Ion-beam sculpting at nanometre length scales

Empowering protein single-molecule sequencing: nanopore technology toward sensing gene sequences

The investigation of proteins at the single-molecule level is urgent to reveal the relationship between their structure and function. Unlike traditional techniques for attaining the overall average effect of group systems, nanopore sensing mode can provide information on the characteristics of proteins at the single-molecule level. Assisting with the intensity, frequency, and period of current changes, nanopore sequencing technology is rapidly advancing due to its merits, including fast readout, high accuracy, low cost, and portability. In particular, the single-molecule nanopore sequencing mode enables in-depth studies of DNA-protein interactions, protein conformation, DNA sequencing, and microbial assay, including genome sequencing of new species. This review summarizes the sensing mechanisms of nanopore sequencing technology in DNA damage, DNA methylation, RNA sequencing, and protein post-translational modifications and unfolding, covering both biological and solid-state nanopores. Due to these significant advantages, nanopore sequencing provides new insights into complex biological processes and enables more precise real-time monitoring of molecular changes. Its applications extend to clinical diagnostics, environmental monitoring, food safety, and forensic analysis. Moreover, the review outlines the present challenges faced by nanopore sequencing patterns, such as the choice of raw reagents and the design of special construction, offering a deep understanding of nanoporous single-molecule sensing toward protein sequence information and structure prediction.

Exploring a solid-state nanopore approach for single-molecule protein detection from single cells

Direct protein analysis from complex cellular samples is crucial for understanding cellular diversity and disease mechanisms. Here, we explored the potential of SiN x solid-state nanopores for single-molecule protein analysis from complex cellular samples. Using the LOV2 protein as a model, we designed a nanopore electrophoretic driver protein and fused it with LOV2, thereby enhancing the capture efficiency of the target protein. Then, we performed ex situ single-cell protein analysis by directly extracting the contents of individual cells using glass nanopipette-based single-cell extraction and successfully identified and monitored the conformational changes of the LOV2 protein from single-cell extracts using SiN x nanopores. Our results reveal significant differences between proteins measured directly from single cells and those obtained from purified samples. This work demonstrates the potential of solid-state nanopores as a powerful tool for single-cell, single-molecule protein analysis, opening avenues for investigating protein dynamics and interactions at the cellular level.

Stereochemistry at the Single-Molecule Level: From Monitoring to Regulation

Traditional stereochemistry analysis is crucial for understanding the molecular behavior, but relies on measurements that encompass multiple molecules and obscure individual molecular dynamics. Single-molecule techniques enable real-time tracking of stereochemical transformations. These techniques include electrical methods (such as scanning probe microscopy, single-molecule junction techniques, and nanopore technology) and non-electrical approaches (such as circular dichroism spectroscopy and surface-enhanced Raman spectroscopy). This review highlights recent advances in monitoring and regulation of stereochemical properties at the single-molecule level. Techniques that bridge macroscopic observations with molecular-scale dynamics are emphasized. Key isomerization phenomena (constitutional, configurational, and conformational isomerizations) are explored to demonstrate how light, electric field, and mechanical force regulate molecular states. The use of chiral molecules in optical tweezers, chiral-modified scanning tunneling microscopies, and graphene-based single-molecule junctions to leverage the chirality-induced spin selectivity effect for enantiomer discrimination and manipulation is highlighted. Despite progress in this field, challenges persist in resolving ultrafast isomerization pathways, understanding chiral origin mechanisms, and integrating single-molecule devices. Emerging strategies combining multimodal stimuli, machine learning, and nanofabrication are promising for advancing stereochemical research and applications in molecular electronics and nanotechnology. This work underscores the transformative potential of single-molecule techniques in unveiling fundamental chemical dynamics and designing functional molecular systems.

Nanopore Environmental Analysis

As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.

Insights on using plastic-based dual in-plane nanopore sensors for differentiation and shape determinations of single protein molecules

Techniques to analyze proteins often involves complex workflows and/or sophisticated equipment with modest limits-of-detection. While fluorescence spectroscopy can interrogate single molecules, it often requires fluorescence labeling with lasers and microscopes. We report herein a label-free approach for analyzing intact proteins using resistive pulse sensing (RPS). RPS data were secured using a unique RPS device, which we call a dual in-plane nanopore sensor, fabricated in a thermoplastic. The nanopore sensor was produced via nano-injection molding with critical structures of 30 nm, enabling the detection of individual protein molecules and providing an approach toward their identification. Following nano-injection molding, the pore size could be reduced to ∼ 10 nm using thermal fusion bonding of a cover plate to the molded substrate. The device architecture contained two in-plane nanopores flanking a nanochannel (50 × 50 nm width × depth and 5 µm length) that facilitated the measurement of the apparent electrophoretic mobilities of protein molecules in a label free manner via their molecular-dependent time-of-flight (ToF; time-difference between two consecutive RPS events-peak pair). We investigated four model proteins and collected multiple characteristics including RPS peak amplitude and dwell time, as well as an RPS-independent value, which was the ToF. Furthermore, we analyzed the temporal profiles of RPS events revealing distinct peak shapes for spherical and non-spherical proteins that were influenced by their rotational motion when resident within the nanopore.

Single-molecule resolution of macromolecules with nanopore devices

Nanopore-based electrical detection technology holds single-molecule resolution and combines the advantages of high sensitivity, high throughput, rapid analysis, and label-free detection. It is widely applied in the determination of organic and biological macromolecules, small molecules, and nanomaterials, as well as in nucleic acid and protein sequencing. There are a wide variety of organic polymers and biopolymers, and their chemical structures, and conformation in solution directly affect their ensemble properties. Currently, there is limited approach available for the analysis of single-molecule conformation and self-assembled topologies of polymers, dendrimers and biopolymers. Nanopore single-molecule platform offers unique advantages over other sensing technologies, particularly in molecular size differentiation of macromolecules and complex conformation analysis. In this review, the classification of nanopore devices, including solid-state nanopores (SSNs), biological nanopores, and hybrid nanopores is introduced. The recent developments and applications of nanopore devices are summarized, with a focus on the applications of nanopore platform in the resolution of the structures of synthetic polymer, including dendritic, star-shaped, block copolymers, as well as biopolymers, including polysaccharides, nucleic acids and proteins. The future prospects of nanopore sensing technique are ultimately discussed.

Probing nanopores: molecular dynamics insights into the mechanisms of DNA and protein translocation through solid-state and biological nanopores

Nanopore sequencing technology has revolutionized single-molecule analysis through its unique capability to detect and characterize individual biomolecules with unprecedented precision. This perspective provides a comprehensive analysis of molecular dynamics (MD) simulations in nanopore research, with particular emphasis on comparing molecular transport mechanisms between biological and solid-state platforms. We first examine how MD simulations at atomic resolution reveal distinct characteristics: biological nanopores exhibit sophisticated molecular recognition through specific amino acid interactions, while solid-state nanopores demonstrate advantages in structural stability and geometric control. Through detailed analysis of simulation methodologies and their applications, we show how computational approaches have advanced our understanding of critical phenomena such as ion selectivity, conformational dynamics, and surface effects in both nanopore types. Despite computational challenges including limited simulation timescales and force field accuracy constraints, recent advances in high-performance computing and artificial intelligence integration have significantly improved simulation capabilities. By synthesizing perspectives from physics, chemistry, biology, and computational science, this perspective provides both theoretical insights and practical guidelines for developing next-generation nanopore platforms. The integration of computational and experimental approaches discussed here offers promising directions for advancing nanopore technology in applications ranging from DNA/RNA sequencing and protein post-translational modification analysis to disease diagnosis and drug screening.

Accurate Molecular Sensing based on a Modular and Customizable CRISPR/Cas-Assisted Nanopore Operational Nexus (CANON)

Solid-state nanopore is a promising single molecular detection technique, but is largely limited by relatively low resolution to small-size targets and laborious design of signaling probes. Here we establish a universal, CRISPR/Cas-Assisted Nanopore Operational Nexus (CANON), which can accurately transduce different targeting sources/species into different DNA structural probes via a "Signal-ON" mode. Target recognition activates the cleavage activity of a Cas12a/crRNA system and then completely digest the blocker of an initiator. The unblocked initiator then triggers downstream DNA assembly reaction and generate a large-size structure easy for nanopore detection. Such integration of Cas12a/crRNA with DNA assembly establishes an accurate correspondence among the input targets, output DNA structures, and the ultimate nanopore signals. We demonstrated dsDNA, long RNA (i.e., Flu virus gene), short microRNA (i.e., let-7d) and non-nucleic acids (i.e., Pb2+) as input paradigms. Various structural assembly reactions, such as hybridization chain reaction (HCR), G-HCR and duplex polymerization strategy (DPS), are adapted as outputs for nanopore signaling. Simultaneous assay is also verified via transferring FluA and FluB genes into HCR and G-HCR, respectively. CANON is thus a modular sensing platform holding multiple advantages such as high accuracy, high resolution and high universality, which can be easily customized into various application scenes.

A long-term stable solid-state nanopore for the dynamic monitoring of DNA synthesis

BACKGROUND

Solid-state nanopores are more suitable than biological nanopores for applications requiring durability and operation across a wider range of external parameters. However, the current solid-state nanopores prepared by various methods have the problem of poor stability, which limits the reproducibility of solid-state nanopore experiments and further wide application in the field of biochemical detection. So far, the problem of poor stability of nanopores has not been effectively solved. Therefore, it is still an urgent problem to explore effective experimental protocols to obtain solid-state nanopores with high stability.

RESULTS

In this study, we dynamically monitored the instability of solid-state nanopores by high-resolution transmission electron microscopy and examined the effect of instability on the open-pore conductance of solid-state nanopores. In order to obtain long-term stability of solid-state nanopores, we used a chemical modification protocol to cover the surface of the solid-state nanopores with a dense protective film and demonstrated the reproducibility of our protocol through TEM characterization and extensive data statistics. Finally, we used long-lived solid-state nanopores to dynamically monitor the process of DNA synthesis by polymerase for more than 10 h, and calculated that the synthesis rate of polymerase was about 1.33-1.78 kb/min.

SIGNIFICANCE

Long-term stability of solid-state nanopores are essential for its future development. Our observation of the unstable behavior of solid-state nanopores and the exploration of solutions will promote the wider application of solid-state nanopores in biochemical detection and other fields.

Advances and Challenges in Solid-State Nanopores for DNA Sequencing

Solid-state nanopore sensing, a state-of-the-art technology for single-molecule detection, has rapidly advanced in recent years and demonstrates significant potential in DNA sequencing. This technology determines the nucleotide sequences by analyzing the electrical or optical signal variations that occur when DNA molecules pass through the nanopore. It offers notable advantages, including high-throughput, single-molecule detection, real-time monitoring, and the elimination of the need for polymerase chain reaction (PCR) amplification, thereby presenting broad application prospects in areas such as the diagnosis and treatment of genetic diseases. This paper reviews the solid-state nanopore DNA sequencing technology by discussing advancements in nanopore types, preparation techniques, and sequencing detection methods. It examines various nanopore materials, including silicon-based materials and two-dimensional (2D) materials, as well as preparation techniques such as transmission electron microscopy (TEM), focused ion beam (FIB) etching, and controlled breakdown (CBD). Additionally, it elucidates sequencing detection mechanisms, including ion-current blockade, transverse-current detection, and optical detection. However, this technology faces numerous challenges in its implementation and future commercialization. For instance, limited spatial resolution hampers single-base identification; the rapid translocation speed of DNA impacts time resolution; and various types of noise significantly disrupt detection signals. In response, researchers have proposed several solutions, including local thinning of the film, adjustment of surface charges, and optimization of detection materials and structures. With interdisciplinary integration and technological innovation, solid-state nanopore DNA sequencing technology is expected to make breakthroughs, bringing transformations to life sciences research and medical diagnosis.

Electric Field Mediated Unclogging of Angstrom-Scale Channels

Angstrom-scale fluidic channels offer immense potential for applications in areas such as desalination, molecular sieving, biomolecular sequencing, and dialysis. Inspired by biological ion channels, nano- and angstrom (Å)-scale channels are fabricated that mimic these molecular or atomic-scale dimensions. At the Å-scale, these channels exhibit unique phenomena, including selective ion transport, osmotic energy generation, fast water and gas flows, and neuromorphic ion memory. However, practical utilization of Å-scale channels is often hindered by contamination, which can clog these nanochannels. In this context, a promising technique is introduced here for unclogging 2D channels, particularly those with sub-nanometre dimensions (≈6.8 Å). The voltage-cycling method emerges as an efficient and reliable solution for this challenge. The electric field effectively dislodges contaminants from the clogged Å-scale channels, facilitating ion and molecular transport. This study provides practical guidelines for reviving clogged nano- and Å-scale channels, thereby enhancing their applicability in various ion and molecular transport applications.

Impact of Translocation Dynamics and Bandwidth on the Readout of DNA Structural Barcodes with Membrane-Based Solid-State Nanopores

Recent advances in nanopore technology have promoted significant progress in single-molecule detection and analysis. In particular, membrane-based solid-state nanopores show promise as highly scalable readout platforms. This study explores the detection performance of this class of nanopores, with a focus on their application in molecular sensing schemes using DNA structural barcodes. The barcode structures, here specifically a series of dumbbell-shaped hairpins, encode information in a dumbbell-bit, which modulates the nanopore ionic current during translocation for readout. Our experiments evaluate the detection capabilities of membrane-based solid-state nanopores with a diameter of ∼15 nm. We investigate the detection success rates of individual dumbbell-bits with lengths ranging from 5 dumbbells (∼35 nm) to 29 dumbbells (∼195 nm) and with varying transmembrane potential. Longer dumbbell-bits exhibit a quasi-constant detection rate, whereas shorter bits show a significant decrease in the detection rate with increasing voltage. The observed dependencies are shown to be due to the increasing translocation velocity with voltage, in combination with the temporal resolution limit of the measurement system. Moreover, we show that a local increase of the effective charge at the dumbbell-bits leads to a proportionally increased local translocation velocity. This local velocity increase further degrades the detection success rate for dumbbell-bits. The findings in this study enhance our understanding of the fundamental limitations and capabilities of nanopore technology in high-throughput biosensing applications and have important implications for the design and optimization of future molecular assays and solid-state nanopore readout platforms.

Localized Nanopore Fabrication in Silicon Nitride Membranes by Femtosecond Laser Exposure and Subsequent Controlled Breakdown

Controlled breakdown has emerged as an effective method for fabricating solid-state nanopores in thin suspended dielectric membranes for various biomolecular sensing applications. On an unpatterned membrane, the site of nanopore formation by controlled breakdown is random. Nanopore formation on a specific site on the membrane has previously been realized using local thinning of the membrane by lithographic processes or laser-assisted photothermal etching under immersion in an aqueous salt solution. However, these approaches require elaborate and expensive cleanroom-based lithography processes or involve intricate procedures using custom-made equipment. Here, we present a rapid cleanroom-free approach using single pulse femtosecond laser exposures of 50 nm thick silicon nitride membranes in air to localize the site of nanopore formation by subsequent controlled breakdown to an area less than 500 nm in diameter on the membrane. The precise positioning of the nanopores on the membrane could be produced both using laser exposure powers which caused significant thinning of the silicon nitride membrane (up to 60% of the original thickness locally), as well as at laser powers which caused no visible modification of the membrane at all. We show that nanopores made using our approach can work as single-molecule sensors by performing dsDNA translocation experiments. Due to the applicability of femtosecond laser processing to a wide range of membrane materials, we expect our approach to simplify the fabrication of localized nanopores by controlled breakdown in a variety of thin film material stacks, thereby enabling more sophisticated nanopore sensors.

Graphite-Based Bio-Mimetic Nanopores for Protein Sequencing and Beyond

Protein sequencing using nanopores represents the next frontier in bio-analytics. However, linearizing unfolded proteins and controlling their translocation speed through solid-state nanopores pose significant challenges in protein sequencing. In order to address these issues, this work proposes a biomimetic graphite-based nanopore construction. These nanopores feature a nanometer-sized pore with a constriction zone, mimicking the structure of the α-hemolysin protein pore. Our all-atom Molecular Dynamics simulations demonstrate the high practical potential of these nanopores by revealing how their charge state renders them complete ion-selective and generates an electro-osmotic flow. This study shows that this nanopore construction can detect peptides at the single amino acid level by analyzing the ionic current traces generated as peptides traverse the nanopore. The novelty of the proposed nanopore lies in its ability to modulate the hydrodynamic drag induced by electro-osmotic flow, relative to the electro-phoretic force. This investigation reveals that tuning these forces helps to linearize translocating peptides and extend the residence time of individual amino acids at the constriction zone of the pore. This significantly enhances the detection and sequencing efficiency of the pore. Furthermore, the high relevance of the proposed nanopores is underscored for seawater desalination through electrodialysis and extends to ion separation under salinity gradients.

Scalable integration of photoresponsive highly aligned nanochannels for self-powered ionic devices

Artificial ionic nanochannels with light perception capabilities hold promise for creating ionic devices. Nevertheless, most research primarily focuses on regulating single nanochannels, leaving the cumulative effect of numerous nanochannels and their integration underexplored. We herein develop a biomimetic photoreceptor based on photoresponsive highly aligned nanochannels (pHANCs), which exhibit uniform channel heights, phototunable surface properties, and excellent compatibility with microfabrication techniques, enabling the scalable fabrication and integration into functional ionic devices. These pHANCs demonstrate exceptional ion selectivity and permeability due to the high surface charges and well-ordered conduits, resulting in outstanding energy harvesting from concentration gradients. Large-scale fabrication of pHANCs has been successfully realized, wherein hundreds of biomimetic photoreceptors produce an ultrahigh voltage over 76 volts, which has not been achieved previously. In addition, we demonstrate that the biomimetic photoreceptor can be further upscaled to be a self-powered ionic image sensor, capable of sensing and decoding incident light information.

2D Materials for Potable Water Application: Basic Nanoarchitectonics and Recent Progresses

Water polluted by toxic chemicals due to waste from chemical/pharmaceuticals and harmful microbes such as E. Coli bacteria causes several fatal diseases; and therefore, water filtration is crucial for accessing clean and safe water necessary for good health. Conventional water filtration technologies include activated carbon filters, reverse osmosis, and ultrafiltration. However, they face several challenges, including high energy consumption, fouling, limited selectivity, inefficiencies in removing certain contaminants, dimensional control of pores, and structural/chemical changes at higher thermal conditions and upon prolonged usage of water filter. Recently, the advent of 2D materials such as graphene, BN, MoS2, MXenes, and so on opens new avenues for advanced water filtration systems. This review delves into the nanoarchitectonics of 2D materials for water filtration applications. The current state of water filtration technologies is explored, the inherent challenges they face are outlines, and the unique properties and advantages of 2D materials are highlighted. Furthermore, the scope of this review is discussed, which encompasses the synthesis, characterization, and application of various 2D materials in water filtration, providing insights into future research directions and potential industrial applications.

Single-Molecule Bioelectronic Sensors with AI-Aided Data Analysis: Convergence and Challenges

Single-molecule bioelectronic sensing, a groundbreaking domain in biological research, has revolutionized our understanding of molecules by revealing deep insights into fundamental biological processes. The advent of emergent technologies, such as nanogapped electrodes and nanopores, has greatly enhanced this field, providing exceptional sensitivity, resolution, and integration capabilities. However, challenges persist, such as complex data sets with high noise levels and stochastic molecular dynamics. Artificial intelligence (AI) has stepped in to address these issues with its powerful data processing capabilities. AI algorithms effectively extract meaningful features, detect subtle changes, improve signal-to-noise ratios, and uncover hidden patterns in massive data. This review explores the synergy between AI and single-molecule bioelectronic sensing, focusing on how AI enhances signal processing and data analysis to boost accuracy and reliability. We also discuss current limitations and future directions for integrating AI, highlighting its potential to advance biological research and technological innovation.

Nanomechanical thermometry for probing sub-nW thermal transport

Accurate local temperature measurement at micro and nanoscales requires thermometry with high resolution because of ultra-low thermal transport. Among the various methods for measuring temperature, optical techniques have shown the most precise temperature detection, with resolutions reaching (~10-9 K). In this work, we present a nanomechanical device with nano-Kelvin resolution (~10-9 K) at room temperature and 1 atm. The device uses a 20 nm thick silicon nitride (SiN) membrane, forming an air chamber as the sensing area. The presented device has a temperature sensing area >1 mm2 for micro/nanoscale objects with reduced target placement constraints as the target can be placed anywhere on the >1 mm2 sensing area. The temperature resolution of the SiN membrane device is determined by deflection at the center of the membrane. The temperature resolution is inversely proportional to the membrane's stiffness, as detailed through analysis and measurements of stiffness and noise equivalent temperature (NET) in the pre-stressed SiN membrane. The achievable heat flow resolution of the membrane device is 100 pW, making it suitable for examining thermal transport on micro and nanoscales.

Nanopore-based sensors for DNA sequencing: a review

Nanopore sensors, owing to their distinctive structural properties, can be used to detect biomolecular translocation events. These sensors operate by monitoring variations in electric current amplitude and duration, thereby enabling the calibration and distinction of various biomolecules. As a result, nanopores emerge as a potentially powerful tool in the field of deoxyribonucleic acid (DNA) sequencing. However, the interplay between testing bandwidth and noise often leads to the loss of part of the critical translocation signals, presenting a substantial challenge for the precise measurement of biomolecules. In this context, innovative detection mechanisms have been developed, including optical detection, tunneling current detection, and nanopore field-effect transistor (FET) detection. These novel detection methods are based on but beyond traditional nanopore techniques and each of them has unique advantages. Notably, nanopore FET sensors stand out for their high signal-to-noise ratio (SNR) and high bandwidth measurement capabilities, overcoming the limitations typically associated with traditional solid-state nanopore (SSN) technologies and thus paving the way for new avenues to biomolecule detection. This review begins by elucidating the fundamental detection principles, development history, applications, and fabrication methods for traditional SSNs. It then introduces three novel detection mechanisms, with a particular emphasis on nanopore FET detection. Finally, a comprehensive analysis of the advantages and challenges associated with both SSNs and nanopore FET sensors is performed, and then insights into the future development trajectories for nanopore FET sensors in DNA sequencing are provided. This review has two main purposes: firstly, to provide researchers with a preliminary understanding of advancements in the nanopore field, and secondly, to offer a comprehensive analysis of the fabrication techniques, transverse current detection principles, challenges, and future development trends in the field of nanopore FET sensors. This comprehensive analysis aims to help give researchers in-depth insights into cutting-edge advancements in the field of nanopore FET sensors.

Review of single-molecule immunoassays: Non-chip and on-chip Assays

Enhancing the sensitivity of immunoassays is an important requirement in the field of immunology, especially in light of rapid developments in genetic testing, making the detection of low-abundance protein biomarkers crucial. Therefore, innovations in highly sensitive immunoassays are imperative. This demand has led to the emergence of single-molecule immunoassays (SMIs), driving advancements in early diagnostic techniques, and ushering in a new era of immunoassays. This review begins by tracing the development of immunoassays and offers a detailed discussion of SMI technology across two distinct pathways: non-chip (SMI without microfluidic chips) and on-chip (SMI with microfluidic chips). Furthermore, we evaluated and compared these methods using two pathways. In addition, this review discusses the significance of SMI techniques in the diagnosis of various diseases and their current applications in laboratory and clinical settings. The progress of SMI in commercial applications and suggestions for innovative directions are also summarized. Despite the considerable potential of SMI, these technologies face challenges in practical application, particularly in developing countries and economically disadvantaged regions. The final section of this review addresses the challenges and prospects of these technologies.

Sequence-Dependent Single-Molecule DNA Sensing Using Covalent Organic Framework Nanopores

Enzyme-free single-molecule sequencing has the potential to significantly expand the application of nanopore technology to DNA, proteins, and saccharides. Despite their advantages over biological nanopores and natural suitability for enzyme-free single-molecule sequencing, conventional solid-state nanopores have not yet achieved single-molecule DNA sequencing. The biggest challenge for the accuracy of single-molecule sequencing using solid-state nanopores lies in the precise control of the pore size and conformity. In this study, we fabricated nanopore devices by covering the tip of a quartz nanopipette with ultrathin two-dimensional (2D) covalent organic framework (COF) nanosheets (pore size ≈ 1.1 nm). The size of the periodically arranged nanopores in COF is comparable to that of protein nanopores, and the structure of each COF nanopore is consistent at the atomic scale. The COF nanopore device could roughly distinguish dAMP, dCMP, dGMP, and dTMP. Furthermore, a certain percentage of the current blockades originating from 150 nucleotides model DNA molecules (13.5% for dA50dC50dA50 and 11.1% for dC50dA50dC50) show distinct DNA sequence-specific concave and convex resistive current patterns. The finite element simulation confirmed that the current blockade pattern of a DNA molecule passing through a COF nanopore is dependent on the relative location of the nanopore with respect to the wall of the nanopipette. Our study is a significant step toward single-molecule DNA sequencing by solid-state nanopores.

Multiple applications of metal-organic frameworks (MOFs) in the treatment of orthopedic diseases

Pharmacologic treatment of orthopedic diseases is a common challenge for clinical orthopedic surgeons, and as an important step in the stepwise treatment of orthopedic diseases, it is often difficult to achieve satisfactory results with existing pharmacologic treatments. Therefore, it is increasingly important to find new ways to effectively improve the treatment pattern of orthopedic diseases as well as to enhance the therapeutic efficacy. It has been found that metal-organic frameworks (MOFs) possess the advantages of high specific surface area, high porosity, chemical stability, tunability of structure and biocompatibility. Therefore, MOFs are expected to improve the conventional traditional treatment modality for bone diseases. This manuscript reviewed the applications of MOFs in the treatment of common clinical bone diseases and look forward to its future development.

Registration of activity of a single molecule of horseradish peroxidase using a detector based on a solid-state nanopore

This work demonstrates the use of a solid-state nanopore detector to monitor the activity of a single molecule of a model enzyme, horseradish peroxidase (HRP). This detector includes a measuring cell, which is divided into cis- and trans- chambers by a silicon nitride chip (SiN structure) with a nanopore of 5 nm in diameter. To entrap a single HRP molecule into the nanopore, an electrode had been placed into the cis-chamber; HRP solution was added into this chamber after application of a negative voltage. The reaction of the HRP substrate, 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), oxidation by the enzyme molecule was performed in the presence of hydrogen peroxide. During this reaction, the functioning of a single HRP molecule, entrapped in the nanopore, was monitored by recording the time dependence of the ion current flowing through the nanopore. The approach proposed in our work is applicable for further studies of functioning of various enzymes at the level of single molecules, and this is an important step in the development of single-molecule enzymology.

Using Nanoscale Passports To Understand and Unlock Ion Channels as Gatekeepers of the Cell

Natural ion channels are proteins embedded in the cell membrane that control many aspects of cell and human physiology by acting as gatekeepers, regulating the flow of ions in and out of cells. Advances in nanotechnology have influenced the methods for studying ion channels in vitro, as well as ways to unlock the delivery of therapeutics by modulating them in vivo. This review provides an overview of nanotechnology-enabled approaches for ion channel research with a focus on the synthesis and applications of synthetic ion channels. Further, the uses of nanotechnology for therapeutic applications are critically analyzed. Finally, we provide an outlook on the opportunities and challenges at the intersection of nanotechnology and ion channels. This work highlights the key role of nanoscale interactions in the operation and modulation of ion channels, which may prompt insights into nanotechnology-enabled mechanisms to study and exploit these systems in the near future.

Research Progress on Saccharide Molecule Detection Based on Nanopores

Saccharides, being one of the fundamental molecules of life, play essential roles in the physiological and pathological functions of cells. However, their intricate structures pose challenges for detection. Nanopore technology, with its high sensitivity and capability for single-molecule-level analysis, has revolutionized the identification and structural analysis of saccharide molecules. This review focuses on recent advancements in nanopore technology for carbohydrate detection, presenting an array of methods that leverage the molecular complexity of saccharides. Biological nanopore techniques utilize specific protein binding or pore modifications to trigger typical resistive pulses, enabling the high-sensitivity detection of monosaccharides and oligosaccharides. In solid-state nanopore sensing, boronic acid modification and pH gating mechanisms are employed for the specific recognition and quantitative analysis of polysaccharides. The integration of artificial intelligence algorithms can further enhance the accuracy and reliability of analyses. Serving as a crucial tool in carbohydrate detection, we foresee significant potential in the application of nanopore technology for the detection of carbohydrate molecules in disease diagnosis, drug screening, and biosensing, fostering innovative progress in related research domains.

Technologies for investigating single-molecule chemical reactions

Single molecules, the smallest independently stable units in the material world, serve as the fundamental building blocks of matter. Among different branches of single-molecule sciences, single-molecule chemical reactions, by revealing the behavior and properties of individual molecules at the molecular scale, are particularly attractive because they can advance the understanding of chemical reaction mechanisms and help to address key scientific problems in broad fields such as physics, chemistry, biology and materials science. This review provides a timely, comprehensive overview of single-molecule chemical reactions based on various technical platforms such as scanning probe microscopy, single-molecule junction, single-molecule nanostructure, single-molecule fluorescence detection and crossed molecular beam. We present multidimensional analyses of single-molecule chemical reactions, offering new perspectives for research in different areas, such as photocatalysis/electrocatalysis, organic reactions, surface reactions and biological reactions. Finally, we discuss the opportunities and challenges in this thriving field of single-molecule chemical reactions.

A Simple Cost-Effective Method to Fabricate Single Nanochannels by Embedding Electrospun Polyethylene Oxide Nanofibers

Solid state nanochannels provide significant practical advantages in many fields due to their interesting properties, such as controllable shape and size, robustness, ion selectivity. But their complex preparation processes severely limit their application. In this study, a simple cost-effective method to fabricate single nanochannel by embedding a single polyethylene oxide (PEO) nanofiber is presented. Firstly, PEO nanofibers are prepared by electrospinning, and then a single PEO nanofiber are precisely transferred to the target sample using a micromanipulation platform. Then, PDMS is used for embedding, and finally, the PEO nanofiber is dissolved to obtain a single nanochannel. Unlike other methods of preparing nanochannels by embedding nanofibers, this method can prepare single nanochannel. The diameter of nanochannel can be as fine as 100 nm, and the length can reach several micrometers. The power generation between two potassium chloride solutions with various combinations of concentrations was investigated using the nanochannel. This low-cost flexible nanochannel can also be used in various applications, including DNA sequencing and biomimetic ion channel.

Immunological assay using a solid-state pore with a low limit of detection

Emerging infectious diseases, cancer, and other diseases are quickly tested mainly via immune reactions based on specific molecular recognition between antigens and antibodies. By changing the diameter of solid-state pores, biomolecules of various sizes can be rapidly detected at the single-molecule level. The combination of immunoreactions and solid-state pores paves the way for an efficient testing method with high specificity and sensitivity. The challenge in developing this method is achieving quantitative analysis using solid-state pores. Here, we demonstrate a method with a low limit of detection for testing tumor markers using a combination of immunoreactions and solid-state pore technology. Quantitative analysis of the mixing ratio of two and three beads with different diameters was achieved with an error rate of up to 4.7%. The hybrid solid-state pore and immunoreaction methods with prostate-specific antigen (PSA) and anti-PSA antibody-modified beads achieved a detection limit of 24.9 fM PSA in 30 min. The hybrid solid-state pore and immunoreaction enabled the rapid development of easy-to-use tests with lower limit of detection and greater throughput than commercially available immunoassay for point-of-care testing.

Integrated In-Plane Nanofluidic Devices for Resistive-Pulse Sensing

Single-particle (or digital) measurements enhance sensitivity (10- to 100-fold improvement) and uncover heterogeneity within a population (one event in 100 to 10,000). Many biological systems are significantly influenced by rare or infrequent events, and determining what species is present, in what quantity, and the role of that species is critically important to unraveling many questions. To develop these measurement systems, resistive-pulse sensing is used as a label-free, single-particle detection technique and can be combined with a range of functional elements, e.g., mixers, reactors, filters, separators, and pores. Virtually, any two-dimensional layout of the micro- and nanofluidic conduits can be envisioned, designed, and fabricated in the plane of the device. Multiple nanopores in series lead to higher-precision measurements of particle size, shape, and charge, and reactions coupled directly with the particle-size measurements improve temporal response. Moreover, other detection techniques, e.g., fluorescence, are highly compatible with the in-plane format. These integrated in-plane nanofluidic devices expand the toolbox of what is possible with single-particle measurements.

Advances in Two-Dimensional Ion-Selective Membranes: Bridging Nanoscale Insights to Industrial-Scale Salinity Gradient Energy Harvesting

Salinity gradient energy, often referred to as the Gibbs free energy difference between saltwater and freshwater, is recognized as "blue energy" due to its inherent cleanliness, renewability, and continuous availability. Reverse electrodialysis (RED), relying on ion-selective membranes, stands as one of the most prevalent and promising methods for harnessing salinity gradient energy to generate electricity. Nevertheless, conventional RED membranes face challenges such as insufficient ion selectivity and transport rates and the difficulty of achieving the minimum commercial energy density threshold of 5 W/m2. In contrast, two-dimensional nanostructured materials, featuring nanoscale channels and abundant functional groups, offer a breakthrough by facilitating rapid ion transport and heightened selectivity. This comprehensive review delves into the mechanisms of osmotic power generation within a single nanopore and nanochannel, exploring optimal nanopore dimensions and nanochannel lengths. We subsequently examine the current landscape of power generation using two-dimensional nanostructured materials in laboratory-scale settings across various test areas. Furthermore, we address the notable decline in power density observed as test areas expand and propose essential criteria for the industrialization of two-dimensional ion-selective membranes. The review concludes with a forward-looking perspective, outlining future research directions, including scalable membrane fabrication, enhanced environmental adaptability, and integration into multiple industries. This review aims to bridge the gap between previous laboratory-scale investigations of two-dimensional ion-selective membranes in salinity gradient energy conversion and their potential large-scale industrial applications.

Detection and identification of single ribonucleotide monophosphates using a dual in-plane nanopore sensor made in a thermoplastic via replication

We report the generation of ∼8 nm dual in-plane pores fabricated in a thermoplastic via nanoimprint lithography (NIL). These pores were connected in series with nanochannels, one of which served as a flight tube to allow the identification of single molecules based on their molecular-dependent apparent mobilities (i.e., dual in-plane nanopore sensor). Two different thermoplastics were investigated including poly(methyl methacrylate), PMMA, and cyclic olefin polymer, COP, as the substrate for the sensor both of which were sealed using a low glass transition cover plate (cyclic olefin co-polymer, COC) that could be thermally fusion bonded to the PMMA or COP substrate at a temperature minimizing nanostructure deformation. Unique to these dual in-plane nanopore sensors was two pores flanking each side of the nanometer flight tube (50 × 50 nm, width × depth) that was 10 μm in length. The utility of this dual in-plane nanopore sensor was evaluated to not only detect, but also identify single ribonucleotide monophosphates (rNMPs) by using the travel time (time-of-flight, ToF), the resistive pulse event amplitude, and the dwell time. In spite of the relatively large size of these in-plane pores (∼8 nm effective diameter), we could detect via resistive pulse sensing (RPS) single rNMP molecules at a mass load of 3.9 fg, which was ascribed to the unique structural features of the nanofluidic network and the use of a thermoplastic with low relative dielectric constants, which resulted in a low RMS noise level in the open pore current. Our data indicated that the identification accuracy of individual rNMPs was high, which was ascribed to an improved chromatographic contribution to the nano-electrophoresis apparent mobility. With the ToF data only, the identification accuracy was 98.3%. However, when incorporating the resistive pulse sensing event amplitude and dwell time in conjunction with the ToF and analyzed via principal component analysis (PCA), the identification accuracy reached 100%. These findings pave the way for the realization of a novel chip-based single-molecule RNA sequencing technology.

Conformation Influence of DNA on the Detection Signal through Solid-State Nanopores

The detection and identification of nanoscale molecules are crucial, but traditional technology comes with a high cost and requires skilled operators. Solid-state nanopores are new powerful tools for discerning the three-dimensional shape and size of molecules, enabling the translation of molecular structural information into electric signals. Here, DNA molecules with different shapes were designed to explore the effects of electroosmotic forces (EOF), electrophoretic forces (EPF), and volume exclusion on electric signals within solid-state nanopores. Our results revealed that the electroosmotic force was the main driving force for single-stranded DNA (ssDNA), whereas double-stranded DNA (dsDNA) was primarily dominated by electrophoretic forces in nanopores. Moreover, dsDNA caused greater amplitude signals and moved faster through the nanopore due to its larger diameter and carrying more charges. Furthermore, at the same charge level and amount of bases, circular dsDNA exhibited a tighter structure compared to brush DNA, resulting in a shorter length. Consequently, circular dsDNA caused higher current-blocking amplitudes and faster passage speeds. The characterization approach based on nanopores allows researchers to get molecular information about size and shape in real time. These findings suggest that nanopore detection has the potential to streamline nanoscale characterization and analysis, potentially reducing both the cost and complexity.

The single strand template shortening strategy improves the sensitivity and specificity of solid-state nanopore detection

Through controlling the ssDNA product length of rolling circle amplification with AcyNTP, here we develop a nanopore signal enhancement strategy (STSS), which can successfully transfer the short oligonucleotide targets into long ssDNAs with appropriate lengths that can generate significant translocation currents. By labelling the RCA product with tags such as tetrahedral structures and isothermal amplicons, the resolution, signal specificity, and target range of the STSS can be further extended.

Electron beam lithography on nonplanar and irregular surfaces

E-beam lithography is a powerful tool for generating nanostructures and fabricating nanodevices with fine features approaching a few nanometers in size. However, alternative approaches to conventional spin coating and development processes are required to optimize the lithography procedure on irregular surfaces. In this review, we summarize the state of the art in nanofabrication on irregular substrates using e-beam lithography. To overcome these challenges, unconventional methods have been developed. For instance, polymeric and nonpolymeric materials can be sprayed or evaporated to form uniform layers of electron-sensitive materials on irregular substrates. Moreover, chemical bonds can be applied to help form polymer brushes or self-assembled monolayers on these surfaces. In addition, thermal oxides can serve as resists, as the etching rate in solution changes after e-beam exposure. Furthermore, e-beam lithography tools can be combined with cryostages, evaporation systems, and metal deposition chambers for sample development and lift-off while maintaining low temperatures. Metallic nanopyramids can be fabricated on an AFM tip by utilizing ice as a positive resistor. Additionally, Ti/Au caps can be patterned around a carbon nanotube. Moreover, 3D nanostructures can be formed on irregular surfaces by exposing layers of anisole on organic ice surfaces with a focused e-beam. These advances in e-beam lithography on irregular substrates, including uniform film coating, instrumentation improvement, and new pattern transferring method development, substantially extend its capabilities in the fabrication and application of nanoscale structures.

Controllable Fabrication of Sub-10 nm Graphene Nanopores via Helium Ion Microscopy and DNA Detection

Solid-state nanopores have become a prominent tool in the field of single-molecule detection. Conventional solid-state nanopores are thick, which affects the spatial resolution of the detection results. Graphene is the thinnest 2D material and has the highest spatial detection resolution. In this study, a graphene membrane chip was fabricated by combining a MEMS process with a 2D material wet transfer process. Raman spectroscopy was used to assess the quality of graphene after the transfer. The mechanism behind the influence of the processing dose and residence time of the helium ion beam on the processed pore size was investigated. Subsequently, graphene nanopores with diameters less than 10 nm were fabricated via helium ion microscopy. DNA was detected using a 5.8 nm graphene nanopore chip, and the appearance of double-peak signals on the surface of 20 mer DNA was successfully detected. These results serve as a valuable reference for nanopore fabrication using 2D material for DNA analysis.

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.

Nanopore Fabrication Made Easy: A Portable, Affordable Microcontroller-Assisted Approach for Tailored Pore Formation via Controlled Breakdown

With growing interest in solid-state nanopore sensing─a single-molecule technique capable of profiling a host of analyte classes─establishing facile and scalable approaches for fabricating molecular-size pores is becoming increasingly important. The introduction of nanopore fabrication by controlled breakdown (CBD) has transformed the economics and accessibility of nanopore fabrication. Here, we introduce the design of an Arduino-based, portable USB-powered CBD device, with an estimated cost of <150 USD, which is ≈10-100× cheaper than most commercial solutions, capable of fabricating single nanopores conducive for single molecule sensing experiments. We demonstrate the facile fabrication of 60 tailored nanopores (∼2.6-12.6 nm) with ∼80% of the pores within 1 nm of the target diameter. Selected pores were then tested with double-stranded DNA, the canonical molecular ruler, demonstrating their performance for single-molecule sensing applications. The device is constructed with off-the-shelf readily available components and controlled using a highly customizable MATLAB application, which has capabilities encompassing pore fabrication, pore enlargement, and current-voltage acquisition for pore size estimation. When combined with a portable amplifier, this device also provides a fully portable sensing platform, an important step toward portable solid-state nanopore sensing applications.

Surface-dominant micro/nanofluidics for efficient green energy conversion

Green energy conversion in aqueous systems has attracted considerable interest owing to the sustainable clean energy demand resulting from population and economic growth and urbanization, as well as the significant potential energy from water resources and other regenerative sources coupled with fluids. In particular, molecular motion based on intrinsic micro/nanofluidic phenomena at the liquid-solid interface (LSI) is crucial for efficient and sustainable green energy conversion. The electrical double layer is the main factor affecting transport, interaction between molecules and surfaces, non-uniform ion distribution, synthesis, stimulated reactions, and motion by external renewable resources in both closed nanoconfinement and open surfaces. In this review, we summarize the state-of-the-art progress in physical and chemical reaction-based green energy conversion in LSI, including nanoscale fabrication, key mechanisms, applications, and limitations for practical implementation. The prospects for resolving critical challenges in this field and inspiring other promising research areas in the infancy stage (studying chemical and biological dynamics at the single-molecule level and nanofluidic neuromorphic computing) are also discussed.

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

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

Solid-State Nanopores for Biomolecular Analysis and Detection

Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.

Aggregation and Oligomerization Characterization of ß-Lactoglobulin Protein Using a Solid-State Nanopore Sensor

Protein aggregation is linked to many chronic and devastating neurodegenerative human diseases and is strongly associated with aging. This work demonstrates that protein aggregation and oligomerization can be evaluated by a solid-state nanopore method at the single molecule level. A silicon nitride nanopore sensor was used to characterize both the amyloidogenic and native-state oligomerization of a model protein ß-lactoglobulin variant A (βLGa). The findings from the nanopore measurements are validated against atomic force microscopy (AFM) and dynamic light scattering (DLS) data, comparing βLGa aggregation from the same samples at various stages. By calibrating with linear and circular dsDNA, this study estimates the amyloid fibrils' length and diameter, the quantity of the βLGa aggregates, and their distribution. The nanopore results align with the DLS and AFM data and offer additional insight at the level of individual protein molecular assemblies. As a further demonstration of the nanopore technique, βLGa self-association and aggregation at pH 4.6 as a function of temperature were measured at high (2 M KCl) and low (0.1 M KCl) ionic strength. This research highlights the advantages and limitations of using solid-state nanopore methods for analyzing protein aggregation.

Recognition of Oligonucleotide C by Polydopamine-Coated Solid-State Nanopores

Selective recognition of short oligonucleotides at the single-molecule level is particularly important for early disease detection and treatment. In this work, polydopamine (PDA)-coated nanopores were prepared via self-polymerization as a solid-state nanopore sensing platform for the recognition of oligonucleotide C (PolyC). The PDA coating possesses abundant active sites, such as indole, amino, carboxyl, catechol, and quinone structures, which had interactions with short oligonucleotides to slow down the translocation rate. PDA-coated nanopores selectively interact with PolyC20 by virtue of differences in hydrogen bonding forces, generating a larger blocking current, while polyA and polyT demonstrated very small blockings. At the same time, PDA-coated nanopores can sensitively distinguish PolyC with different lengths, such as 20, 14, and 10 nt. The functionalization of PDA on the solid-state nanopore provides an opportunity for the rational design of the recognition surface for biomolecules.

Deciphering DNA nucleotide sequences and their rotation dynamics with interpretable machine learning integrated C3N nanopores

A solid-state nanopore combined with the quantum transport method has garnered substantial attention and intrigue for DNA sequencing due to its potential for providing rapid and accurate sequencing results, which could have numerous applications in disease diagnosis and personalized medicine. However, the intricate and multifaceted nature of the experimental protocol poses a formidable challenge in attaining precise single nucleotide analysis. Here, we report a machine learning (ML) framework combined with the quantum transport method to accelerate high-throughput single nucleotide recognition with C3N nanopores. The optimized eXtreme Gradient Boosting Regression (XGBR) algorithm has predicted the fingerprint transmission of each unknown nucleotide and their rotation dynamics with root mean square error scores as low as 0.07. Interpretability of ML black box models with the game theory-based SHapley Additive exPlanation method has provided a quasi-explanation for the model working principle and the complex relationship between electrode-nucleotide coupling and transmission. Moreover, a comprehensive ML classification of nucleotides based on binary, ternary, and quaternary combinations shows maximum accuracy and F1 scores of 100%. The results suggest that ML in tandem with a nanopore device can potentially alleviate the experimental hurdles associated with quantum tunneling and facilitate fast and high-precision DNA sequencing.

Nano-injection molding with resin mold inserts for prototyping of nanofluidic devices for single molecular detection

While injection molding is becoming the fabrication modality of choice for high-scale production of microfluidic devices, especially those used for in vitro diagnostics, its translation into the growing area of nanofluidics (structures with at least one dimension <100 nm) has not been well established. Another prevailing issue with injection molding is the high startup costs and the relatively long time between device iterations making it in many cases impractical for device prototyping. We report, for the first time, functional nanofluidic devices with dimensions of critical structures below 30 nm fabricated by injection molding for the manipulation, identification, and detection of single molecules. UV-resin molds replicated from Si masters served as mold inserts, negating the need for generating Ni-mold inserts via electroplating. Using assembled devices with a cover plate via hybrid thermal fusion bonding, we demonstrated two functional thermoplastic nanofluidic devices. The first device consisted of dual in-plane nanopores placed at either end of a nanochannel and was used to detect and identify single ribonucleotide monophosphate molecules via resistive pulse sensing and obtain the effective mobility of the molecule through nanoscale electrophoresis to allow its identification. The second device demonstrated selective binding of a single RNA molecule to a solid phase bioreactor decorated with a processive exoribonuclease, XRN1. Our results provide a simple path towards the use of injection molding for device prototyping in the development stage of any nanofluidic or even microfluidic application, through which rapid scale-up is made possible by transitioning from prototyping to high throughput production using conventional Ni mold inserts.

Registration of Functioning of a Single Horseradish Peroxidase Macromolecule with a Solid-State Nanopore

Currently, nanopore-based technology for the determination of the functional activity of single enzyme molecules continues its development. The use of natural nanopores for studying single enzyme molecules is known. At that, the approach utilizing artificial solid-state nanopores is also promising but still understudied. Herein, we demonstrate the use of a nanotechnology-based approach for the investigation of the enzymatic activity of a single molecule of horseradish peroxidase with a solid-state nanopore. The artificial 5 nm solid-state nanopore has been formed in a 40 nm thick silicon nitride structure. A single molecule of HRP has been entrapped into the nanopore. The activity of the horseradish peroxidase (HRP) enzyme molecule inserted in the nanopore has been monitored by recording the time dependence of the ion current through the nanopore in the course of the reaction of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) oxidation reaction. We have found that in the process of ABTS oxidation in the presence of 2.5 mM hydrogen peroxide, individual HRP enzyme molecules are able to retain activity for approximately 700 s before a decrease in the ion current through the nanopore, which can be explained by structural changes of the enzyme.

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.

Influence of nanopore coating patterns on the translocation dynamics of polyelectrolytes

Polyelectrolytes can electrophoretically be driven through nanopores in order to be detected. The respective translocation events are often very fast and the process needs to be controlled to promote efficient detection. To this end, we attempt to control the translocation dynamics by coating the inner surface of a nanopore. For this, different charge distributions are chosen that result in substantial variations of the pore-polymer interactions. In addition and in view of the existing detection modalities, experimental settings, and nanopore materials, different types of sensors inside the nanopore have been considered to probe the translocation process and its temporal spread. The respective transport of polyelectrolytes through the coated nanopores is modeled through a multi-physics computational scheme that incorporates a mesoscopic/electrokinetic description for the solvent and particle-based scheme for the polymer. This investigation could underline the interplay between sensing modality, nanopore material, and detection accuracy. The electro-osmotic flow and electrophoretic motion in a pore are analyzed together with the polymeric temporal and spatial fluctuations unraveling their correlations and pathways to optimize the translocation speed and dynamics. Accordingly, this work sketches pathways in order to tune the pore-polymer interactions in order to control the translocation dynamics and, in the long run, errors in their measurements.

Extreme Ion-Transport Inorganic 2D Membranes for Nanofluidic Applications

Inorganic 2D materials offer a new approach to controlling mass diffusion at the nanoscale. Controlling ion transport in nanofluidics is key to energy conversion, energy storage, water purification, and numerous other applications wherein persistent challenges for efficient separation must be addressed. The recent development of 2D membranes in the emerging field of energy harvesting, water desalination, and proton/Li-ion production in the context of green energy and environmental technology is herein discussed. The fundamental mechanisms, 2D membrane fabrication, and challenges toward practical applications are highlighted. Finally, the fundamental issues of thermodynamics and kinetics are outlined along with potential membrane designs that must be resolved to bridge the gap between lab-scale experiments and production levels.

Gradient Channel Segmentation in Covalent Organic Framework Membranes with Highly Oriented Nanochannels

Covalent organic frameworks (COFs) offer an exceptional platform for constructing membrane nanochannels with tunable pore sizes and tailored functionalities, making them promising candidates for separation, catalysis, and sensing applications. However, the synthesis of COF membranes with highly oriented nanochannels remains challenging, and there is a lack of systematic studies on the influence of postsynthetic modification reactions on functionality distribution along the nanochannels. Herein, we introduced a "prenucleation and slow growth" approach to synthesize a COF membrane featuring highly oriented mesoporous channels and a high Brunauer-Emmett-Teller surface area of 2230 m2 g-1. Functional moieties were anchored to the pore walls via "click" reactions and coordinated with Cu ions to serve as segmentation functions. This led to a remarkable H2/CO2 separation performance that surpassed the Robeson upper bound. Moreover, we found that the functionalities distributed along the nanochannels could be influenced by functionality flexibility and postsynthetic reaction rate. This strategy paved the way for the accurate design and construction of COF-based artificial solid-state nanochannels with high orientation and precisely controlled channel environments.