Nanopore detection of metal ions: Current status and future directions

A highly sensitive nanopore platform for measuring RNase A activity

Ribonuclease A (RNase A) plays significant roles in several physiological and pathological conditions and can be used as a valuable diagnostic biomarker for human diseases such as myocardial infarction and cancer. Hence, it is of great importance to develop a rapid and cost-effective method for the highly sensitive detection of RNase A. The significance of RNase A assay is further enhanced by the growing attention from the biotechnology and pharmaceutical industries to develop RNA-based vaccines and drugs in large part as a result of the successful development of mRNA vaccines in the COVID-19 pandemic. Herein, we report a label-free method for the detection of RNase A by monitoring its proteolytic cleavage of an RNA substrate in a nanopore. The method is ultra-sensitive with the limit of detection reaching as low as 30 fg per milliliter. Furthermore, sensor selectivity and the effects of temperature, incubation time, metal ion, salt concentration on sensor sensitivity were also investigated.

Ion detection in a DNA nanopore FET device

An ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine sensitivity of the nanodevice to the local cellular environment. Such devices could be integrated into a live cell, creating an abiotic-biotic interface integrated with semiconductor electronics. A continuum model is used to describe the behavior of ions in an electrolyte solution. The drift-diffusion equations are employed to model the ion distribution, taking into account the electric fields and concentration gradients. This was matched to the results from electric double layer theory to verify applicability of the model to a bio-sensing environment. The FET device combined with the nanopore is shown to have high sensitivity to ion concentration and nanopore geometry, with the electrical double layer behavior governing the device characteristics. A logarithmic relationship was found between ion concentration and a single FET current, generating up to 200 nA of current difference with a small applied bias.

Nanopore-based glycan sequencing: state of the art and future prospects

Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.

Probe-assisted detection of Fe3+ ions in a multi-functionalized nanopore

Iron is an essential element that plays critical roles in many biological/metabolic processes, ranging from oxygen transport, mitochondrial respiration, to host defense and cell signaling. Maintaining an appropriate iron level in the body is vital to the human health. Iron deficiency or overload can cause life-threatening conditions. Thus, developing a new, rapid, cost-effective, and easy to use method for iron detection is significant not only for environmental monitoring but also for disease prevention. In this study, we report an innovative Fe3+ detection strategy by using both a ligand probe and an engineered nanopore with two binding sites. In our design, one binding site of the nanopore has a strong interaction with the ligand probe, while the other is more selective toward interfering species. Based on the difference in the number of ligand DTPMPA events in the absence and presence of ferric ions, micromolar concentrations of Fe3+ could be detected within minutes. Our method is selective: micromolar concentrations of Mg2+, Ca2+, Cd2+, Zn2+, Ni2+, Co2+, Mn2+, and Cu2+ would not interfere with the detection of ferric ions. Furthermore, Cu2+, Ni2+, Co2+, Zn2+, and Mn2+ produced current blockage events with quite different signatures from each other, enabling their simultaneous detection. In addition, simulated water and serum samples were successfully analyzed. The nanopore sensing strategy developed in this work should find useful application in the development of stochastic sensors for other substances, especially in situations where multi-analyte concurrent detection is desired.

Protein Deceleration and Sequencing Using Si3N4-CNT Hybrid Nanopores

Protein sequencing is crucial for understanding the complex mechanisms driving biological functions and is of utmost importance in molecular diagnostics and medication development. Nanopores have become an effective tool for single molecule sensing, however, the weak charge and non-uniform charge distribution of protein make capturing and sensing very challenging, which poses a significant obstacle to the development of nanopore-based protein sequencing. In this study, to facilitate capturing of the unfolded protein, highly charged peptide was employed in our simulations, we found that the velocity of unfolded peptide translocating through a hybrid nanopore composed of silicon nitride membrane and carbon nanotube is much slower compared to bare silicon nitride nanopore, it is due to the significant interaction between amino acids and the surface of carbon nanotube. Moreover, by introducing variations in the charge states at the boundaries of carbon nanotube nanopores, the competition and combination of the electrophoretic and electroosmotic flows through the nanopores could be controlled, we then successfully regulated the translocation velocity of unfolded proteins through the hybrid nanopores. The proposed hybrid nanopore effectively retards the translocation velocity of protein through it, facilitates the acquisition of ample information for accurate amino acid identification.

Ion transport in nanofluidics under external fields

Nanofluidic channels with tailored ion transport dynamics are usually used as channels for ion transport, to enable high-performance ion regulation behaviors. The rational construction of nanofluidics and the introduction of external fields are of vital significance to the advancement and development of these ion transport properties. Focusing on the recent advances of nanofluidics, in this review, various dimensional nanomaterials and their derived homogeneous/heterogeneous nanofluidics are first briefly introduced. Then we discuss the basic principles and properties of ion transport in nanofluidics. As the major part of this review, we focus on recent progress in ion transport in nanofluidics regulated by external physical fields (electric field, light, heat, pressure, etc.) and chemical fields (pH, concentration gradient, chemical reaction, etc.), and reveal the advantages and ion regulation mechanisms of each type. Moreover, the representative applications of these nanofluidic channels in sensing, ionic devices, energy conversion, and other areas are summarized. Finally, the major challenges that need to be addressed in this research field and the future perspective of nanofluidics development and practical applications are briefly illustrated.

Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates

Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.

Regenerable and Highly Stable Two-Dimensional Imine-Based Covalent Organic Framework for Simultaneous Rapid Detection and Adsorption of Cu2+ Ions

The development of efficient fluorescent probes and adsorbents for detecting and removing Cu2+, which pose potential environmental and health risks, is a highly active area of research. However, achieving simultaneously improved fluorescence detection efficiency and enhanced adsorption capacity in a single porous probe remains a significant challenge. In this study, we successfully synthesized a two-dimensional imine-based TAP-COF using 2,4,6-triformylphloroglucinol and tri(4-aminophenyl)amine as raw materials. TAP-COF exhibited excellent properties, including a large specific surface area of 685.65 m2·g-1, exceptional thermal stability (>440 °C), chemical stability, temporal stability, and recyclability. Fluorescence testing revealed that TAP-COF exhibited remarkable specificity and high sensitivity for detecting Cu2+. The fluorescence mechanism, in which the excited state intramolecular proton transfer was impeded by the interaction of Cu2+ with C═O and C-N bonds on TAP-COF upon the addition of Cu2+, was further elucidated through experimental and theoretical methods. Furthermore, the adsorption capacity of TAP-COF toward Cu2+ was investigated, confirming the excellence of TAP-COF as a fluorescent probe and adsorbent for the specific detection and removal of Cu2+. This work holds significant implications for improving environmental and human health concerns associated with Cu2+ contamination.

Direct Determination of the Structure of Single Biopolymer Molecules Using Nanopore Sequencing

This review highlights operational principles, features, and modern aspects of the development of third-generation sequencing technology of biopolymers focusing on the nucleic acids analysis, namely the nanopore sequencing system. Basics of the method and technical solutions used for its realization are considered, from the first works showing the possibility of creation of these systems to the easy-to-handle procedure developed by Oxford Nanopore Technologies company. Moreover, this review focuses on applications, which were developed and realized using equipment developed by the Oxford Nanopore Technologies, including assembly of whole genomes, methagenomics, direct analysis of the presence of modified bases.

Confirming Silent Translocation through Nanopores with Simultaneous Single-Molecule Fluorescence and Single-Channel Electrical Recordings

Most of what is known concerning the luminal passage of materials through nanopores arises from electrical measurements. Whether nanopores are biological, solid-state, synthetic, hybrid, glass-capillary-based, or protein ion channels in cells and tissues, characteristic signatures embedded in the flow of ionic current are foundational to understanding functional behavior. In contrast, this work describes passage through a nanopore that occurs without producing an electrical signature. We refer to the phenomenon as "silent translocation." By definition, silent translocations are invisible to the standard tools of electrophysiology and fundamentally require a simultaneous ancillary measurement technique for positive identification. As a result, this phenomenon has been largely unexplored in the literature. Here, we report on a derivative of Cyanine 5 (sCy5a) that passes through the α-hemolysin (αHL) nanopore silently. Simultaneously acquired single-molecule fluorescence and single-channel electrical recordings from bilayers formed over a closed microcavity demonstrate that translocation does indeed take place, albeit infrequently. We report observations of silent translocation as a function of time, dye concentration, and nanopore population in the bilayer. Lastly, measurement of the translocation rate as a function of applied potential permits estimation of an effective energy barrier for transport through the pore as well as the effective charge on the dye, all in the absence of an information-containing electrical signature.

Nanopore discrimination and sensitive plasma detection of multiple natriuretic peptides: The representative biomarker of human heart failure

Natriuretic peptides can relieve cardiovascular stress and closely related to heart failure. Besides, these peptides also have preferable interactions of binding to cellular protein receptors, and subsequently mediate various physiology actions. Hence, detection of these circulating biomarkers could be evaluated as a predictor ("Gold standard") for rapid, early diagnosis and risk stratification in heart failure. Herein, we proposed a measurement to discriminate multiple natriuretic peptides via the peptide-protein nanopore interaction. The nanopore single-molecular kinetics revealed that the strength of peptide-protein interactions was in the order of ANP > CNP > BNP, which was demonstrated by the simulated peptide structures using SWISS-MODEL. More importantly, the peptide-protein interaction analyzing also allowed us to measure the peptide linear analogs and structure damage in peptide by single-chemical bond breakup. Finally, we presented an ultra-sensitive detection of plasma natriuretic peptide using asymmetric electrolyte assay, obtaining a detection limit of ∼770 fM for BNP. At approximately, it is 1597 times lower than that of using symmetric assay (∼1.23 nM), 8 times lower than normal human level (∼6 pM), and 13 times lower than the diagnostic values (∼10.09 pM) complied in the guideline of European Society of Cardiology. That said, the designed nanopore sensor is benefit for natriuretic peptides measurement at single molecule level and demonstrates its potential for heart failure diagnosis.

Recent Advances in Nanopore Technology for Copper Detection and Their Potential Applications

Recently, nanopore technology has emerged as a promising technique for the rapid, sensitive, and selective detection of various analytes. In particular, the use of nanopores for the detection of copper ions has attracted considerable attention due to their high sensitivity and selectivity. This review discusses the principles of nanopore technology and its advantages over conventional techniques for copper detection. It covers the different types of nanopores used for copper detection, including biological and synthetic nanopores, and the various mechanisms used to detect copper ions. Furthermore, this review provides an overview of the recent advancements in nanopore technology for copper detection, including the development of new nanopore materials, improvements in signal amplification, and the integration of nanopore technology with other analytical methods for enhanced detection sensitivity and accuracy. Finally, we summarize the extensive applications, current challenges, and future perspectives of using nanopore technology for copper detection, highlighting the need for further research in the field to optimize the performance and applicability of the technique.

Proton conducting metal-organic frameworks with light response for multistate logic gates

The simulation of neurons receiving stimulation and transmitting signals by proton conduction has great potential applications in electrochemistry and biology. In this work, copper tetrakis(4-carboxyphenyl)porphyrin (Cu-TCPP), which is a proton conductive metal organic framework (MOF) with photothermal response, is adopted as the structural framework, with the in situ co-incorporation of polystyrene sulfonate (PSS) and sulfonated spiropyran (SSP) to prepare the composite membranes. The resultant PSS-SSP@Cu-TCPP thin-film membranes were used as the logic gates i.e., NO gate, NOR gate and NAND gate because of the photothermal effect of Cu-TCPP MOFs and the photoinduced conformational changes of SSP. This membrane exhibits the high proton conductivity of 1.37 × 10^-4 S cm^-1. Under the conditions of 55 °C and 95% relative humidity (RH), using 405 nm laser irradiation with 400 mW cm^-2 and 520 nm laser irradiation with 200 mW cm^-2 as inputs, the device can be adjusted between various steady states, and the value of the conductivity is regarded as the output with different thresholds in different logic gates. Before and after laser irradiation, the electrical conductivity changes dramatically, and the ON/OFF switching ratio reached 1068. The application of three logic gates is realized by constructing circuits with LED lights. Depending on the convenience of light and the easy measurement of conductivity, this kind of device with light source as input and electrical signal as output provides the possibility to realize the remote control of chemical sensors and complex logic gates devices.

Fluids and Electrolytes under Confinement in Single-Digit Nanopores

Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification to new gas permeable materials for water electrolyzers and energy-storage devices. SDNs also present unique opportunities to achieve ultrasensitive and selective chemical sensing at the single-ion and single-molecule limit. In this review article, we summarize the progress on nanofluidics of SDNs, with a focus on the confinement effects that arise in these extremely narrow nanopores. The recent development of precision model systems, transformative experimental tools, and multiscale theories that have played enabling roles in advancing this frontier are reviewed. We also identify new knowledge gaps in our understanding of nanofluidic transport and provide an outlook for the future challenges and opportunities at this rapidly advancing frontier.

Solid-State Nanopore Array: Manufacturing and Applications

Nanopore brings extraordinary properties for a variety of potential applications in various industrial sectors. Since manufacturing of solid-state nanopore is first reported in 2001, solid-state nanopore has become a hot topic in the recent years. An increasing number of manufacturing methods have been reported, with continuously decreased sizes from hundreds of nanometers at the beginning to ≈1 nm until recently. To enable more robust, sensitive, and reliable devices required by the industry, researchers have started to explore the possible methods to manufacture nanopore array which presents unprecedented challenges on the fabrication efficiency, accuracy and repeatability, applicable materials, and cost. As a result, the exploration of fabrication of nanopore array is still in the fledging period with various bottlenecks. In this article, a wide range of methods of manufacturing nanopores are summarized along with their achievable morphologies, sizes, inner structures for characterizing the main features, based on which the manufacturing of nanopore array is further addressed. To give a more specific idea on the potential applications of nanopore array, some representative practices are introduced such as DNA/RNA sequencing, energy conversion and storage, water desalination, nanosensors, nanoreactors, and dialysis.

Fully inkjet-printed paper-based Pb2+ optodes for water analysis without interference from the chloramine disinfectant

We developed a paper-based colorimetric sensor for facile and cost-effective detection of Pb²⁺ in drinking and environmental water samples. The Pb²⁺ ion-selective optodes are fabricated by inkjet printing of ionophore, chromoionophore, and ion exchanger on cellulose paper. Pb²⁺ in water samples induces deprotonation of the pH chromoionophore and changes the optode color, which is acquired and analyzed by a smartphone. The paper-based optode without any plasticizer or polymer has a dynamic range and selectivity comparable to those of traditional optodes using PVC polymer and/or plasticizer. Furthermore, the response time of the plasticizer/polymer-free paper-based optode is much shorter than those of plasticized PVC-based optodes on paper and glass (5 min vs. 15 and 50 min). Moreover, the plasticizer/polymer-free optode preserves the water-wicking capability of porous cellulose paper, allowing for the design of pump-free microfluidic devices. Chloramine, a widely used disinfectant in drinking water, was found to be a strong and generic interference species for heavy metal ion detection via ion-selective optodes. A fully inkjet-printed lateral-flow paper-based device consisting of a sodium thiosulfate-based chloramine elimination zone and a plasticizer/polymer-free sensing zone was designed for Pb²⁺ detection in tap water disinfected by chloramine. The dynamic range of the Pb²⁺ sensor may be shifted from the current 10^-6 to 10^-5 M to lower concentrations by using stronger ionophores, but this work lays a foundation for the design of paper-based heavy metal ion sensors without detrimental interference from disinfectants.

Aerolysin nanopore-based identification of proteinogenic amino acids using a bipolar peptide probe

Nanopore technology has attracted extensive attention due to its rapid, highly sensitive, and label-free performance. In this study, we aimed to identify proteinogenic amino acids using a wild-type aerolysin nanopore. Specifically, bipolar peptide probes were synthesised by linking four aspartic acid residues to the N-terminal and five arginine residues to the C-terminal of individual amino acids. With the help of the bipolar peptide carrier, 9 proteinogenic amino acids were reliably recognised based on current blockade and dwell time using an aerolysin nanopore. Furthermore, by changing the charge of the peptide probe, two of the five unrecognized amino acids above mentioned were identified. These findings promoted the application of aerolysin nanopores in proteinogenic amino acid recognition.

Nanopore Detection Assisted DNA Information Processing

The deoxyribonucleotide (DNA) molecule is a stable carrier for large amounts of genetic information and provides an ideal storage medium for next-generation information processing technologies. Technologies that process DNA information, representing a cross-disciplinary integration of biology and computer techniques, have become attractive substitutes for technologies that process electronic information alone. The detailed applications of DNA technologies can be divided into three components: storage, computing, and self-assembly. The quality of DNA information processing relies on the accuracy of DNA reading. Nanopore detection allows researchers to accurately sequence nucleotides and is thus widely used to read DNA. In this paper, we introduce the principles and development history of nanopore detection and conduct a systematic review of recent developments and specific applications in DNA information processing involving nanopore detection and nanopore-based storage. We also discuss the potential of artificial intelligence in nanopore detection and DNA information processing. This work not only provides new avenues for future nanopore detection development, but also offers a foundation for the construction of more advanced DNA information processing technologies.

Nanopore Identification of Alditol Epimers and Their Application in Rapid Analysis of Alditol-Containing Drinks and Healthcare Products

Alditols, which have a sweet taste but produce much lower calories than natural sugars, are widely used as artificial sweeteners. Alditols are the reduced forms of monosaccharide aldoses, and different alditols are diastereomers or epimers of each other and direct and rapid identification by conventional methods is difficult. Nanopores, which are emerging single-molecule sensors with exceptional resolution when engineered appropriately, are useful for the recognition of diastereomers and epimers. In this work, direct distinguishing of alditols corresponding to all 15 monosaccharide aldoses was achieved by a boronic acid-appended hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore (MspA-PBA). Thirteen alditols including glycerol, erythritol, threitol, adonitol, arabitol, xylitol, mannitol, sorbitol, allitol, dulcitol, iditol, talitol, and gulitol (l-sorbitol) could be fully distinguished, and their sensing features constitute a complete nanopore alditol database. To automate event classification, a custom machine-learning algorithm was developed and delivered a 99.9% validation accuracy. This strategy was also used to identify alditol components in commercially available "zero-sugar" drinks and healthcare products, suggesting their use in rapid and sensitive quality control for the food and medical industry.

Simultaneous Dual-Site Identification of 5mC/8oG in DNA Triplex Using a Nanopore Sensor

DNA triplex participates in delivering site-specific epigenetic modifications critical for the regulation of gene expression. Among these marks, 5mC with 8oG functions comprehensively on gene expression. Recently, few research studies have emphasized the necessity of incorporation detection of 5mC with 8oG using one DNA triplex at the same time. Herein, DNA triplex structure was designed and tailored for the site-specific identification of 5mC with 8oG by means of nanopore electroanalysis. The identification was associated with the distinguishable current modulation types caused by DNA unzipping through the nanopore in an electrical field. Results demonstrated that the epigenetic modification proximity to the latch zone or constriction area of the nanopore enables differentiation of modification series at single nucleotide resolution in one DNA triplex, at both physiological and mildly acidic environment. In addition, our nanopore method enables the kinetic and thermodynamic studies to calculate the free energy of modified DNA triplex with applied potentials. Gibbs' energy provided the direct evidence that the DNA triplex with these epigenetic modifications is more stable in acidic environment. Considering modified DNA functions significantly in gene expression, the presented method may provide future opportunities to understand incorporating epigenetic mechanisms of many dysregulated biological processes on the basis of accurate detection.

Chemistry solutions to facilitate nanopore detection and analysis

Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.

Photoresponsive Solid Nanochannels Membranes: Design and Applications

Light stimuli have notable advantages over other environmental stimuli, such as more precise spatial and temporal regulation, and the ability to serve as an energy source to power the system. In nature, photoresponsive nanochannels are important components of organisms, with examples including the rhodopsin channels in optic nerve cells and photoresponsive protein channels in the photosynthesis system of plants. Inspired by biological channels, scientists have constructed various photoresponsive, smart solid-state nanochannels membranes for a range of applications. In this review, the methods and applications of photosensitive nanochannels membranes are summarized. The authors believe that this review will inspire researchers to further develop multifunctional artificial nanochannels for applications in the fields of biosensors, stimuli-responsive smart devices, and nanofluidic devices, among others.

Recent Progress on Single-Molecule Detection Technologies for Food Safety

Rapid and sensitive detection technologies for food contaminants play vital roles in food safety. Due to the complexity of the food matrix and the trace amount distribution, traditional methods often suffer from unsatisfying accuracy, sensitivity, or specificity. In past decades, single-molecule detection (SMD) has emerged as a way to realize the rapid and ultrasensitive measurement with low sample consumption, showing a great potential in food contaminants detection. For instance, based on the nanopore technique, simple and effective methods for single-molecule analysis of food contaminants have been developed. To our knowledge, there has been a rare review that focuses on SMD techniques for food safety. The present review attempts to cover some typical SMD methods in food safety, including electrochemistry, optical spectrum, and atom force microscopy. Then, recent applications of these techniques for detecting food contaminants such as biotoxins, pesticides, heavy metals, and illegal additives are reviewed. Finally, existing research challenges and future trends of SMD in food safety are also tentatively proposed.

Nanopore detects γ-radiation inhibited HIV-1 protease activity

Inhibition of HIV-1 protease (PR) activity is realized by exposure to ⁶⁰Co γ-radiation. The radiation effects on enzyme kinetics of HIV-1 PR are subsequently monitored using nanopore sensor. Substantial loss of proteolytic efficiency towards GagPol polypeptide is observed due to the radiation treatment. Results shows ~50% of GagPol polypeptide was not involved in HIV-1 PR proteolysis by exposure to ultra-low intensity of γ-radiation (0.1K Gy), and the values reach to over 90% with high γ-ray treatment. Besides, the inactivation effect is also verified in blood samples which contain the virus protease. Our finding provides the potential benefits of γ-radiation to inactivate viral proteinic function, and might be a complementary to the designation of HIV-1 PR inhibitors.

Nanopore sensors for viral particle quantification: current progress and future prospects

Rapid, inexpensive, and laboratory-free diagnostic of viral pathogens is highly critical in controlling viral pandemics. In recent years, nanopore-based sensors have been employed to detect, identify, and classify virus particles. By tracing ionic current containing target molecules across nano-scale pores, nanopore sensors can recognize the target molecules at the single-molecule level. In the case of viruses, they enable discrimination of individual viruses and obtaining important information on the physical and chemical properties of viral particles. Despite classical benchtop virus detection methods, such as amplification techniques (e.g., PCR) or immunological assays (e.g., ELISA), that are mainly laboratory-based, expensive and time-consuming, nanopore-based sensing methods can enable low-cost and real-time point-of-care (PoC) and point-of-need (PoN) monitoring of target viruses. This review discusses the limitations of classical virus detection methods in PoN virus monitoring and then provides a comprehensive overview of nanopore sensing technology and its emerging applications in quantifying virus particles and classifying virus sub-types. Afterward, it discusses the recent progress in the field of nanopore sensing, including integrating nanopore sensors with microfabrication technology, microfluidics and artificial intelligence, which have been demonstrated to be promising in developing the next generation of low-cost and portable biosensors for the sensitive recognition of viruses and emerging pathogens.

A Microfluidic Aptamer-Based Sensor for Detection of Mercury(II) and Lead(II) Ions in Water

Heavy metal contaminants have serious consequences for the environment and human health. Consequently, effective methods for detecting their presence, particularly in water and food, are urgently required. Accordingly, the present study proposes a sensor capable of detecting mercury Hg(II) and lead Pb(II) ions simultaneously, using graphene oxide (GO) as a quenching agent and an aptamer solution as a reagent. In the proposed device, the aptamer sequences are labeled by FAM and HEX fluorescent dyes, respectively, and are mixed well with 500 ppm GO solution before injection into one inlet of the microchannel, and the heavy metal sample solution is injected into another inlet. The presence of Hg(II) and Pb(II) ions is then detected by measuring the change in the fluorescence intensity of the GO/aptamer suspension as the aptamer molecules undergo fluorescence resonance energy transfer (FRET). The selectivity of these two ions is also shown to be clear among other mixed heavy metal ions. The experimental results show that the aptamer sensors have a linear range of 10~250 nM (i.e., 2.0~50 ppb) for Hg(II) ions and 10~100 nM (i.e., 2.1~20.7 ppb) for Pb(II) ions. Furthermore, the limit of detection is around 0.70 ppb and 0.53 ppb for Hg(II) and Pb(II), respectively, which is lower than the maximum limits of 6 ppb and 10 ppb prescribed by the World Health Organization (WHO) for Hg(II) and Pb(II) in drinking water, respectively.

Nanoparticle-assisted detection of nucleic acids in a polymeric nanopore with a large pore size

Rapid and accurate detection of nucleic acids is of paramount importance in many fields, including medical diagnosis, gene therapy and virus identification. In this work, by taking advantage of two DNA hybridization probes, one of which was immobilized on the surface of gold nanoparticles, while the other was free in solution, detection of short length nucleic acids was successfully achieved using a large size (20 nm tip diameter) polyethylene terephythalate (PET) nanopore. The sensor was sensitive and selective: DNA samples with concentrations at as low as 0.5 nM could be detected within minutes and the number of mismatches can be discerned from the translocation frequency. Furthermore, the nanopore can be repeatedly used many times. Our developed large-size nanopore sensing platform offers the potential for fieldable/point-of-care diagnostic applications.

Programmable nano-reactors for stochastic sensing

Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.

Bioinspired Solid-State Nanochannel Sensors: From Ionic Current Signals, Current, and Fluorescence Dual Signals to Faraday Current Signals

Inspired from bioprotein channels of living organisms, constructing "abiotic" analogues, solid-state nanochannels, to achieve "smart" sensing towards various targets, is highly seductive. When encountered with certain stimuli, dynamic switch of terminal modified probes in terms of surface charge, conformation, fluorescence property, electric potential as well as wettability can be monitored via transmembrane ionic current, fluorescence intensity, faraday current signals of nanochannels and so on. Herein, the modification methodologies of nanochannels and targets-detecting application are summarized in ions, small molecules, as well as biomolecules, and systematically reviewed are the nanochannel-based detection means including 1) by transmembrane current signals; 2) by the coordination of current- and fluorescence-dual signals; 3) by faraday current signals from nanochannel-based electrode. The coordination of current and fluorescence dual signals offers great benefits for synchronous temporal and spatial monitoring. Faraday signals enable the nanoelectrode to monitor both redox and non-redox components. Notably, by incorporation with confined effect of tip region of a needle-like nanopipette, glorious in-vivo monitoring is conferred on the nanopipette detector at high temporal-spatial resolution. In addition, some outlooks for future application in reliable practical samples analysis and leading research endeavors in the related fantastic fields are provided.

Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis

Solid-state nanopores have been developed as a prominent tool for single molecule analysis in versatile applications. Although controlled dielectric breakdown (CDB) is the most accessible method for a single nanopore fabrication, it is still necessary to improve the fabrication efficiency and avoid the generation of multiple nanopores. In this work, we treated the SiNx membranes in the air–plasma before the CDB process, which shortened the time-to-pore-formation by orders of magnitude. λ-DNA translocation experiments validated the functionality of the pore and substantiated the presence of only a single pore on the membrane. Our fabricated pore could also be successfully used to detect short single-stranded DNA (ssDNA) fragments. Using to ionic current signals, ssDNA fragments with different lengths could be clearly distinguished. These results will provide a valuable reference for the nanopore fabrication and DNA analysis.

Nanopore Stochastic Sensing Based on Non-covalent Interactions

A variety of species could be detected by using nanopores engineered with various recognition sites based upon non-covalent interactions, including electrostatic, aromatic, and hydrophobic interactions. The existence of these engineered non-covalent bonding sites was supported by the single-channel recording technique. The advantage of the non-covalent interaction-based sensing strategy was that the recognition site of the engineered nanopore was not specific for a particular molecule but instead selective for a class of species (e.g., cationic, anionic, aromatic, and hydrophobic). Since different species produce current modulations with quite different signatures represented by amplitude, residence time, and even characteristic voltage-dependence curve, the non-covalent interaction-based nanopore sensor could not only differentiate individual molecules in the same category but also enable differentiation between species with similar structures or molecular weights. Hence, our developed non-covalent interaction-based nanopore sensing strategy may find useful application in the detection of molecules of medical and/or environmental importance.

Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures

i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3-10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.

Tailoring CO2-Activated Ion Nanochannels Using Macrocyclic Pillararenes

Gas-responsive nanochannels have great relevance for applications in many fields. Inspired by CO₂-sensitive ion channels, herein we present an approach for designing solid-state nanochannels that allow controlled regulation of ion transport in response to alternate CO₂/N₂ stimuli. The pillar[5]arene (P5N) bearing diethylamine groups can convert into the water-soluble host P5C, containing cationic tertiary ammonium salt groups after absorbing CO₂. Subsequently, the nanochannel walls are tailored using P5N-based host-guest chemistry. The ion transport rate of K⁺ in the P5N nanochannels under CO₂ was 1.66 × 10^-4 mol h^-1 m^-2, whereas that under N₂ was 7.98 × 10^-4 mol h^-1 m^-2. Notably, there was no significant change to the ion current after eight cycles, which may indicate the stability and repeatability of CO₂-activated ion nanochannels. It is speculated that the difference in ion conductance resulted from the change in wettability and surface charge within the nanochannels in response to the gas stimuli. Achieving CO₂-activated ion transport in solid-state nanochannels opens new avenues for biomimetic nanopore systems and advanced separation processes.

The Characterization of Electronic Noise in the Charge Transport through Single-Molecule Junctions

With the goal of creating single-molecule devices and integrating them into circuits, the emergence of single-molecule electronics provides various techniques for the fabrication of single-molecule junctions and the investigation of charge transport through such junctions. Among the techniques for characterization of charge transport through molecular junctions, electronic noise characterization is an effective strategy with which issues from molecule-electrode interfaces, mechanisms of charge transport, and changes in junction configurations are studied. Electronic noise analysis in single-molecule junctions can be used to identify molecular conformations and even monitor reaction kinetics. This review summarizes the various types of electronic noise that have been characterized during single-molecule electrical detection, including the functions of random telegraph signal (RTS) noise, flicker noise, shot noise, and their corresponding applications, which provide some guidelines for the future application of these techniques to problems of charge transport through single-molecule junctions.