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.

Functionalized nanopores based on hybridization chain reaction: Fabrication and microRNA sensing

Enzyme-free hybridization chain reaction (HCR) technology is often used as a signal amplification tool for the detection of different targets. In this study, an ultrasensitive and label-free method for detecting miRNA-21 was developed using the nanopore ionic current rectification (ICR) technology coupled with HCR technology. The probe oligonucleotide (DNA1) was combined with the gold-coated nanopore through the Au-S bond to form a DNA1-functionalized gold-coated nanopore (DNA1-Au-coated nanopore). Since miRNA-21 is partially complementary to DNA1, it can be selectively recognized by DNA1-functionalized gold-coated nanopores. The target (miRNA-21) can induce the opening of hairpin DNA and HCR reaction after the introduction of hairpin DNA H1 and H2. The concentration of miRNA-21 will affect the combination of H1 and H2 on the inner wall of the nanopore, and its surface charge will change with the internal modification, thereby changing the ion current rectification ratio. Under the condition that the concentration of H1, H2 and HCR reaction time are constant, the change of ICR ratio is linearly correlated with the logarithm of miRNA-21 concentration within a certain range, which shows that the sensing strategy we designed can achieve target miRNA-21 detection. This ultrasensitive miRNA holds great promise in the field of cancer diagnosis.

Metal-Organic Framework Sub-Nanochannels Formed inside Solid-State Nanopore with Proton Ultra-High Selectivity

Metal-Organic frameworks (MOFs) have the advantages of high porosity, angstrom-scale pore size, and unique structure. In this work, a kind of MOFs, UiO-66 and its derivatives (including aminated UiO-66-(NH2 )2 and sulfonated UiO-66-(NH-SAG)2 ), were constructed on the inner surface of solid-state nanopores for ultra-selective proton transport. UiO-66 and UiO-66-(NH2 )2 nanocrystal particles were in-situ grown at the orifice of glass nanopores firstly, which were used to investigate the ionic current responses in LiCl and HCl solutions when the monovalent anions (Cl- ) were unchanged. Compared with UiO-66-modifed nanopores, the aminated MOFs modification (UiO-66-(NH2 )2 ) can improve the proton selectivity obviously. However, when the UiO-66-(NH-SAG)2 nanopore is prepared by further post-modification with sulfo-acetic acid, lithium ions can hardly pass through the channel, and the interaction between protons and sulfonic acid groups can promote the transport of protons, thus achieving ultra-high selectivity to protons. This work provides a new way to achieve sub-nanochannels with high selectivity, which can widely be used in ion separation, sensing and energy conversion.

An ultrasensitive aptasensor of SARS-CoV-2 N protein based on ion current rectification with nanopipettes

Since the outbreak of COVID-19 in the world, it has spread rapidly all over the world. Rapid and effective detection methods have been a focus of research. The SARS-CoV-2 N protein (NP) detection methods currently in use focus on specific recognition of antibodies, but the reagents are expensive and difficult to be produced. Here, aptamer-functionalized nanopipettes utilize the unique ion current rectification (ICR) of nanopipette to achieve rapid and highly sensitive detection of trace NP, and can significantly reduce the cost of NP detection. In the presence of NP, the surface charge at the tip of the nanopipette changes, which affects ion transport and changes the degree of rectification. Quantitative detection of NP is achieved through quantitative analysis. Relying on the high sensitivity of nanopipettes to charge fluctuations, this sensor platform achieves excellent sensing performance. The sensor platform exhibited a dynamic working range from 10²-10⁶ pg/mL with a detection limit of 73.204 pg/mL, which showed great potential as a tool for rapidly detecting SARS-CoV-2. As parallel and serial testing are widely used in the clinic to avoid missed diagnosis or misdiagnosis, we hope this platform can play a role in controlling the spread and prevention of COVID-19.

Single-Molecule Investigation of the Protein-Aptamer Interactions and Sensing Application Inside the Single Glass Nanopore

Solid-state nanopores offer a nanoconfined space for a single-molecule sensing strategy. Evaluating the behavior of proteins and protein-related interactions at the single-molecule level is becoming more and more important for a better understanding of biological processes and diseases. In this work, the aptamer-functionalized nanopore was prepared as the sensing platform for kinetic analysis of the carcinoembryonic antigen (CEA) with its aptamers, which is an important cancer biomarker. CEA molecules were captured by the aptamers immobilized on the inner surface of the nanopore, and there was a complicated interaction between the CEA molecules and the aptamer, which is the process of association and dissociation. This could be used to measure the dynamics of aptamer-protein interactions without labeling. The kinetic analysis could be evaluated at the single-molecule level to interpret the dissociation constants of the binding and dissociation processes. Results showed that the translocation of CEA molecules in a functionalized nanopore had a deep blockades degree and long duration compared with nanopore modified with bare gold, which could be used for CEA sensing. This protein and protein-related interaction we designed provides new insights for evaluating the binding affinity, which will be beneficial for protein sensing and immunoassays.

Nanopore-Based Single-Entity Electrochemistry for the Label-Free Monitoring of Single-Molecule Glycoprotein-Boronate Affinity Interaction and Its Sensing Application

Nanopipettes provide a promising confined space that enables advances in single-molecule analysis, and their unique conical tubular structure is also suitable for single-cell analysis. In this work, functionalized-nanopore-based single-entity electrochemistry (SEE) analysis tools were developed for the label-free monitoring of single-molecule glycoprotein-boronate affinity interaction for the first time, and immunoglobulin G (IgG, one of the important biomarkers for many diseases such as COVID-19 and cancers) was employed as the model glycoprotein. The principle of this method is based on a single glycoprotein molecule passing through 4-mercaptophenylboronic acid (4-MPBA)-modified nanopipettes under a bias voltage and in the meantime interacting with the boronate group from modified 4-MPBA. This translocation and affinity interaction process can generate distinguishable current blockade signals. Based on the statistical analysis of these signals, the equilibrium association constant (κ_a) of single-molecule glycoprotein-boronate affinity interaction was obtained. The results show that the κ_a of IgG in the confined nanopore at the single-molecule level is much larger than that measured in the open system at the ensemble level, which is possibly due to the enhanced multivalent synergistic binding in the restricted space. Moreover, the functionalized-nanopore-based SEE analysis tools were further applied for the label-free detection of IgG, and the results indicate that our method has potential application value for the detection of glycoproteins in real samples, which also paves way for the single-cell analysis of glycoproteins.

Confined Synthesis of Silver Wire at the Nanopipette-Liquid/Liquid Interface

Herein, silver wire is synthesized electrochemically within a nanopipette using the nanopipette-liquid/liquid interface. The i-t curve characterizes the growth state of the silver wire. The higher rate of current increase indicates the faster electron transfer and the faster growth of the silver wire; conversely, when the current does not increase significantly with time, i.e., the rate of increase of the current is small, the growth rate of the silver wire is slow. The main driving force for the growth of silver into a linear structure is the theoretical current differential between the water and oil, caused by the concentration difference between the silver nitrate and ferrocene. The growth of the silver wire is also influenced by the shape of the nanopipette. If the diameter of the pipet increases quickly, silver wire tends to produce multibranched structures, while a smaller diameter makes it easier to obtain silver wire with fewer branches due to the confinement effect. This method is also applicable to the synthesis of gold within a nanopipette. The combination of nanopipette and metallic material using a liquid-liquid interface results in a broader application of nanopipettes for nanopore sensors, nanopore electrodes, bipolar electrodes, etc.

Acceleration of DNA Hybridization Chain Reactions on 3D Nanointerfaces of Magnetic Particles and Their Direct Application in the Enzyme-Free Amplified Detection of microRNA

Accelerated DNA hybridization chain reactions (HCRs) using DNA origami as a scaffold have received considerable attention in dynamic DNA nanotechnology. However, tailor-made designs are essential for DNA origami scaffolds, hampering the practical application of accelerated HCRs. Here, we constructed the semilocalized HCR and localized HCR systems using magnetic beads (MBs) as a simple scaffold to explore them for the enzyme-free miR-21 detection. The semilocalized HCR system relied on free diffusing one hairpin DNA and MBs immobilized with another hairpin DNA, and the localized HCR system relied on MBs coimmobilized with two hairpin DNAs. We demonstrated that the DNA density on MBs plays a critical role in HCR kinetics and limit of detection (LOD). Among semilocalized HCR systems, MBs with a medium DNA density showed a faster HCR and lower LOD (10 pM) than the diffusive (conventional) HCR system (LOD: 86 pM). In contrast, the HCR further accelerated for the localized HCR systems as the DNA density increased. The localized HCR system with the highest DNA density showed the fastest HCR and the lowest LOD (533 fM). These findings are of great importance for the rational design of accelerated HCRs using simple scaffolds for practical applications.

Single gold nanoclusters: Formation and sensing application for isonicotinic acid hydrazide detection

Nano-sized electrodes have their special advantages for sensing applications, such as small overall dimension, fast response and low background current. In this work, single gold nanoclusters (AuNCs) were controllably prepared on single Pt nanoelectrode surface by electrodeposition method. The AuNCs covered Pt nanoelectrode (AuNCs/PtNE) had steady-state voltammetric response in redox species solution, which was similar to micro-/nano-sized electrodes. It was interesting to find isonicotinic acid hydrazide (INH, also known as isoniazid) showed good electrochemical response on AuNCs/PtNE surface, which had investigated carefully by square wave voltammetry (SWV) and chronoamperometry. Moreover, the prepared single AuNCs/PtNEs showed the capability for INH sensing with good sensitivity, reproducibility and selectivity, which was demonstrated for INH detection in human urine samples.

Analytes Triggered Conformational Switch of i-Motif DNA inside Gold-Decorated Solid-State Nanopores

The nanopore-based technique is a useful tool for single-molecule sensing and characterization. In this work, we have developed a new DNA-functionalized gold-modified nanopore, and analytes can induce the conformational switch of i-motif DNA formed on the inner surface of the nanopore. i-Motif DNA structure can be formed in the presence of silver ions (Ag⁺), which will result in the change in surface charge and structure of the nanopore tip and ion current rectification (ICR) ratio. The i-motif DNA structure on nanopore surface will be destroyed after the addition of glutathione (GSH) due to the strong interaction of Ag-S bond, which results in the recovery of surface charge, steric hindrance, and ICR ratio. This analyte-triggered conformational switch of i-motif DNA can help us deeply understand the DNA technology inside single nanopore and will benefit the possible applications in an ultrasensitive detection and biological/chemical analysis.

Simple Single-Legged DNA Walkers at Diffusion-Limited Nanointerfaces of Gold Nanoparticles Driven by a DNA Circuit Mechanism

We designed and prepared a single-legged DNA walker that relies on the creation of a simple diffusion-limited nanointerface on a gold nanoparticle (DNA/PEG⁽⁺⁾-GNP) track co-modified with fluorescence-labeled hairpin DNA and poly(ethylene glycol) (PEG) containing a positively charged amino group at one end. The movement of our single-legged DNA walker is driven by an enzyme-free DNA circuit mechanism through cascading toehold mediated DNA displacement reactions (TMDRs) using fuel hairpin DNAs. The acceleration of TMDRs was observed for the DNA/PEG⁽⁺⁾-GNP track through electrostatic interaction between the positively charged track and negatively charged DNAs, resulting in the acceleration of the DNA circuit and amplification of the fluorescence signal. Furthermore, the DNA/PEG⁽⁺⁾-GNP track allowed autonomous and persistent movement of a walker DNA strand on the same GNP track, because the intraparticle DNA circuit occurred preferentially by preventing diffusion of the negatively charged free walker DNA strand from near the positively charged tracks into solution through electrostatic interaction. Based on comparative study of kinetics of TMDRs and DNA walking behaviors, it is to be noted that the DNA/PEG⁽⁺⁾-GNP track showed the fastest DNA circuit reaction (walking rate) and the largest number of steps taken by the walker DNA strand compared to other GNP tracks with varying nanointerfaces that differ in terms of their type of charges (no and negative charges), density of positive charges, and number of hairpin DNAs per GNP track. These facts reveal that the positive charges on the GNP track play an important role in the acceleration of the DNA circuit, as well as the successful walking motion of the single-legged DNA strand. By using the fluorescence signal amplification functions, our single-legged DNA walker could be applied directly and successfully to enzyme-free miRNA-detection systems. The miRNA-detection system provided higher discrimination of other mismatched miRNAs and higher sensitivity (the lowest LOD: 4.0 pM) when compared to other miRNA-detection systems based on other GNP tracks without positive charges. Unlike existing single-legged DNA walkers, our single-legged DNA walkers do not require complex processes, such as immobilization of the walker DNA strand on the tracks and precise adjustment of the sequence of walker DNA. Therefore, our strategy, based on the creation of diffusion-limited nanointerfaces, has enormous potential for the applications of single-legged DNA walkers to biosensors, bioimaging, and computing.