Fabrication and Use of Nanopipettes in Chemical Analysis

Nanopipette dynamic microscopy unveils nano coffee ring

Liquid-phase electron microscopy (LP-EM) imaging has revolutionized our understanding of nanosynthesis and assembly. However, the current closed geometry limits its application for open systems. The ubiquitous physical process of the coffee-ring phenomenon that underpins materials and engineering science remains elusive at the nanoscale due to the lack of experimental tools. We introduce a quartz nanopipette liquid cell with a tunable dimension that requires only standard microscopes. Depending on the imaging condition, the open geometry of the nanopipette allows the imaging of evaporation-induced pattern formation, but it can also function as an ordinary closed-geometry liquid cell where evaporation is negligible despite the nano opening. The nano coffee-ring phenomenon was observed by tracking individual nanoparticles in an evaporating nanodroplet created from a thin liquid film by interfacial instability. Nanoflows drive the assembly and disruption of a ring pattern with the absence of particle-particle correlations. With surface effects, nanoflows override thermal fluctuations at tens of nanometers, in which nanoparticles displayed a "drunken man trajectory" and performed work at a value much smaller than kBT.

Solid-State Glass Nanopipettes: Functionalization and Applications

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

Dynamic and Asymmetrical Ion Concentration Polarization in Dual Nanopipettes

Dual nanopipettes with two channels have been receiving great attention due to the convenient experimental setup and multiple measuring channels in sensing applications at nanoscale, while the involved dynamic and asymmetrical ion transport processes have not been fully elucidated. In this paper, both experimental and simulation methods are used to investigate the dynamic mass transport processes inside dual nanopipettes with two well-separated channels. The results present that the ion transport resistance through the two channels (R12) is always the add-up of the individual ones (R13 + R23) with respect to the bulk solutions, at various ionic strengths and scan rates. A constant zero-current potential is obtained when loading an asymmetrical electrolyte concentration in the two channels, and the zero-potential current displays a good linear relationship with the bulk concentration outside the pipet. Besides revealing the dynamic and asymmetrical concentration polarization in the dual nanopipettes, these results would also further promote the better usage of dual nanopipettes in electrochemical sensing and imaging applications.

Rectifying artificial nanochannels with multiple interconvertible permeability states

Transmembrane channels play a vital role in regulating the permeation process, and have inspired recent development of biomimetic channels. Herein, we report a class of artificial biomimetic nanochannels based on DNAzyme-functionalized glass nanopipettes to realize delicate control of channel permeability, whereby the surface wettability and charge can be tuned by metal ions and DNAzyme-substrates, allowing reversible conversion between different permeability states. We demonstrate that the nanochannels can be reversibly switched between four different permeability states showing distinct permeability to various functional molecules. By embedding the artificial nanochannels into the plasma membrane of single living cells, we achieve selective transport of dye molecules across the cell membrane. Finally, we report on the advanced functions including gene silencing of miR-21 in single cancer cells and selective transport of Ca2+ into single PC-12 cells. In this work, we provide a versatile tool for the design of rectifying artificial nanochannels with on-demand functions.

Low-cost and convenient fabrication of polymer micro/nanopores with the needle punching process and their applications in nanofluidic sensing

Solid-state micro/nanopores play an important role in the sensing field because of their high stability and controllable size. Aiming at problems of complex processes and high costs in pore manufacturing, we propose a convenient and low-cost micro/nanopore fabrication technique based on the needle punching method. The thin film is pierced by controlling the feed of a microscale tungsten needle, and the size variations of the micropore are monitored by the current feedback system. Based on the positive correlation between the micropore size and the current threshold, the size-controllable preparation of micropores is achieved. The preparation of nanopores is realized by the combination of needle punching and chemical etching. First, a conical defect is prepared on the film with the tungsten needle. Then, nanopores are obtained by unilateral chemical etching of the film. Using the prepared conical micropores, resistive-pulse detection of nanoparticles is performed. Significant ionic current rectification is also obtained with our conical nanopores. It is proved that the properties of micro/nanopores prepared by our method are comparable to those prepared by the track-etching method. The simple and controllable fabrication process proposed here will advance the development of low-cost micro/nanopore sensors.

Thermoelectric Nanofluidics Probing Thermal Heterogeneity inside Single Cells

Accurate temperature measurement in one living cell is of great significance for understanding biological functions and regulation. Here, a nanopipet electric thermometer (NET) is established for real-time intracellular temperature measurement. Based on the temperature-controlled ion migration, the temperature change in solution results in altered ion mobilities and ion distributions, which can be converted to the thermoelectric responses of NET in a galvanostatic configuration. The exponential relationship between the voltage and the temperature promises highly sensitive thermoelectric responses up to 11.1 mV K-1, which is over an order of magnitude higher than previous thermoelectric thermometry. Moreover, the NET exhibits superior thermal resolution of 25 mK and spatiotemporal resolution of 100 nm and 0.9 ms as well as excellent stability and reproducibility. Benefiting from these unique features, both thermal fluctuations in steady-state cells and heat generation and dissipation upon drug administration can be successfully monitored, which are hardly achieved by current methods. By using NET, thermal heterogeneities of single cancer cells during immunotherapy were reported first in this work, in which the increased intracellular temperature was demonstrated to be associated with the survival benefit and resistance of cancer cells in immunotherapy. This work not only provides a reliable method for microscopic temperature monitoring but also gains new insights to elucidate the mechanism of immune evasion and therapeutic resistance.

Nanofluidic diodes based on asymmetric bio-inspired surface coatings in straight glass nanochannels

In this study, we present nanofluidic diodes fabricated from straight glass nanochannels and functionalized using bio-inspired polydopamine (PDA) and poly-L-lysine (PLL) coatings. The resulting PDA coatings are shown to be asymmetric due to a combination of transport considerations which can be leveraged to provide a measure of control over the effective channel geometry. By subsequently introducing a layer of amine-bearing PLL chains covalently bound to the PDA, we enhance heterogeneities in the charge and ion distributions within the channel and enable significant current rectification between forward-bias and reverse-bias modes; our PDA-PLL-coated channels yielded a rectification ratio greater than 1000 in a 100 nm channel filled with 0.01× phosphate-buffered saline solution (PBS). We further demonstrated that at higher ionic strength conditions, reducing the solution pH increased the number of protonated amines within the PLL layer, amplifying the charge disparities along the channel and leading to greater rectification. As nanofluidic diodes with bipolar surface charge distributions tend to provide superior performance compared to those with a single wall charge polarity, we imposed a more bipolar charge distribution in our devices by partially coating our PDA-PLL-coated channels with negatively charged polyacrylic acid (PAA). These enhanced bipolar channels exhibited greater current rectification than the PDA-PLL-coated channels, reaching rectification ratios in excess of 100 even in more physiologically-relevant 1× PBS solutions. Our fabrication approach and the results herein provide a promising platform from which the scientific community can build upon in the relentless endeavor for improved sensitivity in biosensors and other analytical devices.

The Modification and Applications of Nanopipettes in Electrochemical Analysis

Nanopipette, which is fabricated by glasses and possesses a nanoscale pore in the tip, has been proven to be immensely useful in electrochemical analysis. Numerous nanopipette-based sensors have emerged with improved sensitivity, selectivity, ease of use, and miniaturization. In this minireview, we provide an overview of the recent developments of nanopipette-based electrochemical sensors based on different types of nanopipettes, including single-nanopipettes, self-referenced nanopipettes, dual-nanopipettes, and double-barrel nanopipettes. Several important modification materials for nanopipette functionalization are highlighted, such as conductive materials, macromolecular materials, and functional molecules. These materials can improve the sensing performance and targeting specificities of nanopipettes. We also discuss examples of related applications and the future development of nanopipette-based strategies.

Real-Time Monitoring of Exosomes Secretion from Single Cell Using Dual-Nanopore Biosensors

Exosomes secreted from cells carry rich information from their parent cells, representing a promising biomarker for investigation of diseases. We develop a dual-nanopore biosensor using DNA aptamers to specifically recognize CD63 protein on the exosome's surface, which enables label-free exosome detection based on ionic current change. The sensor allows for sensitive detection of exosomes with a detection limit of 3.4 × 10⁶ particles/mL. The dual-nanopore biosensor was able to form an intrapipette electric circuit for ionic current measurement due to its unique structure, which is crucial to achieve detection of exosome secretion from a single cell. We utilized a microwell array chip to entrap a single cell into a confined microwell with small volume, enabling the accumulation of exosomes with high concentration. The dual-nanopore biosensor was positioned into the microwell with a single cell, and monitoring of exosome secretion from a single cell in different cell lines and under different stimulations has been achieved. Our design may provide a useful platform for developing nanopore biosensors for detecting cell secretions from a single living cell.

Multivalent Ion-Modulated Electron Transfer Processes in Carbon Nanopipettes

Conductive nanopipettes with both an electroactive interface and a pipet geometry have been recognized as powerful multifunctional probes in various electrochemical sensing and imaging applications. As confined inside the nanopipette, the excess surface charges at the solid/solution interface would then play a dominant role in the resulting charge transport processes. Herein, the effects of a multivalent ion on the resulting electron transfer (ET) processes in the carbon nanopipettes are investigated with both experimental and simulation methods. The multivalent cations (i.e., Ca²⁺, Mg²⁺, Co²⁺, and Ni²⁺) are shown to strongly adsorb at the negatively charged carbon surface and attract more Fe(CN)₆^4- ions inside the cavity, as indicated by the increasing ET current responses. In addition to elucidating the fundamental charge transport processes in conductive nanopipettes to afford better usage as electrochemical probes, these results could also help in the development of new sensing methods for measuring the non-electroactive ions in biological or environmental systems.

Specially Resolved Single Living Cell Perfusion and Targeted Fluorescence Labeling Based on Nanopipettes

Targeted delivery and labeling of single living cells in heterogeneous cell populations are of great importance to understand the molecular biology and physiological functions of individual cells. However, it remains challenging to perfuse fluorescence markers into single living cells with high spatial and temporal resolution without interfering neighboring cells. Here, we report a single cell perfusion and fluorescence labeling strategy based on nanoscale glass nanopipettes. With the nanoscale tip hole of 100 nm, the use of nanopipettes allows special perfusion and high-resolution fluorescence labeling of different subcellular regions in single cells of interest. The dynamic of various fluorescent probes has been studied to exemplify the feasibility of nanopipette-dependent targeted delivery. According to experimental results, the cytoplasm labeling of Sulfo-Cyanine5 and fluorescein isothiocyanate is mainly based on the Brownian movement due to the dyes themselves and does not have a targeting ability, while the nucleus labeling of 4',6-diamidino-2-phenylindole (DAPI) is originated from the adsorption between DAPI and DNA in the nucleus. From the finite element simulation, the precise manipulation of intracellular delivery is realized by controlling the electro-osmotic flow inside the nanopipettes, and the different delivery modes between nontargeting dyes and nucleus-targeting dyes were compared, showcasing the valuable ability of nanopipette-based method for the analysis of specially defined subcellular regions and the potential applications for single cell surgery, subcellular manipulation, and gene delivery.

Fabrication of solid-state nanopores

Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.

Visualization of Ion Fluxes in Nanopipettes: Detection and Analysis of Electro-osmosis of the Second Kind

Nanopipettes are finding increasing use as nano "test tubes", with reactions triggered through application of an electrochemical potential between electrodes in the nanopipette and a bathing solution (bath). Key to this application is an understanding of how the applied potential induces mixing of the reagents from the nanopipette and the bath. Here, we demonstrate a laser scanning confocal microscope (LSCM) approach to tracking the ingress of dye into a nanopipette (20-50 nm diameter end opening). We examine the case of dianionic fluorescein under alkaline conditions (pH 11) and large applied tip potentials (±10 V), with respect to the bath, and surprisingly find that dye ingress from the bath into the nanopipette is not observed under either sign of potential. Finite element method (FEM) simulations indicate this is due to the dominance of electro-osmosis in mass transport, with electro-osmotic flow in the conventional direction at +10 V and electro-osmosis of the second kind acting in the same direction at -10 V, caused by the formation of significant space charge in the center of the orifice. The results highlight the significant deviation in mass transport behavior that emerges at the nanoscale and the utility of the combined LSCM and FEM approach in deepening understanding, which in turn should promote new applications of nanopipettes.

Discerning Tyrosine Phosphorylation from Multiple Phosphorylations Using a Nanofluidic Logic Platform

Discerning tyrosine phosphorylation (pTyr) catalyzed by Tyr kinase is central to the revelation of oncogenic mechanisms and the development of targeted anticancer drugs. Despite some techniques, this goal remains challenging, especially when faced with the interference of multiple phosphorylation events, including serine (pSer) and threonine phosphorylation (pThr). We describe here a functional polymer-modified artificial ion nanochannel, which enables the sensitive and selective recognition of phosphotyrosine (pY) peptide by the distinct ionic current change. Such a recognition effect allows for the nanochannel to work in a complex protein digest condition. Further, the implementation of nanofluidic logic functions with the addition of Ca²⁺ dramatically improves the selectivity of the nanochannel to pY peptide and thus can discern pTyr by the Tyr kinase from pSer by the Ser/Thr kinase through simultaneously monitoring multisite phosphorylation at the same or different peptide substrates in one-pot. This logic sensing platform displays the potential in differentiating Tyr kinase and Ser/Thr kinase and assessing multi-kinase activities in multi-targeted drug design.

Quantification of the charge transport processes inside carbon nanopipettes

Conductive nanopipettes have been extensively used as powerful multifunctional probes for electrochemical and ion transport measurements, while the involved charge transfer processes have not been fully explored. In this paper, we use both experimental and simulation methods to de-convolute and quantify the respective electron transfer (ET) and ion transport (IT) contributions to the resulting current signals in carbon nanopipettes (CNPs). The results present that the current signals in CNPs are determined by ET in the case of low solution depth and long timescales, while IT becomes dominant at short timescales or high solution depth. In addition, the electrochemically and chemically irreversible ET processes in CNPs were also quantified. The elucidated and quantified charge transport processes inside CNPs will help control and optimize the IT and ET processes at the nanoscale, promoting better and broad usage of conductive nanopipettes in single-entity sensing and imaging applications.

The coupled electron transfer (ET) and ion transport (IT) processes in conductive nanopipettes, at both steady and transient states, are elucidated and quantified by experiments and simulation.

Scanning Ion Conductance Microscopy

Scanning ion conductance microscopy (SICM) has emerged as a versatile tool for studies of interfaces in biology and materials science with notable utility in biophysical and electrochemical measurements. The heart of the SICM is a nanometer-scale electrolyte filled glass pipette that serves as a scanning probe. In the initial conception, manipulations of ion currents through the tip of the pipette and appropriate positioning hardware provided a route to recording micro- and nanoscopic mapping of the topography of surfaces. Subsequent advances in instrumentation, probe design, and methods significantly increased opportunities for SICM beyond recording topography. Hybridization of SICM with coincident characterization techniques such as optical microscopy and faradaic electrodes have brought SICM to the forefront as a tool for nanoscale chemical measurement for a wide range of applications. Modern approaches to SICM realize an important tool in analytical, bioanalytical, biophysical, and materials measurements, where significant opportunities remain for further exploration. In this review, we chronicle the development of SICM from the perspective of both the development of instrumentation and methods and the breadth of measurements performed.

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

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

Etching-Engineered Low-Voltage Dielectrophoretic Nanotweezers for Trapping of Single Molecules

Understanding the functions of biomolecules at the single-molecule level is crucial due to their important and diverse roles in cell regulation. Recently, nanotweezers made of dual carbon nanoelectrodes have been developed for single-cell biopsies by applying a high alternating voltage. However, high electric voltage can induce Joule heating, water electrolysis, and other side effects on cell activity, which may be unfavorable for cellular applications. Here, we report a low-voltage nanotweezer for trapping of single DNA molecules using etching-engineered nanoelectrodes which effectively reduce the minimum trapping voltage by six times. Meanwhile, the low-voltage nanotweezer displays an improved trapping stiffness. Based on the finite element method simulations, we attribute the mechanism for the low-voltage nanotweezers to the increase in spatial heterogeneity and nonuniformity of electric field by etching of quartz near the nanoelectrodes. This work opens a new dimension for noninvasive single-molecule manipulation in solution and potential applications in single-cell biopsies.

Single plasmonic nanostructures for biomedical diagnosis

The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.

Low-Noise Solid-State Nanopore Enhancing Direct Label-Free Analysis for Small Dimensional Assemblies Induced by Specific Molecular Binding

Solid-state nanopores show special potential as a new single-molecular characterization for nucleic acid assemblies and molecular machines. However, direct recognition of small dimensional species is still quite difficult due the lower resolution compared with biological pores. We recently reported a very efficient noise-reduction and resolution-enhancement mechanism via introducing high-dielectric additives (e.g., formamide) into conical glass nanopore (CGN) test buffer. Based on this advance, here, for the first time, we apply a bare CGN to directly recognize small dimensional assemblies induced by small molecules. Cocaine and its split aptamer (Capt assembly) are chosen as the model set. By introducing 20% formamide into CGN test buffer, high cocaine-specific distinguishing of the 113 nt Capt assembly has been realized without any covalent label or additional signaling strategies. The signal-to-background discrimination is much enhanced compared with control characterizations such as gel electrophoresis and fluorescence resonance energy transfer (FRET). As a further innovation, we verify that low-noise CGN can also enhance the resolution of small conformational/size changes happening on the side chain of large dimensional substrates. Long duplex concatamers generated from the hybridization chain reaction (HCR) are selected as the model substrates. In the presence of cocaine, low-noise CGN has sensitively captured the current changes when the 26 nt aptamer segment is assembled on the side chain of HCR duplexes. This paper proves that the introduction of the low-noise mechanism has significantly improved the resolution of the solid-state nanopore at smaller and finer scales and thus may direct extensive and deeper research in the field of CGN-based analysis at both single-molecular and statistical levels, such as molecular recognition, assembly characterization, structure identification, information storage, and target index.

Ion Selective Detection Based on the Nuances of the Kinetic Fingerprint for Ion Transfer at Soft Interfaces

A novel approach has been developed for the selective determination of cations or anions based on the application of Fourier transformed staircase sinusoidal voltammetry (FT-SC-SV) in combination with the interface between two immiscible electrolyte solutions (ITIES) in the four-electrode configuration. The electrochemistry at the ITIES provides a very simple yet sensitive platform for the detection of a broad spectrum of redox inactive ions and even the neutral (bio)molecules that can be charged (e.g., protonated in appropriate pH). FT-SC-SV employs a complex potential excitation, i.e., a large-amplitude sine wave superimposed onto a dc bias potential that is stepped/scanned throughout the potential window. The response current is subsequently analyzed in the frequency domain by FT. Although the ions have close standard/formal transfer potential, discrimination and selective detection can be achieved by the higher harmonics. Feasibility and reliability of the proposed approach were verified with two pairs of ions that have very close transfer potentials across the ITIES and were chosen as the model systems. Besides, the additivity of the ionic current magnitude on concentration measured either in the mixture of ionic analytes or in individually prepared solutions containing the separate ionic analyte was tested. The experimental results prove that the principle of additivity holds. Compared with the traditional voltammetry, FT-SC-SV is simpler and more efficient in discrimination and quantification of apparently indistinguishable ion transfer from the viewpoint of thermodynamics. This demonstration may provide a new way for analytical detection of a broad range of redox inactive ions in terms of both fundamentals and applications.

Target-Triggered Assembly in a Nanopipette for Electrochemical Single-Cell Analysis

Engineered nanopipette tools have recently emerged as a powerful approach for electrochemical nanosensing, which has major implications in both fundamental biological research and biomedical applications. Herein, we describe a generic method of target-triggered assembly of aptamers in a nanopipette for nanosensing, which is exemplified by sensitive and rapid electrochemical single-cell analysis of adenosine triphosphate (ATP), a ubiquitous energy source in life and important signaling molecules in many physiological processes. Specifically, a layer of thiolated aptamers is immobilized onto a Au-coated interior wall of a nanopipette tip. With backfilled pairing aptamers, the engineered nanopipette is then used for probing intracellular ATP via the ATP-dependent linkage of the split aptamers. Due to the higher surface charge density from the aptamer assembly, the nanosensor would exhibit an enhanced rectification signal. Besides, this ATP-responsive nanopipette tool possesses excellent selectivity and stability as well as high recyclability. This work provides a practical single-cell nanosensor capable of intracellular ATP analysis. More generally, integrated with other split recognition elements, the proposed mechanism could serve as a viable basis for addressing many other important biological species.

Ribosome Fingerprinting with a Solid-State Nanopore

Nanopores hold great potential for the analysis of complex biological molecules at the single-entity level. One particularly interesting macromolecular machine is the ribosome, responsible for translating mRNAs into proteins. In this study, we use a solid-state nanopore to fingerprint 80S ribosomes and polysomes from a human neuronal cell line andDrosophila melanogaster cultured cells and ovaries. Specifically, we show that the peak amplitude and dwell time characteristics of 80S ribosomes are distinct from polysomes and can be used to discriminate ribosomes from polysomes in mixed samples. Moreover, we are able to distinguish large polysomes, containing more than seven ribosomes, from those containing two to three ribosomes, and demonstrate a correlation between polysome size and peak amplitude. This study highlights the application of solid-state nanopores as a rapid analytical tool for the detection and characterization of ribosomal complexes.

The double life of conductive nanopipette: a nanopore and an electrochemical nanosensor

The continuing interest in nanoscale research has spurred the development of nanosensors for liquid phase measurements. These include nanopore-based sensors typically employed for detecting nanoscale objects, such as nanoparticles, vesicles and biomolecules, and electrochemical nanosensors suitable for identification and quantitative analysis of redox active molecules. In this Perspective, we discuss conductive nanopipettes (CNP) that can combine the advantages of single entity sensitivity of nanopore detection with high selectivity and capacity for quantitative analysis offered by electrochemical sensors. Additionally, the small physical size and needle-like shape of a CNP enables its use as a tip in the scanning electrochemical microscope (SECM), thus, facilitating precise positioning and localized measurements in biological systems.

In situ detection of hydroxyl radicals in mitochondrial oxidative stress with a nanopipette electrode

A nanopipette sensor was designed for the in situ detection of ˙OH around mitochondria with high selectivity and sensitivity.

The fabrication of a gold nanoelectrode–nanopore nanopipette for dopamine enrichment and multimode detection

It is important to further improve the electrophysiology and electrochemistry techniques of neurotransmitter detection.

Rational Design of Stimuli-Responsive Polymers Modified Nanopores for Selective and Sensitive Determination of Salivary Glucose

The great pain and stress from finger-prick glucose measurements have resulted in great motivation to find noninvasive glucose monitoring technologies where salivary glucose measurement is desirable. However, the relative low concentration of glucose and coexisting chemicals in saliva challenges the sensitive and selective salivary glucose detection. In this article, we have rationally designed and constructed a salivary glucose sensor by modifying the inner wall of the Au-decorated glass nanopore with stimuli-responsive copolymer poly(3-(acryloylthioureido) phenylboronic acid-co-N-isopropylacrylamide) (denoted as PATPBA-co-PNIPAAm) via Au-S interaction. Notably, upon recognition of glucose, the copolymer could undergo a wettability switch and pKa shifts in the boronic acid functional groups, which significantly regulated the ion transport through nanopores, thus showing improved sensitivity with the detection limit of 1 nM. Moreover, benefiting from the multivalent boronic acid-glucose interaction and the cooperation of thiourea units, the copolymer exhibited good selectivity for glucose detection against the coexisting saccharides and other biological molecules in saliva. The nanopores with well-demonstrated analytical performance were finally applied for monitoring glucose in saliva. Together, this work unveiled a new platform for glucose detection in saliva, and promised to provide a new strategy for detecting other biomolecules in accessible biofluid involved in physiological and pathological events.

Mechanistic Study of Oxygen Reduction at Liquid/Liquid Interfaces by Hybrid Ultramicroelectrodes and Mass Spectrometry

Proton-coupled electron transfer (PCET) reactions at various interfaces (liquid/membrane, solid/electrolyte, liquid/liquid) lie at the heart of many processes in biology and chemistry. Mechanistic study can provide profound understanding of PCET and rational design of new systems. However, most mechanisms of PCET reactions at a liquid/liquid interface have been proposed based on electrochemical and spectroscopic data, which lack direct evidence for possible intermediates. Moreover, a liquid/liquid interface as one type of soft interface is dynamic, making the investigation of interfacial reactions very challenging. Herein a novel electrochemistry method coupled to mass spectrometry (EC-MS) was introduced for in situ study of the oxygen reduction reaction (ORR) by ferrocene (Fc) under catalysis from cobalt tetraphenylporphine (CoTPP) at liquid/liquid interfaces. The key units are two types of gel hybrid ultramicroelectrodes (agar-gel/organic hybrid ultramicroelectrodes and water/PVC-gel hybrid ultramicroelectrodes), which were made based on dual micro- or nanopipettes. A solidified liquid/liquid interface can be formed at the tip of these pipettes, and it serves as both an electrochemical cell and a nanospray emitter for mass spectrometry. We demonstrated that the solidified L/L interfaces were very similar to typical L/L interfaces. Key CoTPP intermediates of the ORR at the liquid/liquid interfaces were identified for the first time, and the four-electron oxygen reduction pathway predominated, which provides valuable insights into the mechanism of the ORR. Theoretical simulation has further supported the possibility of formation of intermediates. This type of platform is promising for in situ tracking and identifying intermediates to study complicated reactions at liquid/liquid interfaces or other soft interfaces.

Wireless nanopore electrodes for analysis of single entities

Measurements of a single entity underpin knowledge of the heterogeneity and stochastics in the behavior of molecules, nanoparticles, and cells. Electrochemistry provides a direct and fast method to analyze single entities as it probes electron/charge-transfer processes. However, a highly reproducible electrochemical-sensing nanointerface is often hard to fabricate because of a lack of control of the fabrication processes at the nanoscale. In comparison with conventional micro/nanoelectrodes with a metal wire inside, we present a general and easily implemented protocol that describes how to fabricate and use a wireless nanopore electrode (WNE). Nanoscale metal deposition occurs at the tip of the nanopipette, providing an electroactive sensing interface. The WNEs utilize a dynamic ionic flow instead of a metal wire to sense the interfacial redox process. WNEs provide a highly controllable interface with a 30- to 200-nm diameter. This protocol presents the construction and characterization of two types of WNEs-the open-type WNE and closed-type WNE-which can be used to achieve reproducible electrochemical measurements of single entities. Combined with the related signal amplification mechanisms, we also describe how WNEs can be used to detect single redox molecules/ions, analyze the metabolism of single cells, and discriminate single nanoparticles in a mixture. This protocol is broadly applicable to studies of living cells, nanomaterials, and sensors at the single-entity level. The total time required to complete the protocol is ~10-18 h. Each WNE costs ~$1-$3.

An investigation of solid-state nanopores on label-free metal-ion signalling via the transition of RNA-cleavage DNAzyme and the hybridization chain reaction

Recent advances have proven solid-state nanopores as a powerful analysis platform that enables label-free and separation-free single-molecule analysis. However, the relatively low resolution still limits its application because many chemicals or targets with small sizes could not be recognized in a label-free condition. In this paper, we provide a possible solution that uses solid-state nanopores for small species signaling via the transition of huge DNA assembly products. DNAzyme responding to metal ions and the hybridization chain reaction (HCR) generating nanopore-detectable dsDNA concatamers are used as the transition model set. By the two-step DNAzyme-HCR transition, Pb2+ that was too tiny to be sensed was successfully recognized by the nanopore. The whole process happened in a completely homogeneous solution without any chemical modification. During condition optimization, we also discussed one possible application challenge that may affect the HCR signal-background distinction. Solid-state nanopores provide a potential solution to this challenge due to its ability to profile product length or even 3D structure information.

One-Dimensional Assemblies of a DNA Tetrahedron: Manipulations on the Structural Conformation and Single-Molecule Behaviors

DNA nanotechnology can construct various nanostructures with diverse functionalities. However, conformation fluctuations due to the structural flexibility of duplex DNA compromise the efficiency to realize the functionality and reactivity of DNA nanostructures. To understand and control the structural deviation from the design represents a major challenge as well as an opportunity for DNA nanotechnology. In the present work, two series of one-dimensional assemblies of DNA tetrahedrons (DTHs) were fabricated and applied to demonstrate the manipulations of conformation dynamics of a one-dimensional DTH assembly by simple variation on linkage styles at single-molecule resolution. A stepwise strategy allows both nanoassembly with a high fidelity in the number and sequence of DTH units to be assembled with a minimum number of linkage sequences. The characterization for these nanostructures with atomic force microscope (AFM) and a solid-state nanopore technique indicates the difference in conformation dynamics and bending stiffness between two analogous nanoassemblies both in the immobilized state on the surface and free state in solution. This work showed the power of fine-tuning the dynamic conformation of the nanostructures and could see the applications in single-molecule biosensing and functionalization of DNA nanostructures.

Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit

Recent advances have proven that using solid-state nanopores is a promising single molecular technique to enrich the DNA assembly signaling library. Other than using them for distinguishing structures, here we innovatively adapt solid-state nanopores for use in analyzing assembly mixtures, which is usually a tougher task for either traditional characterization techniques or nanopores themselves. A trigger induced DNA step polymerization (SP-CHA), producing three-way-DNA concatemers, is designed as a model. Through counting and integrating the translocation-induced current block when each concatemer passes through a glass conical glass nanopore, we propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the "base-pair distribution" of SP-CHA concatemer mixtures. Due to the higher sensitivity, a number of super long concatemers that were previously difficult to detect via gel electrophoresis are also revealed. These ultra-concatemers, longer than 2 kbp, could provide a much enhanced signal-to-noise ratio for nanopores and are thus believed to be more accurate indicators for the existence of a trigger, which may be of benefit for further applications, such as molecular machines or biosensors.

Nanopore-Based Confined Spaces for Single-Molecular Analysis

The field of nanopore sensing at the single-molecular level is in a "boom" period. Such nanopores, which are either composed of biological materials or are fabricated from solid-state substrates, offer a unique confined space that is compatible with the single-molecular scale. Under the influence of an electrical field, such single-biomolecular interfaces can read single-molecular information and, if appropriately fine-tuned, each molecule plays its individual ionic rhythm to compose a "molecular symphony". Over the past few decades, many research groups have worked on nanopore-based single-molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore-based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.

Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging

Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.