Scaling of ionic conductance in a fluctuating single-layer nanoporous membrane

Single-layer membranes have emerged as promising candidates for applications requiring high transport rates due to their low resistance to molecular transport. Owing to their atomically thin structure, these membranes experience significant microscopic fluctuations, emphasizing the need to explore their impact on ion transport processes. In this study, we investigate the effects of membrane fluctuations on the elementary scaling behavior of ion conductance [Formula: see text] as a function of ion concentration [Formula: see text], represented as [Formula: see text], using molecular dynamics simulations. Our findings reveal that membrane fluctuations not only alter the conductance coefficient [Formula: see text] but also the power-law exponent [Formula: see text]. We identify two distinct frequency regimes of membrane fluctuations, GHz-scale and THz-scale fluctuations, and examine their roles in conductance scaling. Furthermore, we demonstrate that the alteration of conductance scaling arises from the non-linearity between ion conductance and membrane shape. This work provides a fundamental understanding of ion transport in fluctuating membranes.

High Accuracy Protein Identification: Fusion of Solid-State Nanopore Sensing and Machine Learning

Proteins are arguably one of the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analyzing biomolecules such as proteins at single-molecule level. While molecular-level information on size, shape, and charge of proteins can be assessed by nanopores, the identification of proteins with comparable sizes remains a challenge. Here, solid-state nanopore sensing is combined with machine learning to address this challenge. The translocations of four similarly sized proteins is assessed using amplifiers with bandwidths (BWs) of 100 kHz and 10 MHz, the highest bandwidth reported for protein sensing, using nanopores fabricated in <10 nm thick silicon nitride membranes. F-values of up to 65.9% and 83.2% (without clustering of the protein signals) are achieved with 100 kHz and 10 MHz BW measurements, respectively, for identification of the four proteins. The accuracy of protein identification is further enhanced by classifying the signals into different clusters based on signal attributes, with F-value and specificity of up to 88.7% and 96.4%, respectively, for combinations of four proteins. The combined use of high bandwidth instruments, advanced clustering and machine learning methods allows label-free identification of proteins with high accuracy.

Unit-cell-thick zeolitic imidazolate framework films for membrane application

Zeolitic imidazolate frameworks (ZIFs) are a subset of metal-organic frameworks with more than 200 characterized crystalline and amorphous networks made of divalent transition metal centres (for example, Zn2+ and Co2+) linked by imidazolate linkers. ZIF thin films have been intensively pursued, motivated by the desire to prepare membranes for selective gas and liquid separations. To achieve membranes with high throughput, as in ångström-scale biological channels with nanometre-scale path lengths, ZIF films with the minimum possible thickness-down to just one unit cell-are highly desired. However, the state-of-the-art methods yield membranes where ZIF films have thickness exceeding 50 nm. Here we report a crystallization method from ultradilute precursor mixtures, which exploits registry with the underlying crystalline substrate, yielding (within minutes) crystalline ZIF films with thickness down to that of a single structural building unit (2 nm). The film crystallized on graphene has a rigid aperture made of a six-membered zinc imidazolate coordination ring, enabling high-permselective H2 separation performance. The method reported here will probably accelerate the development of two-dimensional metal-organic framework films for efficient membrane separation.

Enzyme-less nanopore detection of post-translational modifications within long polypeptides

Means to analyse cellular proteins and their millions of variants at the single-molecule level would uncover substantial information previously unknown to biology. Nanopore technology, which underpins long-read DNA and RNA sequencing, holds potential for full-length proteoform identification. We use electro-osmosis in an engineered charge-selective nanopore for the non-enzymatic capture, unfolding and translocation of individual polypeptides of more than 1,200 residues. Unlabelled thioredoxin polyproteins undergo transport through the nanopore, with directional co-translocational unfolding occurring unit by unit from either the C or N terminus. Chaotropic reagents at non-denaturing concentrations accelerate the analysis. By monitoring the ionic current flowing through the nanopore, we locate post-translational modifications deep within the polypeptide chains, laying the groundwork for compiling inventories of the proteoforms in cells and tissues.

Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA

The 4-letter DNA alphabet (A, T, G, C) as found in Nature is an elegant, yet non-exhaustive solution to the problem of storage, transfer, and evolution of biological information. Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V). For writing, we devise an enzymatic strategy for inserting a singular, orthogonal xenonucleic acid (XNA) base pair into standard DNA sequences using 2'-deoxy-xenonucleoside triphosphates as substrates. Integrating this strategy with combinatorial oligos generated on a chip, we construct libraries containing single XNA bases for parameterizing kmer basecalling models for commercially available nanopore sequencing. These elementary steps are combined to synthesize and sequence DNA containing 12 letters - the upper limit of what is accessible within the electroneutral, canonical base pairing framework. By introducing low-barrier synthesis and sequencing strategies, this work overcomes previous obstacles paving the way for making expanded alphabets widely accessible.

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.

Feasibility of an implantable bioreactor for renal cell therapy using silicon nanopore membranes

The definitive treatment for end-stage renal disease is kidney transplantation, which remains limited by organ availability and post-transplant complications. Alternatively, an implantable bioartificial kidney could address both problems while enhancing the quality and length of patient life. An implantable bioartificial kidney requires a bioreactor containing renal cells to replicate key native cell functions, such as water and solute reabsorption, and metabolic and endocrinologic functions. Here, we report a proof-of-concept implantable bioreactor containing silicon nanopore membranes to offer a level of immunoprotection to human renal epithelial cells. After implantation into pigs without systemic anticoagulation or immunosuppression therapy for 7 days, we show that cells maintain >90% viability and functionality, with normal or elevated transporter gene expression and vitamin D activation. Despite implantation into a xenograft model, we find that cells exhibit minimal damage, and recipient cytokine levels are not suggestive of hyperacute rejection. These initial data confirm the potential feasibility of an implantable bioreactor for renal cell therapy utilizing silicon nanopore membranes.

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.

Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates

The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.

Metal-Organic Framework Sub-Nanochannels Formed inside Solid-State Nanopore with Proton Ultra-High Selectivity

Metal-Organic frameworks (MOFs) have the advantages of high porosity, angstrom-scale pore size, and unique structure. In this work, a kind of MOFs, UiO-66 and its derivatives (including aminated UiO-66-(NH2 )2 and sulfonated UiO-66-(NH-SAG)2 ), were constructed on the inner surface of solid-state nanopores for ultra-selective proton transport. UiO-66 and UiO-66-(NH2 )2 nanocrystal particles were in-situ grown at the orifice of glass nanopores firstly, which were used to investigate the ionic current responses in LiCl and HCl solutions when the monovalent anions (Cl- ) were unchanged. Compared with UiO-66-modifed nanopores, the aminated MOFs modification (UiO-66-(NH2 )2 ) can improve the proton selectivity obviously. However, when the UiO-66-(NH-SAG)2 nanopore is prepared by further post-modification with sulfo-acetic acid, lithium ions can hardly pass through the channel, and the interaction between protons and sulfonic acid groups can promote the transport of protons, thus achieving ultra-high selectivity to protons. This work provides a new way to achieve sub-nanochannels with high selectivity, which can widely be used in ion separation, sensing and energy conversion.

Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures

Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.

Protein Sizing with 15 nm Conical Biological Nanopore YaxAB

Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.

Single-Nanoparticle-Based Nanomachining for Fabrication of a Uniform Nanochannel Sensor

The structure of nanomaterials and nanodevices determines their functionality and applications. A single uniform nanochannel with a high aspect ratio is an attractive structure due to its unique rigid structures, easy preparation, and diverse pore structures and it holds significant promising importance in fields such as nanopore sensing and nanomanufacturing. Although the metal-nanoparticle-assistant silicon etching technique can produce uniform nanochannels, however, the fabrication of single through nanochannels remains a challenge thus far. A simple and versatile strategy is developed that allows for the retention of individual gold nanoparticle on a substrate, enabling single-nanoparticle nanomachining. This method involves three steps: the formation of a carbon protective layer on individual nanoparticles via electron-beam irradiation, selective removal of unprotected nanoparticles using a corrosive agent, and subsequent elimination of the carbon layer. This enables the fabrication of a single submillimeter-long uniform through nanochannel in the silicon wafer, which can be employed for nanopore sensing and shape-based nanoparticle distinguishing. The developed method can also facilitate single-nanoparticle studies and nanomachining for a broad application in materials science, electronics, micro/nano-optics, and catalysis.

Over One Million DNA and Protein Events Through Ultra-Stable Chemically-Tuned Solid-State Nanopores

Stability, long lifetime, resilience against clogging, low noise, and low cost are five critical cornerstones of solid-state nanopore technology. Here, a fabrication protocol is described wherein >1 million events are obtained from a single solid-state nanopore with both DNA and protein at the highest available lowpass filter (LPF, 100 kHz) of the Axopatch 200B-the highest event count mentioned in literature. Moreover, a total of ≈8.1 million events are reported in this work encompassing the two analyte classes. With the 100 kHz LPF, the temporally attenuated population is negligible while with the more ubiquitous 10 kHz, ≈91% of the events are attenuated. With DNA experiments, the pores are operational for hours (typically >7 h) while the average pore growth is merely ≈0.16 ± 0.1 nm h-1 . The current noise is exceptionally stable with traces typically showing <10 pA h-1 increase in noise. Furthermore, a real-time method to clean and revive pores clogged with analyte with the added benefit of minimal pore growth during cleaning (< 5% of the original diameter) is showcased. The enormity of the data collected herein presents a significant advancement to solid-state pore performance and will be useful for future ventures such as machine learning where large amounts of pristine data are a prerequisite.

Discrimination between Alpha-Synuclein Protein Variants with a Single Nanometer-Scale Pore

Alpha-synuclein is one of several key factors in the regulation of nerve activity. It is striking that single- or multiple-point mutations in the 140-amino-acid-long protein can change its structure, which leads to the protein's aggregation and fibril formation (which is associated with several neurodegenerative diseases, e.g., Parkinson's disease). We recently demonstrated that a single nanometer-scale pore can identify proteins based on its ability to discriminate between protease-generated polypeptide fragments. We show here that a variation of this method can readily discriminate between the wild-type alpha synuclein, a known deleterious point mutation of the glutamic acid at position 46 replaced with a lysine (E46K), and post-translational modifications (i.e., tyrosine Y39 nitration and serine 129 phosphorylation).

Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End

The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.

Duplex Polymerization Strategy for General, Programmable and High-Resolution Nanopore Detection

Nanopore sensing is highly promising in single molecular analysis but their broad applications have been challenged by the limited strategies that can transduce a target-of-interest into a specific and anti-false/inference signal, especially for solid-state nanopores with relatively lower resolution and higher noise. Here we report a high-resolution signal-production concept named target-induced duplex polymerization strategy (DPS). Through linking the same or different duplex substrates (DSs) with a special linker (L) and an optional structure tag (ST), the DPS can generate target-specific DS polymers with highly controllable duration times, duration intervals and even distinguished secondary tagging currents. Experimentally, DPS mono-polymerization of single DS and co-polymerization of multiple DSs has verified the duration time of a DPS product is the sum of those for each DS monomer. Tetrahedron-DNA structures with different sizes are used as the STs to provide needle-like secondary peaks for further resolution enhancement and multiplex assay. With these examples DPS represents a general, programmable and advanced strategy that may simultaneously provide size-amplification, concentration amplification, and signal-specificity for molecular recognition. It is also promisingly in various applications regarding to single molecular investigation, such as polymerization degree, structure/side chain conformation, programmable multiplex decoding and information index.

Reductive Sequestration of Cr(VI) and Immobilization of C during the Microbially Mediated Transformation of Ferrihydrite-Cr(VI)-Fulvic Acid Coprecipitates

Cr(VI) detoxification and organic matter (OM) stabilization are usually influenced by the biological transformation of iron (Fe) minerals; however, the underlying mechanisms of metal-reducing bacteria on the coupled kinetics of Fe minerals, Cr, and OM remain unclear. Here, the reductive sequestration of Cr(VI) and immobilization of fulvic acid (FA) during the microbially mediated phase transformation of ferrihydrite with varying Cr/Fe ratios were investigated. No phase transformation occurred until Cr(VI) was completely reduced, and the ferrihydrite transformation rate decreased as the Cr/Fe ratio increased. Microscopic analysis was uncovered, which revealed that the resulting Cr(III) was incorporated into the lattice structure of magnetite and goethite, whereas OM was mainly adsorbed on goethite and magnetite surfaces and located within pore spaces. Fine line scan profiles showed that OM adsorbed on the Fe mineral surface had a lower oxidation state than that within nanopores, and C adsorbed on the magnetite surface had the highest oxidation state. During reductive transformation, the immobilization of FA by Fe minerals was predominantly via surface complexation, and OM with highly aromatic and unsaturated structures and low H/C ratios was easily adsorbed by Fe minerals or decomposed by bacteria, whereas Cr/Fe ratios had little effect on the binding of Fe minerals and OM and the variations in OM components. Owing to the inhibition of crystalline Fe minerals and nanopore formation in the presence of Cr, Cr sequestration and C immobilization can be synchronously favored at low Cr/Fe ratios. These findings provide a profound theoretical basis for Cr detoxification and synchronous sequestration of Cr and C in anoxic soils and sediments.

High-Sensitivity and Fast-Speed UV Photodetectors Based on Asymmetric Nanoporous-GaN/Graphene Vertical Junction

GaN-based photodetectors are strongly desirable in many advanced fields, such as space communication, environmental monitoring, etc. However, the slow photo-response speed in currently reported high-sensitivity GaN-based photodetectors still hinders their applications. Here, we demonstrate a high-sensitivity and fast-speed UV photodetector based on asymmetric Au/nanoporous-GaN/graphene vertical junctions. The nanoporous GaN-based vertical photodetector shows an excellent rectification ratio up to ∼10⁵ at +4 V/-4 V. The photo-responsivity and specific detectivity of the device is up to 1.01 × 10⁴ A/W and 7.84 × 10¹⁴ Jones, respectively, more than three orders of magnitude higher than the control planar photodetector. With switching light on and off, the repeatable on/off current ratio of the nanoporous GaN-based vertical photodetector is ∼4.32 × 10³, which is about 1.51 × 10³ times to that of the control planar device. The measured rise/decay time is 12.2 μs/14.6 μs, which is the fastest value for the high-sensitivity GaN-based photodetectors to date. These results suggest that the asymmetric Au/nanoporous-GaN/graphene structure can improve the sensitivity and the photo-response speed of GaN-based PDs simultaneously.

Specific Detection of Proteins by a Nanobody-Functionalized Nanopore Sensor

Nanopores are label-free single-molecule analytical tools that show great potential for stochastic sensing of proteins. Here, we described a ClyA nanopore functionalized with different nanobodies through a 5-6 nm DNA linker at its periphery. Ty1, 2Rs15d, 2Rb17c, and nb22 nanobodies were employed to specifically recognize the large protein SARS-CoV-2 Spike, a medium-sized HER2 receptor, and the small protein murine urokinase-type plasminogen activator (muPA), respectively. The pores modified with Ty1, 2Rs15d, and 2Rb17c were capable of stochastic sensing of Spike protein and HER2 receptor, respectively, following a model where unbound nanobodies, facilitated by a DNA linker, move inside the nanopore and provoke reversible blockade events, whereas engagement with the large- and medium-sized proteins outside of the pore leads to a reduced dynamic movement of the nanobodies and an increased current through the open pore. Exploiting the multivalent interaction between trimeric Spike protein and multimerized Ty1 nanobodies enabled the detection of picomolar concentrations of Spike protein. In comparison, detection of the smaller muPA proteins follows a different model where muPA, complexing with the nb22, moves into the pore, generating larger blockage signals. Importantly, the components in blood did not affect the sensing performance of the nanobody-functionalized nanopore, which endows the pore with great potential for clinical detection of protein biomarkers.

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.

Function Investigations and Applications of Membrane Proteins on Artificial Lipid Membranes

Membrane proteins play an important role in key cellular functions, such as signal transduction, apoptosis, and metabolism. Therefore, structural and functional studies of these proteins are essential in fields such as fundamental biology, medical science, pharmacology, biotechnology, and bioengineering. However, observing the precise elemental reactions and structures of membrane proteins is difficult, despite their functioning through interactions with various biomolecules in living cells. To investigate these properties, methodologies have been developed to study the functions of membrane proteins that have been purified from biological cells. In this paper, we introduce various methods for creating liposomes or lipid vesicles, from conventional to recent approaches, as well as techniques for reconstituting membrane proteins into artificial membranes. We also cover the different types of artificial membranes that can be used to observe the functions of reconstituted membrane proteins, including their structure, number of transmembrane domains, and functional type. Finally, we discuss the reconstitution of membrane proteins using a cell-free synthesis system and the reconstitution and function of multiple membrane proteins.

Multi-Stimuli-Responsive and Mechano-Actuated Biomimetic Membrane Nanopores Self-Assembled from DNA

In bioinspired design, biological templates are mimicked in structure and function by highly controllable synthetic means. Of interest are static barrel-like nanopores that enable molecular transport across membranes for use in biosensing, sequencing, and biotechnology. However, biological ion channels offer additional functions such as dynamic changes of the entire pore shape between open and closed states, and triggering of dynamic processes with biochemical and physical stimuli. To better capture this complexity, this report presents multi-stimuli and mechano-responsive biomimetic nanopores which are created with DNA nanotechnology. The nanopores switch between open and closed states, whereby specific binding of DNA and protein molecules as stimuli locks the pores in the open state. Furthermore, the physical stimulus of high transmembrane voltage switches the pores into a closed state. In addition, the pore diameters are larger and more tunable than those of natural templates. These multi-stimuli-responsive and mechanically actuated nanopores mimic several aspects of complex biological channels yet offer easier control over pore size, shape and stimulus response. The designer pores are expected to be applied in biosensing and synthetic biology.

Light-Driven Conversion of Silicon Nitride Nanopore to Nanonet for Single-Protein Trapping Analysis

The single-molecule technique for investigation of an unlabeled protein in solution is very attractive but with great challenges. Nanopore sensing as a label-free tool can be used for collecting the structural information of individual proteins, but currently offers only limited capabilities due to the fast translocation of the target. Here, a reliable and facile method is developed to convert the silicon nitride nanopore to a stable nanonet platform for single-entity sensing by electrophoretic or electroosmotic trapping. A nanonet is fabricated based on a material reorganization process caused by electron-beam and light-irradiation treatment. Using protein molecules as a model, it is revealed that the solid-state nanonet can produce collision and trapping flipping signals of the protein, which provides more structural information than traditional nanopore sensing. More importantly, thanks to the excellent stability of the solid-state silicon nitride nanonet, it is demonstrated that the ultraviolet-light-irradiation-induced structural-change process of an individual protein can be captured. The developed nanonet supplies a robust platform for single-entity studies but is not limited to proteins.