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Protein-protein interactions occur in a wide range of biological processes and are of great significance to life function. Characterization of transient protein-protein interactions remains a significant barrier to our understanding of cellular processes. Nanopores provide unique nanoscale environments that accommodate single molecules from the surrounding bulk solution. This method permits label-free sensing at the single-molecule level with extremely high sensitivity. Herein, the interaction between a single P450cam monooxygenase and its redox partner putidaredoxin (Pdx) was monitored via transient ionic current by using functionalized glass nanopores. Results show that the volume of P450cam determines the blockage current while the interactions between the P450cam and Pdx give a long blockage duration. Our glass nanopore sensor with adjustable diameter could be applied for real-time sensing of protein-protein interactions between individual proteins with a wide range of molecular weight.

The nanopore approach holds the possibility for achieving single-molecule protein sequencing. However, ongoing challenges still remain in the biological nanopore technology, which aims to identify 20 natural amino acids by reading the ionic current difference with the traditional current-sensing model. In this paper, taking aerolysin nanopores as an example, we calculate and compare the current blockage of each of 20 natural amino acids, which are all far from producing a detectable current blockage difference. Then, we propose a modified solution conductivity of σ' in the traditional volume exclusion model for nanopore sensing of a peptide. The σ' value describes the comprehensive result of ion mobility inside a nanopore, which is related to but not limited to nanopore-peptide interactions, and the positions, orientations, and conformations of peptides inside the nanopore. The nanopore experiments of a short peptide (VQIVYK) in wild type and mutant nanopores further demonstrate that the traditional volume exclusion model is not enough to fully explain the current blockage contribution and that many other factors such as enhanced nanopore-peptide interactions could contribute to a dominant part of the current change. This modified sensing model provides insights into the further development of nanopore protein sequencing methods.

The potential distribution at the electrode interface is a core factor in electrochemistry, and it is usually treated by the classic Gouy-Chapman-Stern (G-C-S) model. Yet the G-C-S model is not applicable to nanosized particles collision electrochemistry as it describes steady-state electrode potential distribution. Additionally, the effect of single nanoparticles (NPs) on potential should not be neglected because the size of a NP is comparable to that of an electrode. Herein, a theoretical model termed as Metal-Solution-Metal Nanoparticle (M-S-MNP) is proposed to reveal the dynamic electrode potential distribution at the single-nanoparticle level. An explicit equation is provided to describe the size/distance-dependent potential distribution in single NPs stochastic collision electrochemistry, showing the potential distribution is influenced by the NPs. Agreement between experiments and simulations indicates the potential roles of the M-S-MNP model in understanding the charge transfer process at the nanoscale.

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.

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.

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.

Posttranslational modifications (PTMs) affect protein function/dysfunction, playing important roles in the occurrence and development of tauopathies including Alzheimer's disease. PTM detection is significant and still challenging due to the requirements of high sensitivity to identify the subtle structural differences between modifications. Herein, in terms of the unique geometry of the aerolysin (AeL) nanopore, we elaborately engineered a T232K AeL nanopore to detect the acetylation and phosphorylation of Tau segment (Pep). By replacing neutral threonine (T) with positively charged lysine (K) at the 232 sites, the T232K and K238 rings of this engineered T232K AeL nanopore corporately work together to enhance electrostatic trapping of the acetylated and phosphorylated Tau peptides. Translocation speed of the monophosphorylated Pep-P was decelerated by up to 46 folds compared to the wild-type (WT) AeL nanopore. The prolonged residences within the T232K AeL nanopore enabled to simultaneously identify the monoacetylated Pep-Ac, monophosphorylated Pep-P, di-modified Pep-P-Ac and non-modified Pep. The tremendous potential is demonstrated for PTM sensing by manipulating non-covalent interactions between nanopores and single analytes.

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.

The nanoparticle-based electrocatalysts' performance is directly related to their working conditions. In general, a number of nanoparticles are uncontrollably fixed on a millimetre-sized electrode for electrochemical measurements. However, it is hard to reveal the maximum electrocatalytic activity owing to the aggregation and detachment of nanoparticles on the electrode surface. To solve this problem, here, we take the hydrogen evolution reaction (HER) catalyzed by palladium nanoparticles (Pd NPs) as a model system to track the electrocatalytic activity of single Pd NPs by stochastic collision electrochemistry and ensemble electrochemistry, respectively. Compared with the nanoparticle fixed working condition, Pd NPs in the nanoparticle diffused working condition results in a 2-5 orders magnitude enhancement of electrocatalytic activity for HER at various bias potential. Stochastic collision electrochemistry with high temporal resolution gives further insights into the accurate study of NPs' electrocatalytic performance, enabling to dramatically enhance electrocatalytic efficiency.

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.

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).

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.

Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (ssDNA, >10 nt). Here, we have proposed a novel and robust strategy for the electrostatic focusing of long ssDNA into a lithium-chloride (LiCl)-active AeL. By using this method, for the first time we have demonstrated AeL detection of ssDNA longer than 100 nt. Due to screening more negative charges, LiCl improves AeL capture ability of long ssDNA (i.e. 60 nt) by 2.63- to 10.23-fold compared to KCl. Further calculations and molecular dynamics simulations revealed that strong binding between Li+ and the negatively charged residue neutralized the AeL, leading to a reduction in the energy barrier for ssDNA capture. These findings facilitate the future high-throughput applications of AeL in genetic and epigenetic diagnostics.

Proton transfer has been widely regarded as a key step in many electrochemical and biological processes. However, direct molecular evidence has long been lacking. In this work, we chose the electrochemical oxidation of acetaminophen (APAP) as a model system and utilized in situ liquid time-of-flight secondary ion mass spectroscopy (ToF-SIMS) to molecularly examine proton solvation and transfer in this process. In addition, we successfully captured and identified the transient radical intermediate, providing solid molecular evidence to resolve an important debate in electron transfer-proton transfer oxidation mechanism of APAP. Moreover, the potential-dependent behaviors of both inert ions and electroactive species during the dynamic potential scanning were chemically monitored in real time and the mass diffusion mechanism regarding the electroactive and nonelectroactive species was revealed under polarized conditions. The results are consistent with our computer simulations. The observations in this work greatly improved our understanding of proton transfer and mass dynamics occurring at the electrode-electrolyte interface in complex electrochemical processes.

RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.

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.

Measurement science has been stepping into single entity sensing. Nanopore electrochemistry as a powerful technique is attracting increasing attention for identifying and characterizing single cells, single particles, and even single molecules. Over the past decades, the biological nanopore-based single biomolecule interface has been extensively applied in probing nucleic acids and biomolecular interactions. Thanks to the advanced material science, the development of solid-state nanopores has been greatly promoted, showing new capabilities and features in single molecule analysis and single particle detection. Recently, nanopipettes have exhibited a great advantage in confining strong interactions between pore and analyte, electron-transfer processes and light inside, giving rise to the possibility of adopting nanopore sensing in a wide range of applications, including single-cell manipulating and analysis. Along with the development of nanopore electrochemistry, new data algorithms and high bandwidth instrumentation have also enabled researchers to look deeply into the intrinsic properties of single entities and therefore to associate them with chemical or biological processes. In future, nanopore electrochemistry will open up a new avenue for the better understanding of the chemical and biological world at the single entity level.

In this chapter, we introduce the biological membrane protein-based single-biomolecule interface for single molecule sensing, including DNA and protein detection, using synergic effects from steric volume exclusion and weak interactions between the nanopore and the analyte. More attentions will be focused on the state-of-art detection strategies for the measurement of a variety of biomolecules via nanopore electrochemistry by the selected experimental case studies, in particular for tracing short-lived metastable conformation and recognition of multiple targets for the promising clinical diagnosis. This chapter selects experimental cases in an α-hemolysin nanopore and an aerolysin nanopore to demonstrate the sensing ability of biological nanopores in detail.

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

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...

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

DNA lesion such as metholcytosine(mC), 8-OXO-guanine(OG), inosine(I) etc could cause the 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 remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (mC, OG, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

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...

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.