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Proteins are responsible for the occurrence and treatment of many diseases, and therefore protein sequencing will revolutionize proteomics and clinical diagnostics. Biological nanopore approach has proved successful for single-molecule DNA sequencing, which resolves the identities of 4 natural deoxyribonucleotides based on the current blockages and duration times of their translocations across the nanopore confinement. However, open challenges still remain for biological nanopores to sequentially identify each amino acid (AA) of single proteins due to the inherent complexity of 20 proteinogenic AAs in charges, volumes, hydrophobicity and structures. Herein, we focus on recent exciting advances in biological nanopores for single-molecule protein sequencing (SMPS) from native protein unfolding, control of peptide translocation, AA identification to applications in disease detection.

Single entity electrochemistry (SEE) has emerged as a promising method for precise measurement and fundamental understanding of the heterogeneity of single entities. Herein, we propose the dual responsive SEE sensing of the silver nanoparticles (AgNPs) collisions through a wireless nanopore electrode (WNE). Given the high temporal resolution and low background noise features, the Faradaic and capacitive currents provide the AgNPs' collision response. The electron transfer between the AgNPs and the electrode surface is identified under a bipolar electrochemical mechanism. Compared to the ultramicroelectrode, multistep oxidation of 30 nm AgNPs is observed due to the decreased interaction of the nanoparticles to the electrode. Moreover, the nanoconfinement of WNE plays a vital role in the repeated capturing of nanoparticles from the nontunneling region into the tunneling region until a complete oxidation. As a comparison, the collision of 5 nm AgNPs with higher interaction at the electrode surface shows great decrease in the multistep events. Thus, we propose a nanoconfined interaction based SEE method which could be used for simultaneously capturing the Faradaic and capacitive response. The nanoconfined interaction based SEE method holds great promise in the better understanding of heterogeneity of single particles.

The prompt introduction of single-molecule science into undergraduates’ curricula is an urgent but challenging task. However, the research experiments are often too complicated and the instruments are too expensive to be widely transferred into a compulsory course of undergraduate students. Herein, we introduce a recently developed nanopore technique into an accessible laboratory course for students with the advantages of simple operation, high repeatability, and low cost. The nanopore course serves to help undergraduates in practice to understand single-molecule behaviors, think at a single molecule level, and gradually develop single-molecule solutions for scientific issues. The learning activities for undergraduate students include setup of the instrument, fabrication of a biological nanopore on an artificial lipid bilayer membrane, detection of individual oligonucleotides, and data analysis. An experiment example is single-molecule detection of the model DNA sample poly(dA)n (n = 4, 5) using the aerolysin nanopore. As our developed nanopore sensing system is simple, portable, and easy to handle, the experiment course could be implemented and popularized in undergraduates’ laboratory education. For the undergraduate students who have taken general chemistry and/or biochemistry courses, this hands-on experience of nanopore experiments would benefit them with a better understanding of the chemical world at a single-molecule level and further using single-molecule tools in various applications including DNA and/or protein sequencing.

The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.

Measurements at the single-entity level provide more precise diagnosis and understanding of basic biological and chemical processes. Recent advances in the chemical measurement provide a means for ultra-sensitive analysis. Confining the single analyte and electrons near the sensing interface can greatly enhance the sensitivity and selectivity. In this review, we summarize the recent progress in single-entity electrochemistry of single molecules, single particles, single cells and even brain analysis. The benefits of confining these entities to a compatible size sensing interface are exemplified. Finally, the opportunities and challenges of single entity electrochemistry are addressed.

DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity., Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor DnA lesion into distinguishable electrochemical readouts.

Biological nanopore technology has the advantages of high selectivity and high reproducibility for characterizing single biomolecules. However, it is challenging to achieve protein sequencing owing to the heterogeneous charge distributions of the protein and the small structural difference from each amino acid. Here, we took the inherent electrochemically confined sensing interface of the aerolysin nanopore to enhance its interaction with single amino acids. The results showed that single cysteine molecules, a highly reactive amino acid in aging and neurodegenerative diseases, could be captured and monitored by an aerolysin nanopore as it produced distinctive current blockages with a prolonged statistical duration of 0.11 ± 0.02 ms at +120 mV. This is the first report of the detection of a single amino acid molecule by a biological nanopore directly without any modification and labelling. This study facilitates the direct detection of single amino acids by regulating the characteristic interaction between the single amino acids and the designed sensing interface of aerolysin nanopores.

We have employed glass nanopore as a single molecule technique for direct sensing amyloidosis process of Aβ1–42 peptide, which of great significance in Alzheimer's disease., We have developed a glass nanopore based single molecule tool to investigate the dynamic oligomerization and aggregation process of Aβ1–42 peptides. The intrinsic differences in the molecular size and surface charge of amyloid aggregated states could be distinguished through single molecule induced characteristic current fluctuation. More importantly, our results reveal that the neurotoxic Aβ1–42 oligomer tends to adsorb onto the solid surface of nanopores, which may explain its instability and highly neurotoxic features.

A fundamental question relating to protein folding/unfolding is the time evolution of the folding of a protein into its precisely defined native structure. The proper identification of transition conformations is essential for accurately describing the dynamic protein folding/unfolding pathways. Owing to the rapid transitions and sub-nm conformation differences involved, the acquisition of the transient conformations and dynamics of proteins is difficult due to limited instrumental resolution. Using the electrochemical confinement effect of a solid-state nanopore, we were able to snapshot the transient conformations and trace the multiple transition pathways of a single peptide inside a nanopore. By combining the results with a Markov chain model, this new single-molecule technique is applied to clarify the transition pathways of the β-hairpin peptide, which shows nonequilibrium fluctuations among several blockage current stages. This method enables the high-throughput investigation of transition pathways experimentally to access previously obscure peptide dynamics, which is significant for understanding the folding/unfolding mechanisms and misfolding of peptides or proteins., A solid-state nanopore based method is described for resolving protein-folding-related problems via snapshotting the folding intermediates and characterizing the kinetics of a single peptide.

Nanopore electrochemistry, as one of the promising tools for single molecule sensing, has proved its capability in DNA sequencing and protein analysis. To achieve a high resolution for obtaining molecular information, the nanopore electrochemical technique not only urgently requires an appropriate nanopore sensing interface with atomic resolution but also requires advanced instrumentation and its related data processing methods. In order to reveal the fundamental biological process and process the point-of-care diagnosis, it is necessary to use a nanopore sensing instrument with a high amperometric and temporal resolution as well as high throughput. The development of the instrumentation requires multi-disciplinary collaboration involving preparing a sensitive nanopore interface, low-noise circuit design, and intelligent data analysis. In this review, we have summarized the recent improvements in the nanopore sensing interface as well as discussed the higher throughput achieved by nanopore arrays and intelligent nanopore data analysis methods. The parallelized nanopore instrumentation could be popularized to all ranges of single-molecule applications.

The incidence of disease arising from food-borne pathogens is increasing continuously and has become a global public health problem. Rapid and accurate identification of food-borne pathogens is essential for adopting disease intervention strategies and controlling the spread of epidemics. Surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest due to the attractive features including simplicity, rapid measurement, and high sensitivity. It can be used for rapid in situ sensing of single and multicomponent samples within the nanostructure-based confined space by providing molecular fingerprint information and has been demonstrated to be an effective detection strategy for pathogens. This article aims to review the application of SERS to the rapid sensing of food-borne pathogens in food matrices. The mechanisms and advantages of SERS, and detection strategies are briefly discussed. The latest progress on the use of SERS for rapid detection of food-borne bacteria and viruses is considered, including both the labeled and label-free detection strategies. In closing, according to the current situation regarding detection of food-borne pathogens, the review highlights the challenges faced by SERS and the prospects for new applications in food safety. Graphical abstractIn this review, the advances on the SERS detection of pathogens over the past decades have been reviewed, focusing on the improvements in sensitivity, reproducibility, specificity, and the performance of the SERS-based assay in complex analytical scenarios. Supplementary Information The online version contains supplementary material available at 10.1007/s00604-021-04864-4.

The observation of single-particle surface-enhanced Raman scattering (SERS) has generated considerable interest both in the nanomaterials filed and in the single-particle spectroscopy community. It is a challenge to realize rapid, facile, and high throughput SERS at single nanoparticle level. Here, without the complex experimental device and difficult experimental operations, a general single-particle SERS technique has been achieved by using dark-field-assisted surface-enhanced Raman spectroscopy (DFSERS). This advanced method provides in-situ characterization of the chemical reaction performance at single gold nanorod.

Ensemble averaging measurements obscure the link between the electrochemical performance and the specific properties of an individual because of the interplay of inhomogeneity and heterogeneity. Nanocollision electrochemistry has attracted increasing interest because of its extremely high sensitivity, revealing the intrinsic properties of individual entities that are masked in the traditional ensemble measurements. In this perspective review, we summarized the recent developments in nanocollision-based single entity electrochemistry and photoelectrochemistry, the combined nanocollision electrochemistry with the other complementary techniques, as well as accurate data process. In closing, future challenges, opportunities, and destinations related to nanocollison electrochemistry were discussed.

The hydrogen bond (HB), one of the essential properties of water, tends to link water molecules to form dynamic water clusters. Extrinsic ions could change the size distribution of water clusters b...

Hydrogen evolution reaction (HER) catalyzed by molybdenum sulfide quantum dots (MoS2 QDs) has attracted extensive attention in the energy field. Monitoring HER catalyzed by MoS2 QDs based on a glass nanopore with an electrochemically confined effect was proposed for the first time. MoS2 QDs inside the glass nanopore is driven toward the orifice of the nanopore and bonded with the Ag nanoparticles (Ag NPs) to form a single nanocomposite. When enough voltage is applied across the orifice, the single Ag NP acts as a single nanoparticle electrode to conduct the electrochemically bipolar reaction on its two extremities. In the process, HER is catalyzed by MoS2 QDs, and Ag NPs are oxidized at the same time. The appearance of blockages on the elevated ionic current is attributed to the generation of a H2 bubble. Furthermore, by analyzing the modulations in the ionic current oscillation, the frequency of hydrogen bubble generation that is related to the catalytic efficiency of MoS2 QDs could be estimated. The results reveal the capability of the glass nanopore for the real-time monitoring electrocatalytic behavior, which makes the glass nanopore an ideal candidate to further reveal the heterogeneity of catalytic capability at the single particle level.

Monitoring the dynamic behaviour of a single cell in a natural environment is vital in biological studies and contributes to the understanding of the relationship between the function of single cells and the pathology. The advent of specially designed and sensitive chemical or biological analytical methods that enable the application in single cell analysis is urgently demanded. Confined nanopipettes, a unique microfluidic channel with a tunable size, have been proven to be a facile approach capable of identifying small molecules in a label-free manner. The microfluid in the confined space and the electrochemically confined effect within the nanopipette renders a high sensitivity to the analytes of individual cells. In contrast to ensemble analytical techniques, nanopipettes can precisely manipulate single cells with submicron accuracy. Here, we review the fabrication and characteristics of confined nanopipettes, summarize their application in single cell analysis, and conclude with a perspective for their future development in the single cell analysis area.

Protein kinases play a critical role in regulating virtually all cellular processes. Here, we developed a novel one-step method based on a wild-type aerolysin nanopore, which enables kinase activity detection without labeling/modification, immobilization, cooperative enzymes and complicated procedures. By virtual of the positively charged confinement of the aerolysin nanopore, the kinase-induced phosphopeptides are specially captured while the positively charged substrate peptides might move away from the pore by the electric field. Combining with internal standard method, the event frequency of the phosphopeptides exhibited a dose-dependent response with kinases. The detection limit of 0.005 U/μL has been achieved with protein kinase A as a model target. This method also allowed kinase inhibitor screening, kinase activity sensing in cell lysates and the real-time monitoring of kinase-catalyzed phosphorylation at singe molecule level, which could further benefit fundamental biochemical research, clinical diagnosis and kinase-targeted drug discovery. Moreover, this nanopore sensor shows strong capacity for the other enzymes that altered substrate charge (e.g., sulfonation, carboxylation, or amidation).

Experimental techniques to monitor and visualize the behaviors of single nanoparticles have not only revealed the significant spatial and temporal heterogeneity of those individuals, which are hidden in ensemble methods, but more importantly, they have also enabled researchers to elucidate the origin of such heterogeneity. In pursuing the intrinsic structure-function relations of single nanoparticles, the recently developed stochastic collision approach demonstrated some early promise. However, it was later realized that the appropriate sizing of a single nanoparticle by an electrochemical method could be far more challenging than initially expected owing to the dynamic motion of nanoparticles in electrolytes and complex charge-transfer characteristics at electrode surfaces. This clearly indicates a strong necessity to integrate single nanoparticle electrochemistry with high-resolution optical microscopy. Hence, this review aims to give a timely update of the latest progress for both electrochemically sensing and seeing single nanoparticles. A major focus is on collision-based measurements, where nanoparticles or single entities in solution impact on a collector electrode and the electrochemical response is recorded. These measurements are further enhanced with optical measurements in parallel. For completeness, advances in other related methods for single nanoparticle electrochemistry are also included.

The nanopore technique employs a nanoscale cavity to electrochemically confine individual molecules, achieving ultrasensitive single-molecule analysis based on evaluating the amplitude and duration of the ionic current. However, each nanopore sensing interface has its own intrinsic sensing ability, which does not always efficiently generate distinctive blockade currents for multiple analytes. Therefore, analytes that differ at only a single site often exhibit similar blockade currents or durations in nanopore experiments, which often produces serious overlap in the resulting statistical graphs. To improve the sensing ability of nanopores, herein we propose a novel shapelet-based machine learning approach to discriminate mixed analytes that exhibit nearly identical blockade current amplitudes and durations. DNA oligomers with a single-nucleotide difference, 5'-AAAA-3' and 5'-GAAA-3', are employed as model analytes that are difficult to identify in aerolysin nanopores at 100 mV. First, a set of the most informative and discriminative segments are learned from the time-series data set of blockade current signals using the learning time-series shapelets (LTS) algorithm. Then, the shapelet-transformed representation of the signals is obtained by calculating the minimum distance between the shapelets and the original signals. A simple logistic classifier is used to identify the two types of DNA oligomers in accordance with the corresponding shapelet-transformed representation. Finally, an evaluation is performed on the validation data set to show that our approach can achieve a high

Gold nanoparticles (AuNPs) have been demonstrated to serve as effective nanomaterial-based enzyme mimetics (nanozymes) for a number of enzymatic reactions under mild conditions. The intrinsic glucose oxidase and peroxidase activities of single AuNPs and Ag-Au nanohybrids, respectively, were investigated by single NP collision electrochemical measurements. A significantly high turnover number of nanozymes was obtained from individual catalytic events compared with the results from the classical, ensemble-averaged measurements. The unusual enhancement of catalytic activity of single nanozymes is believed to originate from the high accessible surface area of monodispersed NPs and the high activities of carbon-supported NPs during single-particle collision at a carbon ultramicroelectrode. This work introduces a new method for the precise characterization of the intrinsic catalytic activities of nanozymes, giving further insights to the design of high-efficiency nanomaterial catalysts.

Nanopore is a single-molecule analysis method which also employed electrophoresis has achieved promising single-molecule detections. In this study, we designed two kinds of confined spaces by fabricating solid-state nanopores with desirable diameters to study the structured single-strand DNA of C-rich quadruplex. For the nanopore whose diameter is larger than the quadruplex size, the DNA molecule could directly translocate through the nanopore with extremely high speed. For the nanopore whose diameter is smaller than the quadruplex size, DNA molecule which is captured by nanopore could return to the solution without translocation or unzip the quadruplex structure into single-strand and then pass the nanopore. This study certifies that choosing a suitable sensing interface is the vital importance of observing detailed single-molecule information. The solid-state nanopores hold the great potential to study the structural dynamics of quadruplex DNA molecule.

Our results indicated that a gold electrode participates in the redox reaction of [Fe(CN)6]3/4– by competing with it to form Au(CN)2–., Electrochemical redox conversion between ferricyanide and ferrocyanide on a gold electrode is one of the most classical reactions in electrochemistry. In textbooks, the gold electrode is seen as chemically inert, on which only the adsorption/desorption of [Fe(CN)6]3/4– and electron transfer take place. Here, the electrochemical process of [Fe(CN)6]3/4– on a gold electrode was revisited using a vacuum-compatible microfluidic electrochemical cell in combination with operando liquid ToF-SIMS. An intermediate, Au(CN)2–, was observed in the cyclic voltammetry of ferricyanide with an interesting periodic potential-dependent variation trend. It was demonstrated that the gold electrode participated in the redox reaction of [Fe(CN)6]3/4– by competing with it to form Au(CN)2–, since the formation constant was Fe(CN)63– > Au(CN)2– > Fe(CN)64–. The formation and evolution of Au(CN)2– depends on the ratio of Fe(iii) and Fe(ii) on the surface of the gold electrode, which was determined by the redox conversion between Fe(iii) and Fe(ii) as well as the electric field force-based attraction or repulsion between the gold electrode and [Fe(CN)6]3/4–. Both of these factors were potential-dependent, resulting in the periodic change of Au(CN)2– in the dynamic potential scan of [Fe(CN)6]3/4–. These results provided solid molecular evidence for the participation of the gold electrode in the [Fe(CN)6]3/4– redox system, which will deepen mechanistic understandings of related electrochemical applications.

Summary Muscle tissue performs crucial contraction/extension motions that generate mechanical force and work by consuming chemical energy. Inspired by this naturally created biomolecular machine, artificial molecular muscles are designed and synthesized to undertake linear actuation functions. However, most of these muscle-like actuators are performed at large ensembles, while to realize the nanoscale actuation at the single- to few-molecule level remains challenging. Herein, we developed an artificial muscle-like molecular actuator that can reversibly control the proximity of the attached nano-objects, gold nanoparticles, within the single-molecule length level by its stimuli-responsive muscle-like linear contraction/extension motion. The molecular actuation motion is accompanied by an optical signal output resulting from the plasmonic resonance properties of gold nanoparticles. Meanwhile, the thermal noise of the muscle-like molecular actuator can be overcome by integrating the optical signal over a sufficiently long period.

Alterations in lipid metabolites in coronary artery tissues are phenotypic changes in the progression of atherosclerosis (AS). A full picture of the spatiotemporal distribution of lipid metabolites in coronary AS is needed for a deeper understanding of its pathology and the identification of potential biomarkers of disease progression. In this work, the changes in species, quantity, and distribution of lipid metabolites at different stages of AS, which were standardized by the disease areas, were analyzed through the high spatial resolution- and high sensitivity-time-of-flight secondary ion mass spectrometry (ToF-SIMS) under delayed extraction mode. Based on high lateral resolution imaging, we further analyzed the ToF-SIMS data extracted from the subregions of AS lesion tissues at different disease progression stages by semiquantitative comparison, clustering analysis (t-stochastic neighbor embedding and HCA), and KEGG enrichment. Thus, a much-detailed description of lipids' features in coronary AS was achieved. We constructed a ToF-SIMS mass spectrometry database of coronary AS lipids. 40 specific lipid metabolites with distinctive patterns between different pathological stages were obtained. Chemical imaging unveiled further details regarding the spatial distribution of lipids. Moreover, linoleic acid and arachidonic acid metabolic pathway were predicted to be critical in AS progression.

Water clusters are ubiquitously formed in aqueous solutions by hydrogen bonding, which is quite sensitive to various environment factors such as temperature, pressure, electrolytes, and pH. Investigation of how the environment has impact on water structure is important for further understanding of the nature of water and the interactions between water and solutes. In this work, pH-dependent water structure changes were studied by monitoring the changes for the size distribution of protonated water clusters by in-situ liquid ToF-SIMS. In combination with a light illumination system, in-situ liquid ToF-SIMS was used to real-time measure the changes of a light-activated organic photoacid under different light illumination conditions. Thus, the proton transfer and pH-mediated water cluster changes were analyzed in real-time. It was found that higher concentration of free protons could lead to a strengthened local hydrogen bonding network as well as relatively larger protonated water clusters in both organic acid and inorganic acid. Besides, the accumulation of protons at the liquid-vacuum interface under light illumination was observed owing to the affinity of organic molecules to the low-pressure gas phase. The application of in-situ liquid ToF-SIMS analysis in combination with in-situ light illumination system opened up an avenue to real-time investigate light-activated reactions. Besides, the results regarding water structure changes in acidic solutions showed important insights in related atmospheric and physiochemical processes.

Current strategies for the detection of disease biomarkers often require enzymatic assays that may have limited sensitivity due to inferior stability and vulnerable catalytic activity of the enzyme. A new enzyme-free amplification method for identifying suitable biomarkers is necessary to lower the limit of detection and improve many critical diagnosis applications. Here, we presented an enzyme-free amplified plasmonic immunoassay that enhanced the detection sensitivity of disease biomarkers by combining a novel plasmon-induced silver photoreduction system with a silver nanoparticle (AgNP)-linked immunoassay. The key step to achieving ultrasensitivity was to use Ag

With the development of new instruments and methodologies, the highly dynamic behaviors of nanoparticle at the liquid-solid interface have been studied. However, the dynamic nature of the electrochemical behavior of individual nanoparticles on the electrode interface is still poorly understood. Here, we generalize scaling relations to predict nanoparticle-electrode interactions by examining the adsorption energy of nanoparticles at an ultramicroelectrode interface. Based on the theoretical predictions, we investigate the interaction-modulated dynamic electrochemical behaviors for the oxidation of individual Ag nanoparticles. Typically, significantly distinct current traces are observed owing to the adsorption-mediated motion of Ag nanoparticles. Inspired by restraining the stochastic paths of particles in the vicinity of the electrode interface to produce surface-confined current traces, we successfully realize high-resolution size measurements of Ag nanoparticles in mixed-sample systems. This work offers a better understanding of dynamic interactions of nanoparticles at the electrochemical interface and displays highly valuable applications of single-entity electrochemistry., Single-entity electrochemistry has been proposed for studying properties of single nanoparticles (NPs). Here, the authors make use of adsorption-mediated motion of Ag NPs to take individual NP size measurements using electrochemical impacts with excellent agreement to standard imaging techniques.

Single entity sensing is recently an area of tremendous inter-est in analytical chemistry, such that it is possible to analyze single cells, single particles, and even single molecules. Among diver...

Aggregation-induced emission (AIE) as a unique photophysical process has been intensively explored for their features in fields from optical sensing, bioimaging to optoelectronic devices. However, all AIE luminogens (AIEgens) hardly recover into the initial dispersed state after illuminating at the ultimate aggregated state, which limits AIEgens to achieve reversible sensing and reproducible devices. To real-time manipulate the emission of AIEgen, here we take the advantage of confined space in the quartz nanopore to achieve a nanopore-size-dependent restriction of AIEgens for reversible conversions of “on-to-off” and “off-to-on” emission. By electrochemically manipulating 26 fL AIEgen solution inside nanopore confinement, AIE illuminates while moves along nanopore from the constricted tip to inside cavity at a velocity of 1.4–2.2 μm s−1, and vice versa. We further apply this dynamic manipulation for a target delivery of AIEgen into single cells, which opens up new possibility to design powerful and practical AIE applications., The difficulty in recovering the aggregation-induced emission fluorogens (AIEgens) to the initial dispersed state upon illuminating has limited their applications. Here, the authors employ the confined space in the quartz nanopore to achieve a nanopore-size dependent restriction of AIEgens.

Mimicking cellular transport mechanisms to make solid-state smart nanochannels has long been of great interest for their diverse applications, but it poses a critical synthetic challenge. Covalent organic frameworks (COFs) are porous crystalline materials with tailor-made nanochannels and hold great potential for ion and molecule transport. We demonstrate here for the first time that 2D COFs possess the necessary merits to be promising solid-state nanochannels for selective transport of amino acids, which are the basis for life. By imine condensations of a

Pore-forming confined space, especially at nanoscale, creates a unique environment that is able to controllably and precisely influence the interaction between pores and analytes. Hence, nanopore-based methods offer the possibility to in-situ and operando characterize single particle or molecule at ultra-high temporal and spatial resolutions. This review is to highlight the latest research progress of a typical biological nanopore (aerolysin) as an example to demonstrate the capability of this technique, covering the direct use of wild-type aerolysin nanopores to detect and discriminate nucleotides of difference lengths or with various nucleobases, and the rational mutation of aerolysin nanopores to further enhance the sensitivity and selectivity. These progresses clearly demonstrate the great potential of nanopore or confined space approach in novel electrochemical sensing.

Summary An aerolysin nanopore interface was introduced as a molecular machine to electrically read out the real-time photo-controlled motion of an azobenzene-geared DNA train with high spatial and temporal resolution. Under alternating UV and visible irradiation, each DNA train performed two regulated speeds of 1.9 and 6.3 bases/s corresponding to trans and cis states, respectively, with readily identified current signals. Each train type fell into the ultra-narrow current population with a full-width half maximum of 0.2–0.4 pA. The combination of a model molecular machine system and powerful aerolysin interface enabled the motions of every artificial molecular machine to be followed in real time.

The phosphorylation of oligonucleotides and peptides plays a critical role in regulating virtually all cellular processes. To fully understand these complex and fundamental regulatory pathways, the cellular phosphorylate changes of both oligonucleotides and peptides should be simultaneously identified and characterized. Here, we demonstrated a single-molecule, high-throughput, label-free, general, and one-step aerolysin nanopore method to comprehensively evaluate the phosphorylation of both oligonucleotide and peptide substrates. By virtue of electrochemically confined effects in aerolysin, our results show that the phosphorylation accelerates the traversing speed of a negatively charged substrate for about hundreds of time while significantly enhances the translocation frequency of a positively charged substrate. Thereby, the kinase/phosphatase activity could be directly measured with the aerolysin nanopore from the characteristically dose-dependent event frequency of the substrates. By using this straightforward approach, a model T 4 oligonucleotide kinase (PNK) further achieved the nanopore evaluation of its phosphatase activity and real-time monitoring of its phosphatase-catalyzed dephosphorylation at a single-molecule level. Our study provides a step forward to nanopore enzymology for analyzing the phosphorylation of both oligonucleotides and peptides with significant feasibility in fundamental biochemical researches, clinical diagnosis, and kinase/phosphatase-targeted drug discovery.

Recent advances in nanotechnology have produced plenty of intracellular drug delivery systems based on various functional nanoparticles. Although much progress has been achieved in improving cellular uptake efficiency, the retention time of these engineered nanoparticles in living cells has not yet received wide attention. Here, we report the controllable exocytosis of plasmonic gold nanoparticles (GNPs) based on a microRNA-21 (miRNA-21) targeted binary system. Rapid intracellular accumulation of GNPs was observed in miRNA-21 positive MCF-7 breast cancer cells, which blocked the exocytosis of the GNP aggregates. Under near-infrared (NIR) irradiation, MCF-7 cells were successfully killed due to the far-red and NIR absorption of the GNP aggregates. In contrast, in miRNA-21 negative cells, the dispersive GNPs escaped from the cells after 6 h. The traces of GNPs could be conveniently captured under the dark-field microscope. This work provides a promising platform for the study of controllable aggregation-induced exocytosis inhibition (CAIEI) of nanocarriers, which is inspiring for the design of more effective nanodrugs for the treatment of cancer.

Analysis of nicotinamide adenine dinucleotide (NAD+/NADH)-modified electrodes is important for in vitro monitoring of key biological processes. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to analyze NAD+/NADH-modified gold electrodes. Interestingly, no obvious characteristic peaks of nicotinamide fragment could be observed in the mass spectra of NAD+/NADH in their neutral sodium pyrophosphate form. However, after acidification, the characteristic peaks for both NAD+ and NADH were detected. This was due to the suppression effect of inner pyrophosphoric salts in both neutral molecules. Besides, it was proved that the suppression by inner salt was intramolecular. No obvious suppression was found between neighboring molecules. These results demonstrated the suppression effect of inner salts in ToF-SIMS analysis, providing useful evidence for the study of ToF-SIMS ionization mechanism of organic molecule-modified electrodes. Graphical Abstract ᅟ.

To achieve fast and accurate analysis of weak current signal of nanopore-based single molecule detection, an online data process based on adaptive threshold algorithm with data buffering technique and finite impulse response filtering was designed. A software system based on the data process was developed for online recognition and analysis of nanopore events during nanopore experiment. To testify the performance of the algorithm and software system, ideal signals with different noise level (20–100 pA) were generated at bandwidth ranging from 3 kHz to 100 kHz. The result showed that this software system was stable at different bandwidths and sampling rates and could be used in analyzing the signals at high noise. The proposed software system was further applied to aerolysin nanopore experiment for detection of poly(dA)4 molecules. The results showed that the data process system could be applied in real nanopore recording experiment with high accuracy and speed.

Collision at a single molecule level was achieved based on the nanoimpact of an individual pyrroloquinoline quinone (PQQ) modified multiwalled carbon nanotube (MWCNT) at the carbon fiber ultramicroelectrode (C UME). Electrocatalytic amplification of the current responses was observed when the PQQ-modified MWCNT collided with C UME in the presence of hydrazine (N2H4) in a Tris-HCl buffer solution, which was also supported by the conventional cyclic voltammetry and chronoamperometry techniques. The enhanced catalytic oxidation of N2H4 was due to the “addition-elimination” redox cycling mechanism of PQQ/PQQH2, where the oxidation of N2H4 occurred together with the reduction of PQQ under an external bias, and the formed PQQH2 intermediate would be reoxidized back to PQQ simultaneously. The average collision current, duration, and charge for PQQ-modified MWCNT at 1.0 V vs Ag/AgCl were 105 pA, 0.45 ms, and 49 fC, respectively. As a result, the turnover frequency of electrocatalytic oxidation of N2H4 by PQQ was ...

Monitoring subtle changes in ionic current flow through a nanopore could be applied to observe single molecule reaction. Here, we introduced cysteine to substitute for lysine at position 238 constructing a mutant aerolysin K238C. It could be regarded as a nanoreactor to efficiently visualize chemical bonds making and breaking. The compound 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB) was selected as a reactant coming into collisions on the interface of the pore to occur a reversible reaction. Our results showed that the mutant aerolysin could respond to three molecules of DTNB simultaneously and reflect corresponding levels with distinguishable current signals. Therefore, this method constitutes a simple, generic tool for monitoring single molecule reaction, which evokes a guidance for the mutant aerolysin towards the application of tracking other more reactions at single molecule level.

Quantifying the photoinduced electron transfer properties of a single entity is of paramount importance for clarifying the link between the photoelectrochemical performance and the specific properties of an individual. Here, we successfully monitored the photoelectrochemical behavior of a single dye-sensitized ZnO entity on a Au ultramicroelectrode with different TiO2 film thicknesses. Due to a trap-limited electron diffusion in TiO2 film, a sub-millisecond photocurrent transient was observed for an individual N719@ZnO associated with single-particle photocatalytic water splitting. Furthermore, a Monte Carlo random walk numerical simulation model was developed to simulate the photoinjected electron transport dynamics and recombination in a nanoparticulate TiO2 film. Our approach allowed the photocatalytic properties of N719 at the single-molecule level to be quantified, and electron diffusivity and electron collection efficiency as a function of the film thickness were estimated by simulation analyses. Ex...

An ultrasensitive photoelectrochemical method for achieving real-time detection of single nanoparticle collision events is presented. Using a micrometer-thick nanoparticulate TiO2-filmed Au ultra-microelectrode (TiO2@Au UME), a sub-millisecond photocurrent transient was observed for an individual N719-tagged TiO2 (N719@TiO2) nanoparticle and is due to the instantaneous collision process. Owing to a trap-limited electron diffusion process as the rate-limiting step, a random three-dimensional diffusion model was developed to simulate electron transport dynamics in TiO2 film. The combination of theoretical simulation and high-resolution photocurrent measurement allow electron-transfer information of a single N719@TiO2 nanoparticle to be quantified at single-molecule accuracy and the electron diffusivity and the electron-collection efficiency of TiO2@Au UME to be estimated. This method provides a test for studies of photoinduced electron transfer at the single-nanoparticle level.

Potential-dependent current traces were first observed for the same sized nanoparticles (NPs) during the dynamic electro-oxidation process of single AgNPs. In this work, we demonstrated that the motion trajectories of NPs, coupled with electrochemical kinetics parameters, qualitatively predicted from the series of the experimentally observed current traces obtained single AgNPs collision behaviors. Based on the Poisson–Boltzmann equation for a general electrochemical reaction, a rate constant of Ag oxidation could be further estimated to be 1 × 10–6 mol·cm–2·s–1 for electron transfer between AgNPs and the Au electrode by comparing the experimental results. Our method provided a meaningful attempt to test electron transfer kinetics and motion behaviors of single NPs using the high-resolution electrochemical signal.

The development of photocatalysts that can effectively harvest visible light is essential for advances in high-efficiency solar-driven hydrogen generation. Herein, we synthesized water soluble CuInS2 (CIS) and Cu-In-Zn-S (CIZS) quantum dots (QDs) by using one-pot aqueous method. The CIZS QDs are well passivated by glutathione ligands and are highly stable in aqueous conditions. We subsequently applied these QDs as a light harvesting material for photocatalytic hydrogen generation. Unlike most small band gap materials that show extremely low efficiency, these new QDs display remarkable energy conversion efficiency in the visible and near-infrared regions. The external quantum efficiency at 650 nm is ∼1.5%, which, to the best of our knowledge, is the highest value achieved until now in the near-infrared region.

Herein, green-fluorescent N-doped carbon quantum dots (N-CQDs) with quantum yield of 30.6% were prepared via a simple bottom-up electrochemical (EC) method using the mixtures of pyrocatechol and ethylenediamine as both precursors and electrolytes. The ON-OFF fluorescence (FL) principle that the FL intensity of the N-CQDs was quenched in the presence of Fe3+ was further extended to the ON-OFF-ON and ON-OFF-ON-OFF ones for pyrophosphate anions (PPi) and alkaline phosphatase (ALP) detection, respectively, based on the specific competitive interaction of N-CQDs with Fe3+ and PPi and the hydrolysis of PPi in the presence ALP. Under the optimized conditions, limit of detection (LOD) of 1.2 μM and 0.5 μM were achieved for assays of Fe3+ and PPi, respectively. Meanwhile, measurable evaluation of ALP activity was reached in a wide range from 5 to 360 U/L with a LOD of 1.1 U/L. The as-proposed sensors showed many advantages including label free, rapid, simple, low-cost, high sensitive, which has great promising application potential in vivo and in vitro clinical diagnosis and will promote the application of EC derived carbon nanomaterials.

The ability of chemical tools to effectively detect malignancy in frozen sections removed from patients during surgery is important for the timely determination of the subsequent surgical program. However, current clinical methods for tissue imaging rely on dye-based staining or antibody-based techniques, which are sluggish and complicated. Methods: Here, we have developed a 2D material-based supramolecular imaging probe for the simple, rapid yet precise diagnosis of hepatocellular carcinoma (HCC). The 2D probe is constructed through supramolecular self-assembly between a water soluble, fluorescent peptide ligand that selectively targets glypican-3 (GPC-3, a specific cell-surface biomarker for HCC) and 2D molybdenum disulfide that acts as a fluorescence quencher as well as imaging enhancer. Results: We show that the 2D imaging probe developed with minimal background fluorescence can sensitively and selectively image cells overexpressing GPC-3 over a range of control cells expressing other membrane proteins. Importantly, we demonstrate that the 2D probe is capable of rapidly (signal became readable within 1 min) imaging HCC tissues over para-carcinoma regions in frozen sections derived from HCC patients; the results are in accordance with those obtained using traditional clinical staining methods. Conclusion: Compared to conventional staining methods, which are laborious (e.g., over 30 min is needed for antibody-based immunosorbent assays) and complex (e.g., diagnosis is based on discrimination of the nucleus morphology of cancer cells from that of normal cells), our probe, with its simplicity and quickness, might become a promising candidate for tumor-section staining as well as fluorescence imaging-guided surgery.

The realization of the reversible inter-conversion between NADH and NAD+ is a long-term challenge in biological and energy-related chemistry. Here, we achieve the electrochemical reversible redox of NAD+/NADH derivatives by the functionalization of a gold electrode with a specially designed NAD+ derivative, and the electrochemical redox products are characterized by time-of-flight secondary ion mass spectrometry (ToF-SIMS).

The chemical components analysis of single cell is important for the understanding of physiological processes such as cell growth, signal transduction and apoptosis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a sensitive surface analysis technique with high spatial resolution, which has been used for single cell and micro-area analysis. However, relatively low ionization yield of biomolecules limited its wide applications in single cell analysis. Herein, we used metal substrate and matrix material to enhance the ionization yield of lipids. The signal intensity of phosphatidylcholine (PC 40:0) casted on the matrix/gold-coated silicon substrate was 65 times higher than that on the silicon wafer. The signal enhancement of phosphatidylcholine (PC 34:1) on single cell surface cultured on matrix/gold-coated silicon substrate was observed as well. Owing to the influence of irregular topography and complex chemical environment of cell, the increase of lipids signal was smaller. Delayed extraction mode of ToF-SIMS overcame the effects of cell topography, leading to further enhancement of the signal intensity of lipids. Meanwhile, simultaneous high spatial resolution of chemical imaging and high mass resolution of the mass spectra of single cells were obtained. Our strategies provided new insights into the study of cell metabolism and cell-environment interactions.

Hydrogen generation based on photocatalytic water splitting is a promising strategy for renewable energy production. Significant efforts have been made to improve the photocatalytic efficiency. However, the light harvesting ability of photocatalytic systems in the visible region still needs to be significantly improved to enable them to be a competitive technology for hydrogen generation. Herein, for the first time, we synthesized 2D Zn–Ag–In–S (ZAIS) nanosheets with strong absorption in the visible region and applied them for photocatalytic hydrogen generation. The exploration of oxygen passivation (O-ZAIS) reduced the defect concentration and nonradiative decay. The hydrogen generation rate is up to 25.2 mmol g−1 h−1, which is 14.7 times higher than that of pristine ZAIS nanosheets. Furthermore, by introducing 2D Co3O4 as the co-catalyst, carrier separation is accelerated, giving rise to a hydrogen generation efficiency of 43.6 mmol g−1 h−1. To the best of our knowledge, this is the highest efficiency reported among all kinds of 2D photocatalysts.