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.

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.

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.

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.

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.

Direct Fabrication of Sub-10 nm Nanopores in WO3 Nanosheets Using Single Swift Heavy Ions.

Extending the fabrication methodology of solid-state nanopores in a wide range of materials is significant in the fields of single molecule detection, nanofluidic devices, and nanofiltration membranes. Here, we demonstrate a new method to directly fabricate size- and density-controllable sub-10 nm nanopores in WO3 nanosheets using single swift heavy ions (SHIs) without any chemical etching process. By selecting ions of different electronic energy losses (Se), nanopores with sizes from 1.8 to 7.4 nm can be created in WO3 nanosheets. The creation efficiency of nanopores achieves ∼100% for Se > 20 keV/nm, and there exists a critical thickness below which nanopores can be created. Combined with molecular dynamics simulations, we propose that the viscosity and surface tension of the transient molten phase caused by SHIs are the key factors for the formation of nanopores. This method paves a way to fabricate solid-state nanopores in materials with a low viscosity and surface tension.

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.

Over 30-Fold Enhancement in DNA Translocation Dynamics through Nanoscale Pores Coated with an Anionic Surfactant.

Solid-state nanopores (ssNPs) are single-molecule sensors capable of label-free quantification of different biomolecules, which have become highly versatile with the introduction of different surface treatments. By modulating the surface charges of the ssNP, the electro-osmotic flow (EOF) can be controlled in turn affecting the in-pore hydrodynamic forces. Herein, we demonstrate that negative charge surfactant coating to ssNPs generates EOF that slows-down DNA translocation speed by >30-fold, without deterioration of the NP noise, hence significantly improving its performances. Consequently, surfactant-coated ssNPs can be used to reliably sense short DNA fragments at high voltage bias. To shed light on the EOF phenomena inside planar ssNPs, we introduce visualization of the electrically neutral fluorescent molecule's flow, hence decoupling the electrophoretic from EOF forces. Finite elements simulations are then used to show that EOF is likely responsible for in-pore drag and size-selective capture rate. This study broadens ssNPs use for multianalyte sensing in a single device.

Concentration-Driven Evolution of Adaptive Artificial Ion Channels or Nanopores with Specific Anticancer Activities.

In nature, ceramides are a class of sphingolipids possessing a unique ability to self-assemble into protein-permeable channels with intriguing concentration-dependent adaptive channel cavities. However, within the realm of artificial ion channels, this interesting phenomenon is scarcely represented. Herein, we report on a novel class of adaptive artificial channels, Pn-TPPs, based on PEGylated cholic acids bearing triphenylphosphonium (TPP) groups as anion binding motifs. Interestingly, the molecules self-assemble into chloride ion channels at low concentrations while transforming into small molecule-permeable nanopores at high concentrations. Moreover, the TPP groups endow the molecules with mitochondria-targeting properties, enabling them to selectively drill holes on the mitochondrial membrane of cancer cells and subsequently trigger the caspase 9 apoptotic pathway. The anticancer efficacies of Pn-TPPs correlate with their abilities to form nanopores. Significantly, the most active ensembles formed by P5-TPP exhibits impressive anticancer activity against human liver cancer cells, with an IC50 value of 3.8 µM. While demonstrating similar anticancer performance to doxorubicin, P5-TPP exhibits a selectivity index surpassing that of doxorubicin by a factor of 16.8.

E. coli outer membrane protein T (OmpT) nanopore for peptide sensing.

Peptide detection methods with facility and high sensitivity are essential for diagnosing disease associated with peptide biomarkers. Nanopore sensing technology had emerged as a low cost, high-throughput, and scalable tool for peptide detection. The omptins family proteins which can form ß-barrel pores have great potentials to be developed as nanopore biosensor. However, there are no study about the channel properties of E. coli OmpT and the development of OmpT as a nanopore biosensor. In this study, the OmpT biological nanopore channel was constructed with a conductance of 1.49 nS in 500 mM NaCl buffer and a three-step gating phenomenon under negative voltage higher than 100 mV and then was developed as a peptide biosensor which can detect peptide without the interfere of ssDNA and dNTPs. The OmpT constructed in this study has potential application in peptide detection, and also provides a new idea for the detection of peptides using the specific binding ability of protease.

Oligomer Dynamics of LL-37 Truncated Fragments Probed by α-Hemolysin Pore and Molecular Simulations.

Oligomerization of antimicrobial peptides (AMPs) is critical in their effects on pathogens. LL-37 and its truncated fragments are widely investigated regarding their structures, antimicrobial activities, and application, such as developing new antibiotics. Due to the small size and weak intermolecular interactions of LL-37 fragments, it is still elusive to establish the relationship between oligomeric states and antimicrobial activities. Here, an α-hemolysin nanopore, mass spectrometry (MS), and molecular dynamic (MD) simulations are used to characterize the oligomeric states of two LL-37 fragments. Nanopore studies provide evidence of trapping events related to the oligomer formation and provide further details on their stabilities, which are confirmed by MS and MD simulations. Furthermore, simulation results reveal the molecular basis of oligomer dynamics and states of LL-37 fragments. This work provides unique insights into the relationship between the oligomer dynamics of AMPs and their antimicrobial activities at the single-molecule level. The study demonstrates how integrating methods allows deciphering single molecule level understanding from nanopore sensing approaches.

Controllable Fabrication and Rectification of Bipolar Nanofluid Diodes in Funnel-Shaped Si3 N4 Nanopores.

Solid-state nanopores attract widespread interest, owning to outstanding robustness, extensive material availability, as well as capability for flexible manufacturing. Bioinspired solid-state nanopores further emerge as potential nanofluidic diodes for mimicking the rectification progress of unidirectional ionic transport in biological K+ channels. However, challenges that remain in rectification are over-reliance on complicated surface modifications and limited control accuracy in size and morphology. In this study, suspended Si3 N4 films of only 100 nm thickness are used as substrate and funnel-shaped nanopores are controllably etched on that with single-nanometer precision, by focused ion beam (FIB) equipped with a flexibly programmable ion dose at any position. A small diameter 7 nm nanopore can be accurately and efficiently fabricated in only 20 ms and verified by a self-designed mathematical model. Without additional modification, funnel-shaped Si3 N4 nanopores functioned as bipolar nanofluidic diodes achieve high rectification by simply filling each side with acidic and basic solution, respectively. Main factors are finely tuned experimentally and simulatively to enhance the controllability. Moreover, nanopore arrays are efficiently prepared to further improve rectification performance, which has great potential for high-throughput practical applications such as extended release of drugs, nanofluidic logic systems, and sensing for environmental monitoring and clinical diagnosis.