Molecule-hugging graphene nanopores

High-Resolution and Low-Noise Single-Molecule Sensing with Bio-Inspired Solid-State Nanopores

Solid-state nanopores have been extensively explored as single-molecule sensors, bearing the potential for the sequencing of DNA. Although they offer advantages in terms of high mechanical robustness, tunable geometry, and compatibility with existing semiconductor fabrication techniques in comparison with their biological counterparts, efforts to sequence DNA with these nanopores have been hampered by insufficient spatial resolution and high noise in the measured ionic current signal. Here we show that these limitations can be overcome by the use of solid-state nanopores featuring a thin, narrow constriction as the sensing region, inspired by biological protein nanopores that have achieved notable success in DNA sequencing. Our extensive molecular dynamics simulations show that these bio-inspired nanopores can provide high spatial resolution equivalent to 2D material nanopores and, meanwhile, significantly inhibit noise levels. A theoretical model is also provided to assess the performance of the bio-inspired nanopore, which could guide its design and optimization.

Single-Molecule Discrimination of Saccharides Using Carbon Nitride Nanopores

Structural complexity brings a huge challenge to the analysis of sugar chains. As a single-molecule sensor, nanopores have the potential to provide fingerprint information on saccharides. Traditionally, direct single-molecule saccharide detection with nanopores is hampered by their small size and weak affinity. Here, a carbon nitride nanopore device is developed to discern two types of trisaccharide molecules (LeApN and SLeCpN) with minor structural differences. The resolution of LeApN and SLeCpN in the mixture reaches 0.98, which has never been achieved in solid-state nanopores so far. Monosaccharide (GlcNAcpN) and disaccharide (LacNAcpN) can also be discriminated using this system, indicating that the versatile carbon nitride nanopores possess a monosaccharide-level resolution. This study demonstrates that the carbon nitride nanopores have the potential for conducting structure analysis on single-molecule saccharides.

Bio-Inspired Subnanofluidics: Advanced Fabrication and Functionalization

Biological ion channels can realize high-speed and high-selective ion transport through the protein filter with the sub-1-nanometer channel. Inspired by biological ion channels, various kinds of artificial subnanopores, subnanochannels, and subnanoslits with improved ion selectivity and permeability are recently developed for efficient separation, energy conversion, and biosensing. This review article discusses the advanced fabrication and functionalization methods for constructing subnanofluidic pores, channels, tubes, and slits, which have shown great potential for various applications. Novel fabrication methods for producing subnanofluidics, including top-down techniques such as electron beam etching, ion irradiation, and electrochemical etching, as well as bottom-up approaches starting from advanced microporous frameworks, microporous polymers, lipid bilayer embedded subnanochannels, and stacked 2D materials are well summarized. Meanwhile, the functionalization methods of subnanochannels are discussed based on the introduction of functional groups, which are classified into direct synthesis, covalent bond modifications, and functional molecule fillings. These methods have enabled the construction of subnanochannels with precise control of structure, size, and functionality. The current progress, challenges, and future directions in the field of subnanofluidic are also discussed.

A Universal Approximation for Conductance Blockade in Thin Nanopore Membranes

Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are inaccurate in critical experimental conditions such as thin and tightly fitting pores. Of the two components of the conductance blockade, channel and access resistance, the access resistance is poorly modeled. We present a comprehensive investigation of the access resistance and associated conductance blockade in thin nanopore membranes. By combining a first-principles approach, multiscale modeling, and experimental validation, we propose a unified theoretical modeling framework. The analytical model derived as a result surpasses current approaches across a broad parameter range. Beyond advancing our theoretical understanding, our framework's versatility enables analyte size inference and predictive insights into conductance blockade behavior. Our results will facilitate the design and optimization of nanopore devices for diverse applications, including nanopore base calling and data storage.

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.

Scaled-Up Synthesis of Freestanding Molybdenum Disulfide Membranes for Nanopore Sensing

2D materials are ideal for nanopores with optimal detection sensitivity and resolution. Among these, molybdenum disulfide (MoS₂ ) has gained traction as a less hydrophobic material than graphene. However, experiments using 2D nanopores remain challenging due to the lack of scalable methods for high-quality freestanding membranes. Herein, a site-directed, scaled-up synthesis of MoS₂ membranes on predrilled nanoapertures on 4-inch wafer substrates with 75% yields is reported. Chemical vapor deposition (CVD), which introduces sulfur and molybdenum dioxide vapors across the sub-100 nm nanoapertures results in exclusive formation of freestanding membranes that seal the apertures. Nucleation and growth near the nanoaperture edges is followed by nanoaperture decoration with MoS₂ , which proceeds until a critical flake curvature is achieved, after which fully spanning freestanding membranes form. Intentional blocking of reagent flow through the apertures inhibits MoS₂ nucleation around the nanoapertures, promoting the formation of large-crystal monolayer MoS₂ membranes. The in situ grown membranes along with facile membrane wetting and nanopore formation using dielectric breakdown enables the recording of dsDNA translocation events at an unprecedentedly high 1 MHz bandwidth. The methods presented here are important steps toward the development of scalable single-layer membrane manufacture for 2D nanofluidics and nanopore applications.

An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations

There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.

Membranes for Osmotic Power Generation by Reverse Electrodialysis

In recent years, the utilization of the selective ion transport through porous membranes for osmotic power generation (blue energy) has received a lot of attention. The principal of power generation using the porous membranes is same as that of conventional reverse electrodialysis (RED), but nonporous ion exchange membranes are conventionally used for RED. The ion transport mechanisms through the porous and nonporous membranes are considerably different. Unlike the conventional nonporous membranes, the ion transport through the porous membranes is largely dictated by the principles of nanofluidics. This owes to the fact that the osmotic power generation via selective ion transport through porous membranes is often referred to as nanofluidic reverse electrodialysis (NRED) or nanopore-based power generation (NPG). While RED using nonporous membranes has already been implemented on a pilot-plant scale, the progress of NRED/NPG has so far been limited in the development of small-scale, novel, porous membrane materials. The aim of this review is to provide an overview of the membrane design concepts of nanofluidic porous membranes for NPG/NRED. A brief description of material design concepts of conventional nonporous membranes for RED is provided as well.

Experimental study on single biomolecule sensing using MoS2-graphene heterostructure nanopores

Solid-state nanopores play an important role in sensing single-biomolecules such as DNA and proteins. However, an ultra-short translocation time hinders nanopores from acquiring more detailed information about biomolecules, and further applications such as sequencing and molecular structure analysis are limited. Related studies have shown that MoS₂ has no obvious impediment to biomolecule translocation while graphene may cause obstacles to this process. By combining these two-dimensional materials, nanopores might slow the biomolecule passage. Herein, we fabricated sub-10 nm ultra-thin MoS₂-graphene heterostructure nanopores with high stability and tested both dsDNA and native protein (BSA) at the single-molecule level in experiments for the first time. Some special signals with advanced order are observed, which may reflect the shape change of the BSA molecules during the slow translocation process. The results show that the translocation time of BSA is slowed down up to more than 100 ms and the signal length and form are determined by the extent of interaction between the BSA and the heterostructure nanopore. The weak interaction between the BSA and the MoS₂ layer increases the translocation probability, and meanwhile, the strong interaction of the graphene layer to BSA slows down the translocation and changes its structure. Therefore, our findings indicate the possibilities of slowing down the single-biomolecule translocation and the capability of acquiring more detailed information about biomolecules using MoS₂-graphene heterostructure nanopores.

On the interface between biomaterials and two-dimensional materials for biomedical applications

Two-dimensional (2D) materials have garnered significant attention due to their ultrathin 2D structures with a high degree of anisotropy and functionality. Reliable manipulation of interfaces between 2D materials and biomaterials is a new frontier for biomedical nanoscience and combining biomaterials with 2D materials offers a promising way to fabricate innovative 2D biomaterials composites with distinct functionality for biomedical applications. Here, we focus exclusively on a summary of the current work in the interface investigation of 2D biomaterials. Specifically, we highlight extraordinary features that make 2D materials so desirable, as well as the molecular level interactions between 2D materials and biomaterials that have been studied thus far. Furthermore, the approaches for investigating the interface characteristics of 2D biomaterials are presented and described in depth. To capture the emerging trend in mass manufacturing of 2D materials, we review the research progress on biomaterial-assisted exfoliation. Finally, we present a critical assessment of newly developed 2D biomaterials in biomedical applications.

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.

Angstrom-scale ion channels towards single-ion selectivity

Artificial ion channels with ion permeability and selectivity comparable to their biological counterparts are highly desired for efficient separation, biosensing, and energy conversion technologies. In the past two decades, both nanoscale and sub-nanoscale ion channels have been successfully fabricated to mimic biological ion channels. Although nanoscale ion channels have achieved intelligent gating and rectification properties, they cannot realize high ion selectivity, especially single-ion selectivity. Artificial angstrom-sized ion channels with narrow pore sizes <1 nm and well-defined pore structures mimicking biological channels have accomplished high ion conductivity and single-ion selectivity. This review comprehensively summarizes the research progress in the rational design and synthesis of artificial subnanometer-sized ion channels with zero-dimensional to three-dimensional pore structures. Then we discuss cation/anion, mono-/di-valent cation, mono-/di-valent anion, and single-ion selectivities of the synthetic ion channels and highlight their potential applications in high-efficiency ion separation, energy conversion, and biological therapeutics. The gaps of single-ion selectivity between artificial and natural channels and the connections between ion selectivity and permeability of synthetic ion channels are covered. Finally, the challenges that need to be addressed in this research field and the perspective of angstrom-scale ion channels are discussed.

Two-dimensional material-based virus detection

Cost-effective, rapid, and accurate virus detection technologies play key roles in reducing viral transmission. Prompt and accurate virus detection enables timely treatment and effective quarantine of virus carrier, and therefore effectively reduces the possibility of large-scale spread. However, conventional virus detection techniques often suffer from slow response, high cost or sophisticated procedures. Recently, two-dimensional (2D) materials have been used as promising sensing platforms for the high-performance detection of a variety of chemical and biological substances. The unique properties of 2D materials, such as large specific area, active surface interaction with biomolecules and facile surface functionalization, provide advantages in developing novel virus detection technologies with fast response and high sensitivity. Furthermore, 2D materials possess versatile and tunable electronic, electrochemical and optical properties, making them ideal platforms to demonstrate conceptual sensing techniques and explore complex sensing mechanisms in next-generation biosensors. In this review, we first briefly summarize the virus detection techniques with an emphasis on the current efforts in fighting again COVID-19. Then, we introduce the preparation methods and properties of 2D materials utilized in biosensors, including graphene, transition metal dichalcogenides (TMDs) and other 2D materials. Furthermore, we discuss the working principles of various virus detection technologies based on emerging 2D materials, such as field-effect transistor-based virus detection, electrochemical virus detection, optical virus detection and other virus detection techniques. Then, we elaborate on the essential works in 2D material-based high-performance virus detection. Finally, our perspective on the challenges and future research direction in this field is discussed.

Nanopore Detection of Cancer Biomarkers: A Challenge to Science

Cancer is the most complex and leading cause of fatality worldwide. Despite meritorious research in the field of cancer, it is still a substantial threat to human life. In this article, we address a question on the present strategies and manifest the importance of critical biomarkers for cancer screening and early diagnosis before the symptoms appear. However, this goal can only be achieved if scientists will focus on ultra-sensitive detection techniques such as “Nanopore.” Nanopore sensing is a simple and rapid single-molecule detection technique that can detect multiple cancer biomarkers in femto-Molar concentrations in real time. Last but not least, we propose a systematic policy to win the war against cancer that is a big challenge to science.

Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing

Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.

Recent Progress in the Transfer of Graphene Films and Nanostructures

The one-atom-thick graphene has excellent electronic, optical, thermal, and mechanical properties. Currently, chemical vapor deposition (CVD) graphene has received a great deal of attention because it provides access to large-area and uniform films with high-quality. This allows the fabrication of graphene based-electronics, sensors, photonics, and optoelectronics for practical applications. Zero bandgap, however, limits the application of a graphene film as electronic transistor. The most commonly used bottom-up approaches have achieved efficient tuning of the electronic bandgap by customizing well-defined graphene nanostructures. The postgrowth transfer of graphene films/nanostructures to a certain substrate is crucial in utilizing graphene in applicable devices. In this review, the basic growth mechanism of CVD graphene is first introduced. Then, recent advances in various transfer methods of as-grown graphene to target substrates are presented. The fabrication and transfer methods of graphene nanostructures are also provided, and then the transfer-related applications are summarized. At last, the challenging issues and the potential transfer-free approaches are discussed.

Nonlinear ion transport mediated by induced charge in ultrathin nanoporous membranes

Ultrathin membranes with nanoporous conduits show promise for ionic separations and desalination applications, but the mechanisms underlying the nonlinear ionic transport observed in these systems are not well understood. Here, we demonstrate how induced charge at membrane interfaces can lead to nonlinear ionic transport and voltage-dependent conductance through such channels. The application of an electric field on a polarizable membrane leads to induced charges at the membrane interfaces. The induced charges in turn are screened by diffuse charges in the electrolyte, which are acted upon by the electric field. For extremely thin membranes, the induced charge effect can be significant even for moderate applied voltages commonly used in experiments. We apply a continuum Poisson-Nernst-Planck model to characterize the current-voltage behavior of ultrathin membranes over a wide parameter space. The predictions of the model are compared to recent experiments on graphene and MoS_{2} membranes in an electric field. We expect the role of induced charge to be especially pronounced in the limit of atomically thin membranes.

Nanofluidic osmotic power generators - advanced nanoporous membranes and nanochannels for blue energy harvesting

The increase of energy demand added to the concern for environmental pollution linked to energy generation based on the combustion of fossil fuels has motivated the study and development of new sustainable ways for energy harvesting. Among the different alternatives, the opportunity to generate energy by exploiting the osmotic pressure difference between water sources of different salinities has attracted considerable attention. It is well-known that this objective can be accomplished by employing ion-selective dense membranes. However, so far, the current state of this technology has shown limited performance which hinders its real application. In this context, advanced nanostructured membranes (nanoporous membranes) with high ion flux and selectivity enabling the enhancement of the output power are perceived as a promising strategy to overcome the existing barriers in this technology. While the utilization of nanoporous membranes for osmotic power generation is a relatively new field and therefore, its application for large-scale production is still uncertain, there have been major developments at the laboratory scale in recent years that demonstrate its huge potential. In this review, we introduce a comprehensive analysis of the main fundamental concepts behind osmotic energy generation and how the utilization of nanoporous membranes with tailored ion transport can be a key to the development of high-efficiency blue energy harvesting systems. Also, the document discusses experimental issues related to the different ways to fabricate this new generation of membranes and the different experimental set-ups for the energy-conversion measurements. We highlight the importance of optimizing the experimental variables through the detailed analysis of the influence on the energy capability of geometrical features related to the nanoporous membranes, surface charge density, concentration gradient, temperature, building block integration, and others. Finally, we summarize some representative studies in up-scaled membranes and discuss the main challenges and perspectives of this emerging field.

Two-dimensional materials as solid-state nanopores for chemical sensing

Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.

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

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

Nanopores in Atomically Thin 2D Nanosheets Limit Aqueous Single-Stranded DNA Transport

Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that ssDNA transport through a pore in monolayer hexagonal boron nitride (h-BN) is marked by a basic nanomechanical conflict. It arises from the notably inhomogeneous flexural rigidity of ssDNA and causes high friction via transient DNA desorption costs exacerbated by solvation effects. For a similarly sized pore in bilayer h-BN, its self-passivated atomically smooth edge enables continuous ssDNA transport. Our findings shed light on the fundamental physics of biopolymer transport through pores in 2D materials.

Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants

Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.

Synthesis of holey graphene for advanced nanotechnological applications

Holey or porous graphene, a structural derivative of graphene, has attracted immense attention due to its unique properties and potential applications in different branches of science and technology. In this review, the synthesis methods of holey or porous graphene/graphene oxide are systematically summarized and their potential applications in different areas are discussed. The process–structure–applications are explained, which helps relate the synthesis approaches to their corresponding key applications. The review paper is anticipated to benefit the readers in understanding the different synthesis methods of holey graphene, their key parameters to control the pore size distribution, advantages and limitations, and their potential applications in various fields.

The review paper presents a systematic understanding of different synthesis routes to obtain holey graphene, its properties, and key applications in different fields. The article also evaluates the current progress and future opportunities of HG.

Devices for Nanoscale Guiding of DNA through a 2D Nanopore

We fabricate on-chip solid-state nanofluidic-2D nanopore systems that can limit the range of motion for DNA in the sensing region of a nanopore. We do so by creating devices containing one or more silicon nitride pores and silicon nitride pillars supporting a 2D pore that orient DNA within a nanopore device to a restricted geometry, yet allow the free motion of ions to maintain a high signal-to-noise ratio. We discuss two concepts with two and three independent electrical connections and corresponding nanopore chip device architectures to achieve this goal in practice. Here, we describe device fabrication and transmission electron microscope (TEM) images, and provide simulated translocations based on the finite element analysis in 3D to demonstrate its merit. In both methods, there is a main 2D nanopore which we refer to as a "sensing" nanopore (monolayer MoS₂ in this paper). A secondary layer is either an array of guiding pores sharing the same electrode pair as the sensing pore (Method 1) or a single, independently contacted, guiding pore (Method 2). These pores are constructed parallel to the "sensing" pore and serve as "guiding" elements to stretch and feed DNA into the atomically thin sensing pore. We discuss the practical implementation of these concepts with nanofluidic and Si-based technology, including detailed fabrication steps and challenges involved for DNA applications in solution.

Sub-10-nm-thick SiN nanopore membranes fabricated using the SiO2sacrificial layer process

In our previous studies, ultrathin SiN membranes down to 3 nm in thickness were fabricated using the poly-Si sacrificial layer process, and nanopores were formed in those membranes. The region of the SiN membrane fabricated using this process was small, and the poly-Si sacrificial layer remained throughout the other region. On the other hand, to reduce the noise of the current through the nanopore, it is preferable to reduce the capacitance of the nanopore chip by replacing the poly-Si layer with an insulator with low permittivity, such as SiO₂. Thus, in this study, the fabrication of SiN membranes with thicknesses of 3-7 nm using the SiO₂sacrificial layer process was examined. SiN membranes with thicknesses of less than 5 nm could not be formed when the thickness of the top SiN layer deposited onto the sacrificial layer was 100 nm. In contrast, SiN membranes down to 3.07 nm in thickness could be formed when the top SiN layer was 40 nm in thickness. This is thought to be due to the difference in membrane stress. Nanopores were then fabricated in the membranes via dielectric breakdown. The current noise of the nanopore membranes was approximately 3/5 that of membranes fabricated using the poly-Si sacrificial layer process. Last, ionic current blockades were measured when poly(dT)₆₀passed through the nanopores, and the effective thickness of the nanopores was estimated based on those current-blockade values. The effective thickness was approximately 4.8 nm when the deposited thickness of the SiN membrane was 6.03 nm. On the other hand, the effective thickness and the deposited thickness were almost the same when the deposited thickness was 3.07 nm. This suggests it became difficult to form a shape in which the thickness of the nanopore edge was thinner than the deposited membrane thickness as the deposited thickness decreased.

DNA Knot Malleability in Single-Digit Nanopores

Knots in long DNA molecules are prevalent in biological systems and serve as a model system for investigating static and dynamic properties of biopolymers. We explore the dynamics of knots in double-stranded DNA in a new regime of nanometer-scale confinement, large forces, and short time scales, using solid-state nanopores. We show that DNA knots undergo isomorphic translocation through a nanopore, retaining their equilibrium morphology by swiftly compressing in a lateral direction to fit the constriction. We observe no evidence of knot tightening or jamming, even for single-digit nanopores. We explain the observations as the malleability of DNA, characterized by sharp buckling of the DNA in nanopores, driven by the transient disruption of base pairing. Our molecular dynamics simulations support the model. These results are relevant not only for the understanding of DNA packing and manipulation in living cells but also for the polymer physics of DNA and the development of nanopore-based sequencing technologies.

Nanopores in two-dimensional materials: accurate fabrication

Two-dimensional (2D) materials such as graphene and molybdenum disulfide have been demonstrated with a wide range of applications in electronic devices, chemical catalysis, single-molecule detection, and energy conversion. In the 2D materials, nanopores can be created, and the 2D nanoporous membranes possess many unique properties such as ultrathin thickness, high surface area, and excellent particle sieving capability, showing extraordinary promise in plenty of applications, such as sea water desalination, gas separation, and DNA sequencing. The performances of these membranes are mainly determined by the nanopore size, structure, and density, which, in turn, rely on the fabrication techniques of the nanopores. This review covers the important progress of nanopore fabrication in 2D materials and comprehensively compares these methods for the features of the introduced nanopores and their formation processes. Future perspectives are discussed on the opportunities and challenges in fabricating high-grade 2D nanopores.

Resistive pulse sensing device with embedded nanochannel (nanochannel-RPS) for label-free biomolecule and bionanoparticle analysis

This paper reports an IC-compatible method for fabricating a PDMS-based resistive pulse sensing (RPS) device with embedded nanochannel (nanochannel-RPS) for label-free analysis of biomolecules and bionanoparticles, such as plasmid DNAs and exosomes. Here, a multilayer lithography process was proposed to fabricate the PDMS mold for the microfluidic device, comprising a bridging nanochannel, as the sensing gate. RPS was performed by placing the sensing and excitation electrodes symmetrically upstream and downstream of the sensing gate. In order to reduce the noise level, a reference electrode was designed and placed beside the excitation electrode. To demonstrate the feasibility of the proposed nanochannel-RPS device and sensing system, polystyrene micro- and nanoparticles with diameters of 1μm and 300 nm were tested by the proposed device with signal-to-noise ratios (SNR) ranging from 9.1-30.5 and 2.2-5.9, respectively. Furthermore, a nanochannel with height of 300 nm was applied for 4 kb plasmid DNA detection, implying the potential of the proposed method for label-free quantification of nanoscale biomolecules. Moreover, HeLa cell exosomes, known as a well-studied subtype of extracellular vesicles, were measured and analyzed by their size distribution. The result of the resistive pulse amplitude corresponded well to that of nanoparticle tracking analysis (NTA). The proposed nanochannel-RPS device and the sensing strategy are not only capable of label-free analysis for nanoscale biomolecules and bionanoparticles, but are also cost-effective for large-scale manufacturing.

In situ solid-state nanopore fabrication

Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.

From nanotubes to nanoholes: Scaling of selectivity in uniformly charged nanopores through the Dukhin number for 1:1 electrolytes

Scaling of the behavior of a nanodevice means that the device function (selectivity) is a unique smooth and monotonic function of a scaling parameter that is an appropriate combination of the system's parameters. For the uniformly charged cylindrical nanopore studied here, these parameters are the electrolyte concentration, c, voltage, U, the radius and the length of the nanopore, R and H, and the surface charge density on the nanopore's surface, σ. Due to the non-linear dependence of selectivities on these parameters, scaling can only be applied in certain limits. We show that the Dukhin number, Du=|σ|/eRc∼|σ|λ_D ²/eR (λ_D is the Debye length), is an appropriate scaling parameter in the nanotube limit (H → ∞). Decreasing the length of the nanopore, namely, approaching the nanohole limit (H → 0), an alternative scaling parameter has been obtained, which contains the pore length and is called the modified Dukhin number: mDu ∼ Du H/λ_D ∼ |σ|λ_DH/eR. We found that the reason for non-linearity is that the double layers accumulating at the pore wall in the radial dimension correlate with the double layers accumulating at the entrances of the pore near the membrane on the two sides. Our modeling study using the Local Equilibrium Monte Carlo method and the Poisson-Nernst-Planck theory provides concentration, flux, and selectivity profiles that show whether the surface or the volume conduction dominates in a given region of the nanopore for a given combination of the variables. We propose that the inflection point of the scaling curve may be used to characterize the transition point between the surface and volume conductions.

Measuring trapped DNA at the liquid-air interface for enhanced single molecule sensing

Nanopore sensing is a promising tool with widespread application in single-molecule detection. Borosilicate glass nanopores are a viable alternative to other solid-state nanopores due to low noise and cost-efficient fabrication. For dielectric materials, including borosilicate glass, the capacitive noise is one of the major contributors to noise, which depends on the wall thickness and the surface area submerged in an ionic solution. Here, we investigated the root mean square (I_RMS) noise and ionic conductance for borosilicate nanopores in different depths (i.e., tip submersion depth) ranging from the solution surface (assumed to be zero) to 5000 μm. Our findings demonstrate a decrease in I_RMS noise as the pipette moves toward the surface. We further demonstrate that borosilicate nanopores can detect single lambda DNA (λ-DNA) molecules with a high signal-to noise ratio close to the liquid-air interface. Specifically, our results indicate a higher signal to noise ratio as the submersion depth is reduced owing to the reduced surface area and thus capacitive noise. Further, our experimental results show higher DNA capture frequency at the air-water interface due to a combined effect of evaporation and an evaporation-induced thermal gradient at the surface. Therefore, our findings demonstrate that borosilicate glass nanopores are suitable for studying interfacial concentration gradients of molecules, specifically DNA, with a higher signal to noise.

Engineered two-dimensional nanomaterials: an emerging paradigm for water purification and monitoring

Water scarcity has become an increasingly complex challenge with the growth of the global population, economic expansion, and climate change, highlighting the demand for advanced water treatment technologies that can provide clean water in a scalable, reliable, affordable, and sustainable manner. Recent advancements on 2D nanomaterials (2DM) open a new pathway for addressing the grand challenge of water treatment owing to their unique structures and superior properties. Emerging 2D nanostructures such as graphene, MoS₂, MXene, h-BN, g-C₃N₄, and black phosphorus have demonstrated an unprecedented surface-to-volume ratio, which promises ultralow material use, ultrafast processing time, and ultrahigh treatment efficiency for water cleaning/monitoring. In this review, we provide a state-of-the-art account on engineered 2D nanomaterials and their applications in emerging water technologies, involving separation, adsorption, photocatalysis, and pollutant detection. The fundamental design strategies of 2DM are discussed with emphasis on their physicochemical properties, underlying mechanism and targeted applications in different scenarios. This review concludes with a perspective on the pressing challenges and emerging opportunities in 2DM-enabled wastewater treatment and water-quality monitoring. This review can help to elaborate the structure-processing-property relationship of 2DM, and aims to guide the design of next-generation 2DM systems for the development of selective, multifunctional, programmable, and even intelligent water technologies. The global significance of clean water for future generations sheds new light and much inspiration in this rising field to enhance the efficiency and affordability of water treatment and secure a global water supply in a growing portion of the world.

Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals

The appearance of next generation sequencing technology that features short read length with high measurement throughput and low cost has revolutionized the field of life science, medicine, and even computer science. The subsequent development of the third-generation sequencing technologies represented by nanopore and zero-mode waveguide techniques offers even higher speed and long read length with promising applications in portable and rapid genomic tests in field. Especially under the current circumstances, issues such as public health emergencies and global pandemics impose soaring demand on quick identification of origins and species of analytes through DNA sequences. In addition, future development of disease diagnosis, treatment, and tracking techniques may also require frequent DNA testing. As a result, DNA sequencers with miniaturized size and highly integrated components for personal and portable use to tackle increasing needs for disease prevention, personal medicine, and biohazard protection may become future trends. Just like many other biological and medical analytical systems that were originally bulky in sizes, collaborative work from various subjects in engineering and science eventually leads to the miniaturization of these systems. DNA sequencers that involve nanoprobes, detectors, microfluidics, microelectronics, and circuits as well as complex functional materials and structures are extremely complicated but may be miniaturized with technical advancement. This paper reviews the state-of-the-art technology in developing essential components in DNA sequencers and analyzes the feasibility to achieve miniaturized DNA sequencers for personal use. Future perspectives on the opportunities and associated challenges for compact DNA sequencers are also identified.

Graphene for Biosensing Applications in Point-of-Care Testing

Graphene and graphene-related materials (GRMs) exhibit a unique combination of electronic, optical, and electrochemical properties, which make them ideally suitable for ultrasensitive and selective point-of-care testing (POCT) devices. POCT device-based applications in diagnostics require test results to be readily accessible anywhere to produce results within a short analysis timeframe. This review article provides a summary of methods and latest developments in the field of graphene and GRM-based biosensing in POCT and an overview of the main applications of the latter in nucleic acids and enzymatic biosensing, cell detection, and immunosensing. For each application, we discuss scientific and technological advances along with the remaining challenges, outlining future directions for widespread use of this technology in biomedical applications.

Topological analysis of single-stranded DNA with an alpha-hederin nanopore

Nanopores have been emerged as a powerful tool for analyzing the structural information and interactional properties of a range of biomolecules. The spatial resolution of nanopore is determined by the diameter and effective thickness of its constriction region, but the presence of vestibule or stem structure in protein-based nanopore could negatively affect the sensitivity of the nanopore when applied for genome sequencing and topological analysis of DNA. Recently, alpha-hederin (Ah) has been reported to form a sub-nanometer scale pore structure in lipid membrane. With the simple structure and extremely small effective thickness, the Ah nanopore was shown to discriminate four different types of nucleotides. However, identification of a certain nucleotide in a strand of DNA, which is essential for genome sequencing, remains challenging. Here, we investigated the resolving capability of Ah nanopore to discriminate few nucleotides in a strand of single-stranded DNA, and the factors determining the sensitivity of Ah nanopore. The Ah nanopore was shown to be able to identify as few as three adenosine nucleotides in a strand of poly cytidine, in which the dwell time of the additional current blockade that represents the adenosine residue was in good agreement with their physical length. We also found that the lateral tension and chain pressure generated around the nanopore were influenced by pore's diameter and played as a dependent variables to determine the geometry of nanopore's constriction as well as the spatial resolution of the Ah nanopore.

Functionalized carbon nanotube electrodes for controlled DNA sequencing

In the last decade, solid-state nanopores/nanogaps have attracted significant attention in the rapid detection of DNA nucleotides. However, reducing the noise through controlled translocation of the DNA nucleobases is a central issue for the development of nanogap/nanopore-based DNA sequencing to achieve single-nucleobase resolution. Furthermore, the high reactivity of the graphene pores/gaps causes clogging of the pore/gap, leading to the blockage of the pores/gaps, sticking, and irreversible pore closure. To address the prospective of functionalization of the carbon nanostructure and for accomplishing this objective, herein, we have studied the performance of functionalized closed-end cap armchair carbon nanotube (CNT) nanogap-embedded electrodes, which can improve the coupling through non-bonding electrons and may provide the possibility of N/O-H⋯π interactions with the nucleotides, as single-stranded DNA is transmigrated across the electrode. We have investigated the effect of functionalizing the closed-end cap CNT (6,6) electrodes with purine (adenine, guanine) and pyrimidine (thymine, cytosine) molecules. Weak hydrogen bonds formed between the probe molecule and the target DNA nucleobase enhance the electronic coupling and temporarily stabilize the translocating nucleobase against the orientational fluctuations, which may reduce noise in the current signal during experimental measurements. The findings of our density functional theory and non-equilibrium Green's function-based study indicate that this modeled setup could allow DNA nucleotide sequencing with a better and reliable yield, giving current traces that differ by at least 1 order of current magnitude for all the four target nucleotides. Thus, we feel that the functionalized armchair CNT (6,6) nanogap-embedded electrodes may be utilized for controlled DNA sequencing.

Ion Transport in Electrically Imperfect Nanopores

Ionic transport through a charged nanopore at low ion concentration is governed by the surface conductance. Several experiments have reported various power-law relations between the surface conductance and ion concentration, i.e., G_surf ∝ c₀^α. However, the physical origin of the varying exponent, α, is not yet clearly understood. By performing extensive coarse-grained Molecular Dynamics simulations for various pore diameters, lengths, and surface charge densities, we observe varying power-law exponents even with a constant surface charge and show that α depends on how electrically "perfect" the nanopore is. Specifically, when the net charge of the solution in the pore is insufficient to ensure electroneutrality, the pore is electrically "imperfect" and such nanopores can exhibit varying α depending on the degree of "imperfectness". We present an ionic conductance theory for electrically "imperfect" nanopores that not only explains the various power-law relationships but also describes most of the experimental data available in the literature.

Strategies for development of nanoporous materials with 2D building units

It has already been realized that two-dimensional (2D) materials carry a great potential in energy conversion and storage, gas storage, chemical sensing, and many other applications closely related to human life. These applications benefit from a key feature of 2D materials, namely the large specific surface area, which however can be diminished significantly due to the tendency of these materials to restack. In this review, we revisit the strategies - including soft and hard templating - that have been developed for generating nanoporosity in 3D materials and demonstrate their adaptation for 2D materials using carbon nitride and graphene materials as examples. Owing to the 2D nature of the building units, a new type of nanopore can be generated by perforating the basal planes. These in-plane nanopores are essential in many emerging applications of 2D materials such as semipermeable membranes; hence, their creation methods, including post-synthesis activation, ion bombardment, electron beam drilling, and nanolithography, are worthy of a critical review. Lastly, techniques for preventing the restacking by fabricating 2D-0D, 2D-1D, and 2D-2D layer-by-layer composite structures are discussed. The goal is to promote the use of these methods for creating nanoporosity in more 2D materials.

Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS2 Nanopore

Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS₂ membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS₂ nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.

Computational investigation of geometrical effects in 2D boron nitride nanopores for DNA detection

Nanopore-based DNA detection and analysis have been intensively pursued theoretically and experimentally over the past decade. Owing to their nanometer thickness, 2D nanopores, such as boron nitride nanopores, show great potential for achieving DNA detection at base resolution. Although 2D nanopore devices hold great promise for next-generation DNA detection, efficiently and reliably detecting different DNA sequences is still a challenging problem. To date, most of the investigated nanopores adopt circular shapes. Because of the successful fabrication of triangular nanopores, investigating the shape effect of nanopores for DNA detection has become more and more important. In this study, boron nitride nanopores with circular, hexagonal, quadrangular and triangular shapes were modeled at various sizes. The translocation of homogeneous dsDNA through these nanopores was investigated by all-atom molecular dynamic simulations. The ionic conductivity of these nanopores was characterized and formulas for the total resistance based on the pore and access resistance were derived. The ionic current, dwell time and conductance blockade of homogeneous dsDNA were compared for nanopores with different shapes. We demonstrate that the charge distribution at the pore mouth plays an important role in the transportation of ions and DNA molecules. Our findings may shed light on the design of 2D nanopores and can facilitate the development of fast, low-cost and reliable nanopore-based DNA detection.

Ions and Water Dancing through Atom-Scale Holes: A Perspective toward "Size Zero"

We provide an overview of atom-scale apertures in solid-state membranes, from "pores" and "tubes" to "channels", with characteristic sizes comparable to the sizes of ions and water molecules. In this regime of ∼1 nm diameter pores, water molecules and ions are strongly geometrically confined: the size of water molecules (∼0.3 nm) and the size of "hydrated" ions in water (∼0.7-1 nm) are similar to the pore diameters, physically limiting the ion flow through the hole. The pore sizes are comparable to the classical Debye screening length governing the spatial range of electrostatic interaction, ∼0.3 to 1 nm for 1 to 0.1 M KCl. In such small structures, charges can be unscreened, leading to new effects. We discuss experiments on ∼1 nm diameter nanopores, with a focus on carbon nanotube pores and ion transport studies. Finally, we present an outlook for artificial "size zero" pores in the regime of small diameters and small thicknesses. Beyond mimicking protein channels in nature, solid-state pores may offer additional possibilities where sensing and control are performed at the pore, such as in electrically and optically addressable solid-state materials.

Comparing Current Noise in Biological and Solid-State Nanopores

Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.

Revealing the mechanism of DNA passing through graphene and boron nitride nanopores

Nanopores on 2D materials have great potential for DNA sequencing, which is attributed to their high sequencing speed and reduced cost. However, identifying DNA bases at such a high speed with nanometer precision has remained a big challenge. Here, we implemented theoretical calculations to show the translocation of single-stranded DNA (ssDNA) through solid-state nanopores on a 2D hexagonal boron nitride (h-BN) and graphene sheet. A base-specific ssDNA sequencing technique was devised, based on the individual differences in the ion current responses for the (polyA)₁₆, (polyG)₁₆, (polyC)₁₆, and (polyT)₁₆ bases of ssDNA. Our sequential procedure for sequencing is built on a comparative approach between the current signals obtained from the nanopores to achieve base-specific detection. Our results indicate that at higher voltages (1.0, 1.2, 1.4, 1.6, 1.8 and 2.0 V nm^-1), DNA translocation is tracked though the 1.5 and 2.0 nm nanopores, and at the 1.5 nm pore size, folded ssDNA close to the nanopore accounts for 93% and 81% of events for graphene and h-BN. Our calculations indicate charge transfer from the graphene to ssDNA, while the reverse happens in the case of the h-BN membrane. These results provide critical insights into our understanding of single molecule sequencing through solid-state nanopore research.

High-throughput single nanoparticle detection using a feed-through channel-integrated nanopore

The outstanding sensitivity of solid-state nanopore sensors comes at a price of low detection efficiency due to the lack of active means to transfer objects into the nanoscale sensing zone. Here we report on a key technology for high-throughput single-nanoparticle detection which exploits mutual effects of microfluidics control and multipore electrophoresis in nanopore-in-channel units integrated on a thin Si₃N₄ membrane. Using this novel nanostructure, we demonstrated a proof-of-concept for influenza viruses via hydropressure regulation of mass transport in the fluidic channel for continuous feeding of biosamples into the effective electric field extending out from the nanopores, wherein the feed-through mechanism allowed us to selectively detect charged objects in physiological media such as human saliva. With the versatility of nanopore sensing technologies applicable to analytes of virtually any size from cells to polynucleotides, the present integration strategy may open new avenues for practical ultrasensitive bioanalytical tools.