Controlled Translocation of Proteins through a Biological Nanopore for Single-Protein Fingerprint Identification.

After the successful sequencing of nucleic acids, nanopore technology has now been applied to proteins. Recently, it has been demonstrated that an electro-osmotic flow can be used to induce the transport of unraveled polypeptides across nanopores. Polypeptide translocation, however, is too fast for accurate reading its amino acid compositions. Here, we show that the introduction of hydrophobic residues into the lumen of the nanopore reduces the protein translocation speed. Importantly, the introduction of a tyrosine at the entry of the nanopore and an isoleucine at the entry of the ß-barrel of the nanopore reduced the speed of translocation to ∼10 amino acids/millisecond while keeping a relatively large ionic current, a crucial component for protein identification. These nanopores showed unique features within their current signatures, which may pave the way toward protein fingerprinting using nanopores.

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.

An Ultrasensitive and Efficient microRNA Nanosensor Empowered by the CRISPR/Cas Confined in a Nanopore.

This work presents a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas-nanopipette nano-electrochemistry (Cas = CRISPR-associated proteins) capable of ultrasensitive microRNA detection. Nanoconfinement of the CRISPR/Cas13a within a nanopipette leads to a high catalytic efficacy of ca. 169 times higher than that in bulk electrolyte, contributing to the amplified electrochemical responses. CRISPR/Cas13a-enabled detection of representative microRNA-25 achieves a low limit of detection down to 10 aM. Practical application of this method is further demonstrated for single-cell and real human serum detection. Its general applicability is validated by addressing microRNA-141 and the SARS-CoV-2 RNA gene fragment. This work introduces a new CRISPR/Cas-empowered nanotechnology for ultrasensitive nano-electrochemistry and bioanalysis.

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.

Nanopore Blockade Sensors for Quantitative Analysis Using an Optical Nanopore Assay.

Nanopore sensing is a popular biosensing strategy that is being explored for the quantitative analysis of biomarkers. With low concentrations of analytes, nanopore sensors face challenges related to slow response times and selectivity. Here, we demonstrate an approach to rapidly detect species at ultralow concentrations using an optical nanopore blockade sensor for quantitative detection of the protein vascular endothelial growth factor (VEGF). This sensor relies on monitoring fluorescent polystyrene nanoparticles blocking nanopores in a nanopore array of 676 nanopores. The fluorescent signal is read out using a wide-field fluorescence microscope. Nonspecific blockade events are then distinguished from specific blockade events based on the ability to pull the particles out of the pore using an applied electric field. This allows the detection of VEGF at sub-picomolar concentration in less than 15 min.

Tailored Fabrication of 3D Nanopores Made of Dielectric Oxides for Multiple Nanoscale Applications.

Solid-state nanopores are a key platform for single-molecule detection and analysis that allow engineering of their properties by controlling size, shape, and chemical functionalization. However, approaches relying on polymers have limits for what concerns hardness, robustness, durability, and refractive index. Nanopores made of oxides with high dielectric constant would overcome such limits and have the potential to extend the suitability of solid-state nanopores toward optoelectronic technologies. Here, we present a versatile method to fabricate three-dimensional nanopores made of different dielectric oxides with convex, straight, and concave shapes and demonstrate their functionality in a series of technologies and applications such as ionic nanochannels, ionic current rectification, memristors, and DNA sensing. Our experimental data are supported by numerical simulations that showcase the effect of different shapes and oxide materials. This approach toward robust and tunable solid-state nanopores can be extended to other 3D shapes and a variety of dielectrics.

Preanchoring Enabled Directional Modification of Atomically Thin Membrane for High-Performance Osmotic Energy Generation.

Salinity gradient energy is an environmentally friendly energy source that possesses potential to meet the growing global energy demand. Although covalently modified nanoporous graphene membranes are prospective candidates to break the trade-off between ion selectivity and permeability, the random reaction sites and inevitable defects during modification reduce the reaction efficiency and energy conversion performance. Here, we developed a preanchoring method to achieve directional modification near the graphene nanopores periphery. Numerical simulation revealed that the improved surface charge density around nanopores results in exceptional K+/Cl- selectivity and osmotic energy conversion performance, which agreed well with experimental results. Ionic transport measurements showed that the directionally modified graphene membranes achieved an outstanding power density of 81.6 W m-2 with an energy conversion efficiency of 35.4% under a 100-fold salinity gradient, outperforming state-of-the-art graphene-based nanoporous membranes. This work provided a facile approach for precise modification of nanoporous graphene membranes and opened up new ways for osmotic power harvesting.

Two-Dimensional Sulfonate-Functionalized Metal-Organic Framework Membranes for Efficient Lithium-Ion Sieving.

Two-dimensional (2D) membranes have shown promising potential for ion-selective separation but often suffer from the trade-off between permeability and selectivity. Herein, we report an ultrathin 2D sulfonate-functionalized metal-organic framework (MOF) membrane for efficient lithium-ion sieving. The narrow pores with angstrom precision in the MOF assist hydrated ions to partially remove the hydration shell, according to different hydration energies. The abundant sulfonate groups in the MOF channels serve as hopping sites for fast lithium-ion transport, contributing to a high Li-ion permeability. Then, the difference in affinity of the Li+, Na+, K+, and Mg2+ ions to the terminal sulfonate groups further enhances the Li-ion selectivity. The reported ultrathin MOF membrane overcomes the trade-off between permeability and selectivity and opens up a new avenue for highly permselective membranes.

Next-Generation Nanopore Sensors Based on Conductive Pulse Sensing for Enhanced Detection of Nanoparticles.

Nanopore sensing has been successfully used to characterize biological molecules with single-molecule resolution based on the resistive pulse sensing approach. However, its use in nanoparticle characterization has been constrained by the need to tailor the nanopore aperture size to the size of the analyte, precluding the analysis of heterogeneous samples. Additionally, nanopore sensors often require the use of high salt concentrations to improve the signal-to-noise ratio, which further limits their ability to study a wide range of nanoparticles that are unstable at high ionic strength. Here, a new paradigm in nanopore research that takes advantage of a polymer electrolyte system to comprise a conductive pulse sensing approach is presented. A finite element model is developed to explain the conductive pulse signals observed and compare these results with experiments. This system enables the analytical characterization of heterogeneous nanoparticle mixtures at low ionic strength . Furthermore, the wide applicability of the method is demonstrated by characterizing metallic nanospheres of varied sizes, plasmonic nanostars with various degrees of branching, and protein-based spherical nucleic acids with different oligonucleotide loadings. This system will complement the toolbox of nanomaterials characterization techniques to enable real-time optimization workflow for engineering a wide range of nanomaterials.

Unraveling Clinical Glycoproteome by Integrating Affinity Enrichment with Nanopore Sequencing.

This prospect explores the integration of enrichment strategies with nanopore detection to advance clinical glycoproteomics. Glycoproteins, crucial for understanding biological processes, pose challenges due to their low abundance and structural diversity. Enrichment techniques using lectin affinity, boronate affinity, and hydrazide chemistry and especially molecular imprinted polymers may selectively and specifically isolate glycoproteins from complex samples, while nanopore technology enables label-free, real-time, and single-molecule analysis. This approach holds promise for disease-related glycosylation studies, biomarker discovery, personalized medicine, and streamlined clinical analysis. Standardization, optimization, and data analysis remain challenges, requiring interdisciplinary collaborations and technological advancements. Overall, this integration may offer transformative potential for clinical glycoproteomics and innovative diagnostic and therapeutic strategies.

Performance of single nanopore and multi-pore membranes for blue energy.

The salinity gradient power extracted from the mixing of electrolyte solutions at dierent concentrations through selective nanoporous membranes is a promising route to renewable energy. However, several challenges need to be addressed to make this technology protable, one of the most relevant being the increase of the extractable power per membrane area. Here, the performance of asymmetric conical and bullet-shaped nanopores in a 50 nm thick membrane are studied via electrohydrodynamic simulations, varying the pore radius, curvature, and surface charge. The output power reaches ∼ 60 pW per pore for positively charged membranes (surface charge σw =160 mC/m2 ) and ∼ 30 pW for negatively charges ones, σw =-160 mC/m2 and it is robust to minor variations of nanopore shape and radius. A theoretical argument that takes into account the interaction among neighbour pores allows to extrapolate the single-pore performance to multi-pore membranes showing that power densities from tens to hundreds of W/m2 can be reached by proper tuning of the nanopore number density and the boundary layer thickness. Our model for scaling single-pore performance to multi-pore membrane can be applied also to experimental data providing a simple tool to effectively compare different nanopore membranes in blue energy applications.

Ab Initio Molecular Dynamics Investigation on the Permeation of Sodium and Chloride Ions Through Nanopores in Graphene and Hexagonal Boron Nitride Membranes.

Nanoporous membranes promise energy-efficient water desalination. Hexagonal boron nitride (h-BN), like graphene, exhibits outstanding physical and chemical properties, making it a promising candidate for water treatment. We employed Car-Parrinello molecular dynamics simulations to establish an accurate modeling of Na+ and Cl- permeation through hydrogen passivated nanopores in graphene and h-BN membranes. We demonstrate that ion separation works well for the h-BN system by imposing a barrier of 0.13 eV and 0.24 eV for Na+ and Cl- permeation, respectively. In contrast, for permeation of the graphene nanopore, the Cl- ion faces a minimum of energy of 0.68 eV in the nanopore plane and is prone toward blockade of the nanopore, while the Na+ ion experiences a slight minimum of 0.03 eV. Overall, the desalination performance of h-BN nanopores surpasses that of their graphene counterparts.

Trapping and recapturing single DNA molecules with pore-cavity-pore device.

Single-molecule detection technology is a technique capable of detecting molecules at the single-molecule level, characterized by high sensitivity, high resolution, and high specificity. Nanopore technology, as one of the single-molecule detection tools, is widely used to study the structure and function of biomolecules. In this study, we constructed a small-sized nanopore with a pore-cavity-pore structure, which can achieve a higher reverse capture rate. Through simulation, we investigated the electrical potential distribution of the nanopore with a pore-cavity-pore structure and analyzed the influence of pore size on the potential distribution. Accordingly, different pore sizes can be designed based on the radius of gyration of the target biomolecules, restricting their escape paths inside the chamber. In the future, nanopores with a pore-cavity-pore structure based on two-dimensional thin film materials are expected to be applied in single-molecule detection research, which provides new insights for various detection needs.

Enhanced magnetism derived from pore-edge spins in thin Fe3GeTe2nanomeshes.

The growth of two-dimensional van der Waals magnetic materials presents attractive opportunities for exploring new physical phenomena and valuable applications. Among these materials, Fe3GeTe2(FGT) exhibits a variety of remarkable properties and has garnered significant attention. Herein, we have for the first time created a nanomesh structure-a honeycomb-like array of hexagonal nanopores-with the zigzag pore-edge atomic structure on thin FGT flakes with and without oxidation of the pore edges. It is revealed that the magnitude of ferromagnetism (FM) significantly increases in both samples compared with bulk flakes without nanomeshes. Critical temperature annealing results in the formation of zigzag pore edges and interpore zigzag-edge nanoribbons. We unveil that the non-oxide (O) termination of the Fe dangling bonds on these zigzag edges enhances FM behavior, while O-termination suppresses this FM by introducing antiferromagnetic behavior through edge O-Fe coupling. FGT nanomeshes hold promise for the creation of strong FM and their effective application in magnetic and spintronic systems.

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.

Bottom-up synthesis of graphene films hosting atom-thick molecular-sieving apertures.

Incorporation of a high density of molecular-sieving nanopores in the graphene lattice by the bottom-up synthesis is highly attractive for high-performance membranes. Herein, we achieve this by a controlled synthesis of nanocrystalline graphene where incomplete growth of a few nanometer-sized, misoriented grains generates molecular-sized pores in the lattice. The density of pores is comparable to that obtained by the state-of-the-art postsynthetic etching (1012 cm-2) and is up to two orders of magnitude higher than that of molecular-sieving intrinsic vacancy defects in single-layer graphene (SLG) prepared by chemical vapor deposition. The porous nanocrystalline graphene (PNG) films are synthesized by precipitation of C dissolved in the Ni matrix where the C concentration is regulated by controlled pyrolysis of precursors (polymers and/or sugar). The PNG film is made of few-layered graphene except near the grain edge where the grains taper down to a single layer and eventually terminate into vacancy defects at a node where three or more grains meet. This unique nanostructure is highly attractive for the membranes because the layered domains improve the mechanical robustness of the film while the atom-thick molecular-sized apertures allow the realization of large gas transport. The combination of gas permeance and gas pair selectivity is comparable to that from the nanoporous SLG membranes prepared by state-of-the-art postsynthetic lattice etching. Overall, the method reported here improves the scale-up potential of graphene membranes by cutting down the processing steps.

Analysis of structural defects and their influence on red-emitting γ-Al2O3:Mn4+,Mg2+ nanowires using positron annihilation spectroscopy.

The present paper reported on the analysis of structural defects and their influence on the red-emitting γ-Al2O3:Mn4+,Mg2+ nanowires using positron annihilation spectroscopy (PAS). The nanowires were synthesized by hydrothermal method and low-temperature post-treatment using glucose as a reducing agent. X-ray diffraction (XRD), scanning electron microscopy (SEM), photoluminescence (PL), and photoluminescence excitation (PLE) were utilized, respectively, for determining the structural phase, morphology and red-emitting intensity in studied samples. Three PAS experiments, namely, positron annihilation lifetime (PAL), Doppler broadening (DB), and electron momentum distribution (EMD), were simultaneously performed to investigate the formations of structural defects in synthesized materials. Obtained results indicated that the doping concentration of 0.06% was optimal for the substitution of Mn4+ and Mg2+ to two Al3+ sites and the formation of oxygen vacancy (VO)-rich vacancy clusters (2VAl + 3VO) and large voids (~0.7 nm) with less Al atoms. Those characteristics reduced the energy transfer between Mn4+ ions, thus consequently enhanced the PL and PLE intensities. Moreover, this optimal doping concentration also effectively controlled the size of nanopores (~2.18 nm); hence, it is expected to maintain the high thermal conductivity of γ-Al2O3 nanowire-phosphor. The present study, therefore, demonstrated a potential application of γ-Al2O3 nanowire-phosphor in fabricating the high-performance optoelectronic devices.

Monolayer Fullerene Membranes for Hydrogen Separation.

Hydrogen separation membranes are a critical component in the emerging hydrogen economy, offering an energy-efficient solution for the purification and production of hydrogen gas. Inspired by the recent discovery of monolayer covalent fullerene networks, here we show from concentration-gradient-driven molecular dynamics that quasi-square-latticed monolayer fullerene membranes provide the best pore size match, a unique funnel-shaped pore, and entropic selectivity. The integration of these attributes renders these membranes promising for separating H2 from larger gases such as CO2 and O2. The ultrathin membranes exhibit excellent hydrogen permeance as well as high selectivity for H2/CO2 and H2/O2 separations, surpassing the 2008 Robeson upper bounds by a large margin. The present work points toward a promising direction of using monolayer fullerene networks as membranes for high-permeance, selective hydrogen separation for processes such as water splitting.

Single-Molecule Electrical and Spectroscopic Profiling Protein Allostery Using a Gold Plasmonic Nanopore.

Direct structural and dynamic characterization of protein conformers in solution is highly desirable but currently impractical. Herein, we developed a single molecule gold plasmonic nanopore system for observation of protein allostery, enabling us to monitor translocation dynamics and conformation transition of proteins by ion current detection and SERS spectrum measurement, respectively. Allosteric transition of calmodulin (CaM) was elaborately probed by the nanopore system. Two conformers of CaM were well-resolved at a single-molecule level using both the ion current blockage signal and the SERS spectra. The collected SERS spectra provided structural evidence to confirm the interaction between CaM and the gold plasmonic nanopore, which was responsible for the different translocation behaviors of the two conformers. SERS spectra revealed the amino acid residues involved in the conformational change of CaM upon calcium binding. The results demonstrated that the excellent spectral characterization furnishes a single-molecule nanopore technique with an advanced capability of direct structure analysis.

Enhanced Exciton-to-Trion Conversion by Proton Irradiation of Atomically Thin WS2.

Defect engineering of van der Waals semiconductors has been demonstrated as an effective approach to manipulate the structural and functional characteristics toward dynamic device controls, yet correlations between physical properties with defect evolution remain underexplored. Using proton irradiation, we observe an enhanced exciton-to-trion conversion of the atomically thin WS2. The altered excitonic states are closely correlated with nanopore induced atomic displacement, W nanoclusters, and zigzag edge terminations, verified by scanning transmission electron microscopy, photoluminescence, and Raman spectroscopy. Density functional theory calculation suggests that nanopores facilitate formation of in-gap states that act as sinks for free electrons to couple with excitons. The ion energy loss simulation predicts a dominating electron ionization effect upon proton irradiation, providing further evidence on band perturbations and nanopore formation without destroying the overall crystallinity. This study provides a route in tuning the excitonic properties of van der Waals semiconductors using an irradiation-based defect engineering approach.