable resistive pulse sensing (TRPS) is a relatively recent adaptation to RPS that incorporates a tunable pore that can be altered in real time. Here, we use TRPS to monitor the translocation times of DNA-modified nanoparticles as they traverse the tunable pore membrane as a function of DNA concentration and structure (i.e., single-stranded to double-stranded DNA). TRPS is based on two Ag/AgCl electrodes, separated by an elastomeric pore membrane that establishes a stable ionic current upon an applied electric field. Unlike various optical-based particle characterization technologies, TRPS can characterize individual particles amongst a sample population, allowing for multimodal samples to be analyzed with ease. Here, we demonstrate zeta potential measurements via particle translocation velocities of known standards and apply these to sample analyte translocation times, thus resulting in measuring the zeta potential of those analytes. As well as acquiring mean zeta potential values, the samples are all measured using a particle-by-particle perspective exhibiting more information on a given sample through sample population distributions, for example. Of such, this method demonstrates potential within sensing applications for both medical and environmental fields.

Quantification of Virus Particles Using Nanopore-Based Resistive-Pulse Sensing Techniques

Viruses have drawn much attention in recent years due to increased recognition of their important roles in virology, immunology, clinical diagnosis, and therapy. Because the biological and physical properties of viruses significantly impact their applications, quantitative detection of individual virus particles has become a critical issue. However, due to various inherent limitations of conventional enumeration techniques such as infectious titer assays, immunological assays, and electron microscopic observation, this issue remains challenging. Thanks to significant advances in nanotechnology, nanostructure-based electrical sensors have emerged as promising platforms for real-time, sensitive detection of numerous bioanalytes. In this paper, we review recent progress in nanopore-based electrical sensing, with particular emphasis on the application of this technique to the quantification of virus particles. Our aim is to provide insights into this novel nanosensor technology, and highlight its ability to enhance current understanding of a variety of viruses.

Tunable resistive pulse sensing: potential applications in nanomedicine

An accurate characterization of nanomaterials used in clinical diagnosis and therapeutics is of paramount importance to realize the full potential of nanotechnology in medicine and to avoid unexpected and potentially harmful toxic effects due to these materials. A number of technical modalities are currently in use to study the physical, chemical and biological properties of nanomaterials but they all have advantages and disadvantages. In this review, we discuss the potential of a relative newcomer, tunable resistive pulse sensing, for the characterization of nanomaterials and its applications in nanodiagnostics.

Characterisation of the protein corona using tunable resistive pulse sensing: determining the change and distribution of a particle's surface charge

The zeta potential of the protein corona around carboxyl particles has been measured using tunable resistive pulse sensing (TRPS). A simple and rapid assay for characterising zeta potentials within buffer, serum and plasma is presented monitoring the change, magnitude and distribution of proteins on the particle surface. First, we measure the change in zeta potential of carboxyl-functionalised nanoparticles in solutions that contain biologically relevant concentrations of individual proteins, typically constituted in plasma and serum, and observe a significant difference in distributions and zeta values between room temperature and 37 °C assays. The effect is protein dependent, and the largest difference between the two temperatures is recorded for the γ-globulin protein where the mean zeta potential changes from -16.7 to -9.0 mV for 25 and 37 °C, respectively. This method is further applied to monitor particles placed into serum and/or plasma. A temperature-dependent change is again observed with serum showing a 4.9 mV difference in zeta potential between samples incubated at 25 and 37 °C; this shift was larger than that observed for samples in plasma (0.4 mV). Finally, we monitor the kinetics of the corona reorientation for particles initially placed into serum and then adding 5 % (V/V) plasma. The technology presented offers an interesting insight into protein corona structure and kinetics of formation measured in biologically relevant solutions, i.e. high protein, high salt levels, and its particle-by-particle analysis gives a measure of the distribution of particle zeta potential that may offer a better understanding of the behaviour of nanoparticles in solution. Graphical Abstract The relative velocity of a nanoparticle as it traverses a nanopore can be used to determine its zeta potential. Monitoring the changes in translocation speeds can therefore be used to follow changes to the surface chemistry/composition of 210 nm particles that were placed into protein rich solutions, serum and plasma. The particle-by-particle measurements allow the zeta potential and distribution of the particles to be characterised, illustrating the effects of protein concentration and temperature on the protein corona. When placed into a solution containing a mixture of proteins, the affinity of the protein to the particle's surface determines the corona structure, and is not dependent on the protein concentration.

Particle-by-Particle Charge Analysis of DNA-Modified Nanoparticles Using Tunable Resistive Pulse Sensing

Resistive pulse sensors, RPS, are allowing the transport mechanism of molecules, proteins and even nanoparticles to be characterized as they traverse pores. Previous work using RPS has shown that the size, concentration and zeta potential of the analyte can be measured. Here we use tunable resistive pulse sensing (TRPS) which utilizes a tunable pore to monitor the translocation times of nanoparticles with DNA modified surfaces. We start by demonstrating that the translocation times of particles can be used to infer the zeta potential of known standards and then apply the method to measure the change in zeta potential of DNA modified particles. By measuring the translocation times of DNA modified nanoparticles as a function of packing density, length, structure, and hybridization time, we observe a clear difference in zeta potential using both mean values and population distributions as a function of the DNA structure. We demonstrate the ability to resolve the signals for ssDNA, dsDNA, small changes in base length for nucleotides between 15 and 40 bases long, and even the discrimination between partial and fully complementary target sequences. Such a method has potential and applications in sensors for the monitoring of nanoparticles in both medical and environmental samples.

Observations of Tunable Resistive Pulse Sensing for Exosome Analysis: Improving System Sensitivity and Stability

Size distribution and concentration measurements of exosomes are essential when investigating their cellular function and uptake. Recently, a particle size distribution and concentration measurement platform known as tunable resistive pulse sensing (TRPS) has seen increased use for the characterization of exosome samples. TRPS measures the brief increase in electrical resistance (a resistive pulse) produced by individual submicrometer/nanoscale particles as they translocate through a size-tunable submicrometer/micrometer-sized pore, embedded in an elastic membrane. Unfortunately, TRPS measurements are susceptible to issues surrounding system stability, where the pore can become blocked by particles, and sensitivity issues, where particles are too small to be detected against the background noise of the system. Herein, we provide a comprehensive analysis of the parameters involved in TRPS exosome measurements and demonstrate the ability to improve system sensitivity and stability by the optimization of system parameters. We also provide the first analysis of system noise, sensitivity cutoff limits, and accuracy with respect to exosome measurements and offer an explicit definition of system sensitivity that indicates the smallest particle diameter that can be detected within the noise of the trans-membrane current. A comparison of exosome size measurements from both TRPS and cryo-electron microscopy is also provided, finding that a significant number of smaller exosomes fell below the detection limit of the TRPS platform and offering one potential insight as to why there is such large variability in the exosome size distribution reported in the literature. We believe the observations reported here may assist others in improving TRPS measurements for exosome samples and other submicrometer biological and nonbiological particles.

Quantitative detection of eryptosis in human erythrocytes using tunable resistive pulse sensing and annexin-V-beads

A novel assay using the quantitative tunable resistive pulse sensing technique to detect eryptosis in human RBCs in a non-optical manner.

Applications of tunable resistive pulse sensing

This Review focusses on the recent surge in applied research using tunable resistive pulse sensing, a technique used to analyse submicron colloids in aqueous solutions on a particle-by-particle basis.

Nanomaterials for diagnosis: challenges and applications in smart devices based on molecular recognition

Clinical diagnosis has always been dependent on the efficient immobilization of biomolecules in solid matrices with preserved activity, but significant developments have taken place in recent years with the increasing control of molecular architecture in organized films. Of particular importance is the synergy achieved with distinct materials such as nanoparticles, antibodies, enzymes, and other nanostructures, forming structures organized on the nanoscale. In this review, emphasis will be placed on nanomaterials for biosensing based on molecular recognition, where the recognition element may be an enzyme, DNA, RNA, catalytic antibody, aptamer, and labeled biomolecule. All of these elements may be assembled in nanostructured films, whose layer-by-layer nature is essential for combining different properties in the same device. Sensing can be done with a number of optical, electrical, and electrochemical methods, which may also rely on nanostructures for enhanced performance, as is the case of reporting nanoparticles in bioelectronics devices. The successful design of such devices requires investigation of interface properties of functionalized surfaces, for which a variety of experimental and theoretical methods have been used. Because diagnosis involves the acquisition of large amounts of data, statistical and computational methods are now in widespread use, and one may envisage an integrated expert system where information from different sources may be mined to generate the diagnostics.

Magnetic microbead transport during resistive pulse sensing

Tunable resistive pulse sensing (TRPS) experiments have been used to quantitatively study the motion of 1 μm superparamagnetic beads in a variable magnetic field. Closed-form theory has been developed to interpret the experiments, incorporating six particle transport mechanisms which depend on particle position in and near a conical pore. For our experiments, calculations indicate that pressure-driven flow dominates electrophoresis and magnetism by a factor of ∼100 in the narrowest part of the pore, but that magnetic force should dominate further than ∼1 mm from the membrane. As expected, the observed resistive pulse rate falls as the magnet is moved closer to the pore, while the increase in pulse duration suggests that trajectories in the half space adjacent to the pore opening are important. Aggregation was not observed, consistent with the high hydrodynamic shear near the pore constriction and the high magnetization of aggregates. The theoretical approach is also used to calculate the relative importance of transport mechanisms over a range of geometries and experimental conditions extending well beyond our own experiments. TRPS is emerging as a versatile form of resistive pulse sensing, while magnetic beads are widely used in biotechnology and sensing applications.