Macromolecular Crowding Enhances the Detection of DNA and Proteins by a Solid-State Nanopore

Protein Profiling by Nanopore-Based Technology

Proteins are the molecular foundations of life and disease responsible for understanding most biological processes. Nanopore technology devoted to revealing single-molecule behavior has made great breakthroughs for protein identification, detection and analysis, including protein sequencing. Here, we present an overview of the latest advances in protein profiling by nanopores from the identification and quantification of protein biomarkers and protein enzymes to the delineation of protein conformations and interactions at the single-molecule level, focused on the diverse and exciting approaches to protein sequencing. Furthermore, we discuss the primary challenges associated with nanopore-based protein sensing and recommend potential strategies respond to these challenges from the perspective of nanopore engineering and data processing.

Investigating the impact of Cu2+ on α-synuclein aggregation: A single-molecule approach

Parkinson's disease (PD) is a prevalent neurodegenerative disorder characterized by the abnormal aggregation of α-synuclein. This study investigated the impact of Cu2+ ions on α-synuclein aggregation in oligomer distribution using two single-molecule techniques. The aggregation of α-synuclein monomers with and without Cu2+ revealed that Cu2+ accelerated the formation of ThT-positive β-sheet structured aggregates. Nanopipettes of varying diameters from to 7 to 134 nm were employed to characterize the oligomers formed during the lag phase, demonstrating that Cu2+ generated a wider range of oligomers from 10 nm3 to 20,000 nm3 over time. Confocal fluorescence spectroscopy analysis of ThT-positive fibrils in the plateau phase showed that Cu2+ induces larger oligomers and fewer in number. The introduction of preformed seeds to the control and Cu2+-containing samples further accelerated the aggregation. The combination of seeds and Cu2+ produced structurally distinct oligomers, with seeds catalyzing the formation of small oligomers that detach from the parent fibers and Cu2+, promoting the formation of larger oligomers. These results reveals that seeds and Cu2+ act synergistically, with two different aggregation pathways coexisting in the early phase, leading to an intermediate composition of fibers and clusters at the end of aggregation.

Pressure-Controlled Nanopipette Sensing in the Asymmetric-Conductivity Configuration

Nanopipettes are important tools across diverse disciplines, including biology, physics, and materials science. Precisely controlling their characteristics is crucial for many applications. Recent progress in this endeavor has involved using the asymmetric-conductivity configuration with different electrolyte solutions inside and outside the nanopipette, which can greatly improve nanopipette sensing. However, understanding such measurements remains challenging due to the complex interplay of diffusion, electromigration, and electroosmosis. Here, we systematically explore a fundamental regime of the asymmetric-conductivity configuration where classical ion current rectification due to ion-selective migration is minimized and the effect of electroosmotic flow is maximized. We characterized the current-potential and current-distance relationship and revealed that this experimental configuration exhibits many of the characteristics of traditionally rectifying nanopipettes, such as surface charge sensitivity, while the current response can be understood simply from the rate and direction of solution mixing due to electroosmotic flow. To optimize the sensitivity in the asymmetric-conductivity configuration, we introduced a method that uses external pressure to control the fluid flow rates at the aperture, tuning the local ionic environment in situ.

Nanopore sensing of protein and peptide conformation for point-of-care applications

The global population's aging and growth will likely result in an increase in chronic aging-related diseases. Early diagnosis could improve the medical care and quality of life. Many diseases are linked to misfolding or conformational changes in biomarker peptides and proteins, which affect their function and binding properties. Current clinical methods struggle to detect and quantify these changes. Therefore, there is a need for sensitive conformational sensors that can detect low-concentration analytes in biofluids. Nanopore electrical detection has shown potential in sensing subtle protein and peptide conformation changes. This technique can detect single molecules label-free while distinguishing shape or physicochemical property changes. Its proven sensitivity makes nanopore sensing technology promising for ultra-sensitive, personalized point-of-care devices. We focus on the capability of nanopore sensing for detecting and quantifying conformational modifications and enantiomers in biomarker proteins and peptides and discuss this technology as a solution to future societal health challenges.

Nanopipettes for Chemical Analysis in Life Sciences

Nanopipette-based assays have gained widespread applications in electrochemical and analytical technologies, achieving significant advancements over the past decade in DNA sequencing, biosensing, targeted delivery, and bioimaging. The ultrasmall tip size of nanopipettes bridges the gap between the macro- and nano worlds, which can be attributed to the capability of nanopipettes to transport ultrasmall volumes of liquids, ions, and solutes. In this review, we discuss the fabrication, characterization, and modification of nanopipettes to provide an overview of the recent developments of nanopipette-based sensors and strategies. We also introduce the recent studies developed by our group and other groups using nanopipettes for chemical analysis of life science. Finally, we discuss the future development of nanopipette-based strategies and their exciting potential for studying bioscience and biomedical engineering.

Single-molecule resolution of macromolecules with nanopore devices

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

Specialized ribosomes: integrating new insights and current challenges

Variation in the composition of different ribosomes, termed ribosome heterogeneity, is a now well established phenomenon. However, the functional implications of this heterogeneity on the regulation of protein synthesis are only now beginning to be revealed. While there are numerous examples of heterogeneous ribosomes, there are comparatively few bona fide specialized ribosomes described. Specialization requires that compositionally distinct ribosomes, through their subtly altered structure, have a functional consequence to the translational output. Even for those examples of ribosome specialization that have been characterized, the precise mechanistic details of how changes in protein and rRNA composition enable the ribosome to regulate translation are still missing. Here, we suggest looking at the evolution of specialization across the tree of life may help reveal central principles of translation regulation. We consider functional and structural studies that have provided insight into the potential mechanisms through which ribosome heterogeneity could affect translation, including through mRNA and open reading frame selectivity, elongation dynamics and post-translational folding. Further, we highlight some of the challenges that must be addressed to show specialization and review the contribution of various models. Several studies are discussed, including recent studies that show how structural insight is starting to shed light on the molecular details of specialization. Finally, we discuss the future of ribosome specialization studies, where advances in technology will likely enable the next wave of research questions. Recent work has helped provide a more comprehensive understanding of how ribosome heterogeneity affects translational control.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.

Negative memory capacitance and ionic filtering effects in asymmetric nanopores

The pervasive model for a solvated, ion-filled nanopore is often a resistor in parallel with a capacitor. For conical nanopore geometries, here we propose the inclusion of a Warburg-like element, which is necessary to explain otherwise anomalous observations such as negative capacitance and low-pass filtering of translocation events (we term this phenomenon as Warburg filtering). The negative capacitance observed here has long equilibration times and memory (that is, mem-capacitance) at negative voltages. We used the transient occlusion of the pore using λ-DNA and 10 kbp DNA to test whether events are being attenuated by purely ionic phenomena when there is sufficient amplifier bandwidth. We argue here that both phenomena can be explained by the inclusion of the Warburg-like element, which is mechanistically linked to concentration polarization and activation energy to generate and maintain localized concentration gradients. We conclude the study with insights into the transduction of molecular translocations into electrical signals, which is not simply based on pulse-like resistance changes but instead on the complex and nonlinear storage of ions that enter dis-equilibrium during molecular transit.

Multimodal nanoparticle analysis enabled by a polymer electrolyte nanopore combined with nanoimpact electrochemistry

Nanopores are emerging as a powerful tool for the analysis and characterization of nanoparticles at the single entity level. Here, we report that a PEG-based polymer electrolyte present inside the nanopore enables the enhanced detection of nanoparticles at low ionic strength. We develop a numerical model that recapitulates the electrical response of the glass nanopore system, revealing the response to be sensitive to the position of the polymer electrolyte interface. As proof of concept, we demonstrate the multimodal analysis of a nanoparticle sample by coupling the polymer electrolyte nanopore sensor with nanoimpact electrochemistry. This combination of techniques could deliver the multiparametric analysis of nanoparticle systems complementing electrochemical reactivity data provided by nanoimpact electrochemistry with information on size, shape and surface charge provided by nanopore measurements.

Nafion coated nanopore electrode for improving electrochemical aptamer-based biosensing

The transition to a personalized point-of-care model in medicine will fundamentally change the way medicine is practiced, leading to better patient care. Electrochemical biosensors based on structure-switching aptamers can contribute to this medical revolution due to the feasibility and convenience of selecting aptamers for specific targets. Recent studies have reported that nanostructured electrodes can enhance the signals of aptamer-based biosensors. However, miniaturized systems and body fluid environments pose challenges such as signal-to-noise ratio reduction and biofouling. To address these issues, researchers have proposed various electrode coating materials, including zwitterionic materials, biocompatible polymers and hybrid membranes. Nafion, a commonly used ion exchange membrane, is known for its excellent permselectivity and anti-biofouling properties, making it a suitable choice for biosensor systems. However, the performance and mechanism of Nafion-coated aptamer-based biosensor systems have not been thoroughly studied. In this work, we present a Nafion-coated gold nanoporous electrode, which excludes Nafion from the nanoporous structures and allows the aptamers immobilized inside the nanopores to freely detect chosen targets. The nanopore electrode is formed by a sputtering and dealloying process, resulting in a pore size in tens of nanometers. The biosensor is optimized by adjusting the electrochemical measurement parameters, aptamer density, Nafion thickness and nanopore size. Furthermore, we propose an explanation for the unusual signaling behavior of the aptamers confined within the nanoporous structures. This work provides a generalizable platform to investigate membrane-coated aptamer-based biosensors.

Transmembrane voltage-gated nanopores controlled by electrically tunable in-pore chemistry

Gating is a fundamental process in ion channels configured to open and close in response to specific stimuli such as voltage across cell membranes thereby enabling the excitability of neurons. Here we report on voltage-gated solid-state nanopores by electrically tunable chemical reactions. We demonstrate repetitive precipitation and dissolution of metal phosphates in a pore through manipulations of cation flow by transmembrane voltage. Under negative voltages, precipitates grow to reduce ionic current by occluding the nanopore, while inverting the voltage polarity dissolves the phosphate compounds reopening the pore to ionic flux. Reversible actuation of these physicochemical processes creates a nanofluidic diode of rectification ratio exceeding 40000. The dynamic nature of the in-pore reactions also facilitates a memristor of sub-nanowatt power consumption. Leveraging chemical degrees of freedom, the present method may be useful for creating iontronic circuits of tunable characteristics toward neuromorphic systems.

Solid-State Nanopore Real-Time Assay for Monitoring Cas9 Endonuclease Reactivity

The field of nanopore sensing is now moving beyond nucleic acid sequencing. An exciting avenue is the use of nanopore platforms for the monitoring of biochemical reactions. Biological nanopores have been used for this application, but solid-state nanopore approaches have lagged. This is due to the necessity of using higher salt conditions (e.g., 4 M LiCl) to improve the signal-to-noise ratio which completely abolish the activities of many biochemical reactions. We pioneered a polymer electrolyte solid-state nanopore approach that maintains a high signal-to-noise ratio even at a physiologically relevant salt concentration. Here, we report the monitoring of the restriction enzyme SwaI and CRISPR-Cas9 endonuclease activities under physiological salt conditions and in real time. We investigated the dsDNA cleavage activity of these enzymes in a range of digestion buffers and elucidated the off-target activity of CRISPR-Cas9 ribonucleoprotein endonuclease in the presence of single base pair mismatches. This approach enables the application of solid-state nanopores for the dynamic monitoring of biochemical reactions under physiological salt conditions.

Hydrogel interfaced glass nanopore for high-resolution sizing of short DNA fragments

Solid-state nanopores, known for their label-free detection and operational simplicity, face challenges in accurately sizing the short nucleic acids due to fast translocation and a lack of enzyme-based control mechanisms as compared to their biological counterparts with sizing resolutions still limited to ≥100 bp. Here, we present a facile polyethylene glycol-dimethacrylate (PEG-DMA) hydrogel interfaced glass nanopore (HIGN) system by inserting glass nanopore into the hydrogel to achieve sub-100 base pair (bp) resolution in short DNA sizing analysis. We systematically investigated the effects of hydrogel mesh size, spatial configurations of glass nanopores about the hydrogel, applied bias voltage, and analyte concentration on the transport dynamics of 200 bp double-stranded DNA (dsDNA). A 7.5 w/v% PEG-DMA hydrogel induced ∼11x increase in the mean dwell times compared with bare solution nanopore system. The insertion locations and depths of the glass nanopore into the hydrogel resulted in 7.16% and 5.28% coefficients of variation (CV) for mean normalized event frequencies. This enhancement of dwell times and invariability in translocation characteristics enables precise sizing of dsDNA fragments under 400 bp using HIGN, with an achieved size resolution of 50 bp with observable mean normalized peak amplitude (ΔI/Io) of ∼0.005. Furthermore, we have demonstrated the capability of HIGN to perform multiplex detection of influenza A virus (IAV) and severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) through reverse transcriptase-polymerase chain reaction (RT-PCR). These results demonstrated the potential of HIGN as a versatile tool in nucleic acid analysis and multiplexed label-free molecular diagnostics.

ssDNA Capture Dynamics by Graphene Nanopores: The Role of Electrophoresis and Electro-osmotic Flow

Efficient capture of single-stranded DNA (ssDNA) is crucial for high-throughput sequencing, which influences the speed and accuracy of genetic analysis. Electrophoresis (EP) and electro-osmotic flow (EOF) have a significant impact on the translocation behavior of ssDNA through the nanopore. Experimentally, dynamically tracking these two effects remains challenging, and conventional numerical methods also struggle to capture their dynamic properties in the presence of DNA. We use all-atom molecular dynamics (MD) simulations to study how do EP and EOF play a role in the capture of DNA under different surface charge densities and graphene layer numbers. Our findings indicate that positive surface charge densities work together with electrophoretic forces (FEP) to enhance the EOF, resulting in rapid and efficient ssDNA capture with improved rates of up to 88% and reduced capture times. Electro-osmotic force (FEOF) substantially enhances capture efficiency by not only lowering the energy barrier for ssDNA translocation through the nanopore but also increasing the probability of ssDNA locating and aligning with the pore entrance. Negative charges create a repulsive electrostatic environment. Along with the opposing EOF, this lowers the chances of capture. Additionally, we found that an increased number of graphene layers can shield internal electric fields, affecting ssDNA capture negatively by tempering the effects of EOF. This research highlights the importance of precise control over nanopore surface charge and layers to optimize the performance of graphene nanopore sequencing technologies, offering potential avenues for significant advancements in genomic sequencing.

Enhanced Discriminability of Viral Vectors in Viscous Nanopores

Achieving safe and efficient gene therapy hinges upon the inspection of genomes enclosed within individual nano-carriers to mitigate potential health risks associated with empty or fragment-filled vectors. Here solid-state nanopore sensing is reported for identifications of intermediate adeno-associated virus (AAV) vectors in liquid. The method exploits the phenomenon of translocation slowdown induced by the viscosity of salt water-organic mixtures. This enables real-time ionic current measurements allowing precise tracking of the electroosmotic flow-driven motions of recombinant AAV vectors in a nanopore. The resulting ionic signals facilitate discrimination between replicative intermediates carrying ssDNA fragments and its full vector counterparts based on genome length-derived subtle nanometer differences in the viral diameters. This rapid and non-destructive means of genome analysis within virus capsids provides a promising avenue toward a robust methodology for ensuring the integrity of AAV vectors before administration.

Modulation of Ion Transport in Nanopores Using Polyethylene Glycol

Ion transport in nanopores is crucial for various biological and technological processes, exhibiting unique behaviors compared to bulk solutions. In this study, we systematically explore how polyethylene glycol (PEG) modulates ion transport within a conical nanopore. Our experiments reveal that introducing PEG into the ionic solution induces a reversal in ion current rectification (ICR). We further investigate the impact of PEG concentration, molecular weight, nanopore size, and cation type on ion transport. Additionally, we assess three different configurations of PEG introduction, identifying diffusive flow driven by an asymmetric cation distribution within the nanopore as a dominant transport mechanism. Our results confirm that the interactions between PEG and cations significantly affect ion transport properties. These findings advance our understanding of macromolecular crowding effects on ion transport and suggest potential applications in iontronic devices and biomolecule sensing.

Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches

Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.

Improving macromolecule crowding configurations in nanopores for protein sensing

We show that PEG-induced macromolecular crowding enhances protein detection in nanopores by increasing capture rate and translocation frequency. Experimental data indicate that a PEG concentration gradient boosts capture efficiency, while our theoretical model attributes this enhancement to osmotic flow, offering insights for improving nanopore-based biosensing.

A switchable and facile ionic diode modulated by polyethylene glycol

We introduce a switchable ionic diode modulated by PEG, enabling dynamic control of ion transport and reversible ion flow switching. This system achieves tunable current rectification over two orders of magnitude, simplifying fabrication and offering versatile, scalable solutions for high-performance ionic devices in energy harvesting, nanofluidics, and ionic circuits.

Secondary Nucleation of Aβ Revealed by Single-Molecule and Computational Approaches

Understanding the mechanisms underlying amyloid-β (Aβ) aggregation is pivotal in the context of Alzheimer's disease. This study aims to elucidate the secondary nucleation process of Aβ42 peptides by combining experimental and computational methods. Using a newly developed nanopipette-based amyloid seeding and translocation assay, confocal fluorescence spectroscopy, and molecular dynamics simulations, the influence of the seed properties on Aβ aggregation is investigated. Both fragmented and unfragmented seeds played distinct roles in the formation of oligomers, with fragmented seeds facilitating the formation of larger aggregates early in the incubation phase. The results show that secondary nucleation leads to the formation of oligomers of various sizes and structures as well as larger fibrils structured in β-sheets. From these findings a mechanism of secondary nucleation involving two types of aggregate populations, one released and one growing on the mother fiber is proposed.

Highly Sensitive Detection of Tumor Cell-Derived Exosomes Using Solid-State Nanopores Assisted with a Slight Salt Gradient

As an important biomarker, tumor cell-derived exosomes have substantial application prospects in early cancer screening and diagnosis. However, the unsatisfactory sensitivity and complicated sample pretreatment processes of conventional detection approaches have limited their use in clinical diagnosis. Nanopore sensors, as a highly sensitive, label-free, single-molecule technology, are widely utilized in molecule and bioparticle detection. Nevertheless, the exosome capture rate through nanopores is extremely low due to the low surface charge densities of exosomes and the effects of electrolyte concentration on their structural stability, thereby reducing the detection throughput. Here, we report an approach to improve the capture rate of exosome translocations using silicon nitride (SiNx) nanopores assisted by a slight salt electrolyte gradient. Improvements in exosome translocation event frequency are assessed in electrolyte solutions with different concentration gradients. In the case of asymmetric electrolytes (cis1× PBS and trans0.2 M NaCl, 1× PBS), the event frequency of tumor cell (HepG2)-derived exosome translocations is enhanced by nearly 2 orders of magnitude while maintaining vesicle structure stability. Furthermore, benefiting from the salt gradient effect, tumor cell (AsPC-1 and HCT116)-derived exosome translocations could be discriminated from those of HepG2 cell-derived exosomes. The developed highly sensitive detection method for tumor cell-derived exosomes at the single-particle level provides an approach for early cancer diagnosis.

Enhanced Nanoparticle Sensing in a Highly Viscous Nanopore

Slowing down translocation dynamics is a crucial challenge in nanopore sensing of small molecules and particles. Here, it is reported on nanoparticle motion-mediated local viscosity enhancement of water-organic mixtures in a nanofluidic channel that enables slow translocation speed, enhanced capture efficiency, and improved signal-to-noise ratio by transmembrane voltage control. It is found that higher detection rates of nanoparticles under larger electrophoretic voltage in the highly viscous solvents. Meanwhile, the strongly pulled particles distort the liquid in the pore at high shear rates over 103 s-1 which leads to a counterintuitive phenomenon of slower translocation speed under higher voltage via the induced dilatant viscosity behavior. This mechanism is demonstrated as feasible with a variety of organic molecules, including glycerol, xanthan gum, and polyethylene glycol. The present findings can be useful in resistive pulse analyses of nanoscale objects such as viruses and proteins by allowing a simple and effective way for translocation slowdown, improved detection throughput, and enhanced signal-to-noise ratio.

Sensitive Dual-Signal ELISA Based on Specific Phage-Displayed Double Peptide Probes with Internal Filtering Effect to Assay Monkeypox Virus Antigen

The global spread of monkeypox has become a worldwide public healthcare issue. Therefore, there is an urgent need for accurate and sensitive detection methods to effectively control its spreading. Herein, we screened by phage display two peptides M4 (sequence: DPCGERICSIAL) and M6 (sequence: SCSSFLCSLKVG) with good affinity and specificity to monkeypox virus (MPXV) B21R protein. To simulate the state of the peptide in the phage and to avoid spatial obstacles of the peptide, GGGSK was added at the C terminus of M4 and named as M4a. Molecular docking shows that peptide M4a and peptide M6 are bound to different epitopes of B21R by hydrogen bonds and salt-bridge interactions, respectively. Then, peptide M4a was selected as the capture probe, phage M6 as the detection probe, and carbonized polymer dots (CPDs) as the fluorescent probe, and a colorimetric and fluorescent double-signal capture peptide/antigen/signal peptide-displayed phage sandwich ELISA triggered by horseradish peroxidase (HRP) through a simple internal filtration effect (IFE) was constructed. HRP catalyzes H2O2 to oxidize 3,3',5,5'-tetramethylbenzidine (TMB) to generate blue oxidized TMB, which can further quench the fluorescence of CPDs through IFE, enabling to detect MPXV B21R in colorimetric and fluorescent modes. The proposed simple immunoassay platform shows good sensitivity and reliability in MPXV B21R detection. The limit of detection for colorimetric and fluorescent modes was 27.8 and 9.14 pg/mL MPXV B21R, respectively. Thus, the established double-peptide sandwich-based dual-signal immunoassay provides guidance for the development of reliable and sensitive antigen detection capable of mutual confirmation, which also has great potential for exploring various analytical strategies for other respiratory virus surveillance.

Single molecule delivery into living cells

Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here we describe a platform that uses nanopipettes to deliver defined numbers of macromolecules into cultured cell lines and primary cells at single molecule resolution. In the nanoinjection platform, the nanopipette is used as both a scanning ion conductance microscope (SICM) probe and an injection probe. The SICM is used to position the nanopipette above the cell surface before the nanopipette is inserted into the cell into a defined location and to a predefined depth. We demonstrate that the nanoinjection platform enables the quantitative delivery of DNA, globular proteins, and protein fibrils into cells with single molecule resolution and that delivery results in a phenotypic change in the cell that depends on the identity of the molecules introduced. Using experiments and computational modeling, we also show that macromolecular crowding in the cell increases the signal-to-noise ratio for the detection of translocation events, thus the cell itself enhances the detection of the molecules delivered.

Influence of Seed structure on Volume distribution of α-Synuclein Oligomer at Early Stages of Aggregation using nanopipette

Understanding α-synuclein aggregation is crucial in the context of Parkinson's disease. The objective of this study was to investigate the influence of aggregation induced by preformed seeding on the volume of oligomers during the early stages, using a label-free, single-molecule characterization approach. By utilizing nanopipettes of varying sizes, the volume of the oligomers can be calculated from the amplitude of the current blockade and pipette geometry. Further investigation of the aggregates formed over time in the presence of added seeds revealed an acceleration in the formation of large aggregates and the existence of multiple distinct populations of oligomers. Additionally, we observed that spontaneously formed seeds inhibited the formation of smaller oligomers, in contrast to the effect of HNE seeds. These results suggest that the seeds play a crucial role in the formation of oligomers and their sizes during the early stages of aggregation, whereas the classical thioflavin T assay remains negative.

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.

Macromolecular Crowding Facilitates ssDNA Capture within Biological Nanopores: Role of Size Variation and Solution Heterogeneity

Genetic sequencing is a vital process that requires the transport of charged nucleic acids through transmembrane nanopores. Single-molecule studies show that macromolecular bulk crowding facilitates the capture of these polymers, leading to a high throughput of nanopore sensors. Motivated by these observations, a minimal discrete-state stochastic framework was developed to describe the role of poly(ethylene glycol) (PEG) crowders in varying concentrations in the transport of ssDNA through α-hemolysin nanopores. This theory suggested that the cooperative partitioning of polycationic PEGs controls the capture of ssDNA due to underlying electrostatic interactions. Herein, we investigate the impact of the size variation of PEGs on the capture event. Even though larger crowders attract ssDNA strongly to enhance its capture, our results show that considerable cooperative partitioning of PEGs is also required to achieve high interevent frequency. The exact analytical results are supported by existing single-molecule studies. Since real cellular conditions are heterogeneous, its influence on the ssDNA capture rate is studied by introducing a binary mixture of crowders. Our results indicate that the "polymer-pushing-polymer" concept possibly affects the capture rate depending on the mixture composition. These new findings provide valuable insights into the microscopic mechanism of the capture process, which eventually allows for accurate genome sequencing in crowded solutions.

Bioscreening specific peptide-expressing phage and its application in sensitive dual-mode immunoassay of SARS-CoV-2 spike antigen

Biorecognition components with high affinity and selectivity are vital in bioassay to diagnose and treat epidemic disease. Herein a phage display strategy of combining single-amplification-panning with non-amplification-panning was developed, by which a phage displaying cyclic heptapeptide ACLDWLFNSC (peptide J4) with good affinity and specificity to SARS-CoV-2 spike protein (SP) was identified. Molecular docking suggests that peptide J4 binds to S2 subunit by hydrogen bonding and hydrophobic interaction. Then the J4-phage was used as the capture antibody to establish phage-based chemiluminescence immunoassay (CLIA) and electrochemical impedance spectroscopy (EIS) analytical systems. The as-proposed dual-modal immunoassay platform exhibited good sensitivity and reliability in SARS-CoV-2 SP and pseudovirus assay. The limit of detection for SARS-CoV-2 SP by EIS immunoassay is 0.152 pg/mL, which is dramatically lower than that of 42 pg/mL for J4-phage based CLIA. Further, low to 40 transducing units (TU)/mL, 10 TU/mL SARS-CoV-2 pseudoviruses can be detected by the proposed J4-phage based CLIA and electrochemical immunosensor, respectively. Therefore, the as-developed dual mode immunoassays are potential methods to detect SARS-CoV-2. It is also expected to explore various phages with specific peptides to different targets for bioanalysis.

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.

Abridged solid-phase extraction with alkaline Poly(ethylene) glycol lysis (ASAP) for direct DNA amplification

Complexity of sample preparation decelerate the development of sample-in-answer-out devices for point-of-need nucleic acid amplification testing. Here, we present the consolidation of alkaline poly(ethylene) glycol-based lysis and solid-phase extraction for rapid and simple sample preparation compatible with direct on-bead amplification. Simultaneous cell lysis and binding of DNA were achieved using an optimised reagent comprising 15% PEG8000, 0.5 M NaCl, and 3.5 mM KOH. This was combined with direct, on-bead amplification using 1.5 μg beads per 20 μL PCR reaction mix. The novel single reagent, 5-min method improved the detection limit by 10 and 100-fold compared with commercial DNA extraction kits and the original alkaline PEG lysis method, respectively. The sensitivity can be further enhanced by one amplification cycle with an ethanol wash or by extending the incubation to 10 min before collecting the magnetic particles. Both methods successfully detected a single copy of Escherichia coli DNA. In biological fluids (saliva, sweat, and urine), the 5-min method was delayed by about one cycle compared to the 15-min method. The proposed methods are attractive for incorporation in the workflow for point-of-need testing of biological samples by providing a practical and chemical method for simple alternative DNA sample preparation.

Solid-State Nanopores for Biomolecular Analysis and Detection

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

Nanoconfinement and Crowding Enhanced Single-Molecule Detection of Small Molecules with Nanopipettes

Glass nanopipettes have gained widespread use as a versatile single-entity detector in chemical and biological sensing, analysis, and imaging. Its advantages include low cost, easy accessibility, simplicity of use, and high versatility. However, conventional nanopipettes based on the volume exclusion mechanism have limitations in detecting small biomolecules due to their small volume and high mobility in aqueous solution. To overcome this challenge, we have employed a novel approach by capitalizing on the strong nanoconfinement effect of nanopipettes. This is achieved by utilizing both the hard confinement provided by the long taper nanopipette tip at the cis side and the soft confinement offered by the hydrogel at the trans side. Through this approach, we have effectively slowed down the exit motion of small molecules, allowing us to enrich and jam them at the nanopipette tip. Consequently, we have achieved high throughput detection of small biomolecules with sizes as small as 1 nm, including nucleoside triphosphates, short peptides, and small proteins with excellent signal-to-noise ratios. Furthermore, molecular complex formation through specific intermolecular interactions, such as hydrogen bonding between closely spaced nucleotides in the jam-packed nanopipette tip, has been detected based on the unique ionic current changes.

Insights into In Vivo Environmental Effects on Quantitative Biochemistry in Single Cells

Biomacromolecules exist and function in a crowded and spatially confined intracellular milieu. Single-cell analysis has been an essential tool for deciphering the molecular mechanisms of cell biology and cellular heterogeneity. However, a sound understanding of in vivo environmental effects on single-cell quantification has not been well established. In this study, via cell mimicking with giant unilamellar vesicles and single-cell analysis by an approach called plasmonic immunosandwich assay (PISA) that we developed previously, we investigated the effects of two in vivo environmental factors, i.e., molecular crowding and spatial confinement, on quantitative biochemistry in the cytoplasm of single cells. We find that molecular crowding greatly affects the biomolecular interactions and immunorecognition-based detection while the effect of spatial confinement in cell-sized space is negligible. Without considering the effect of molecular crowding, the results by PISA were found to be apparently under-quantitated, being only 29.5-50.0% of those by the calibration curve considering the effect of molecular crowding. We further demonstrated that the use of a calibration curve established with standard solutions containing 20% (wt) polyethylene glycol 6000 can well offset the effect of intracellular crowding and thereby provide a simple but accurate calibration for the PISA measurement. Thus, this study not only sheds light on how intracellular environmental factors influence biomolecular interactions and immunorecognition-based single-cell quantification but also provides a simple but effective strategy to make the single-cell analysis more accurate.

Single-Molecule Detection of α-Synuclein Oligomers in Parkinson's Disease Patients Using Nanopores

α-Synuclein (α-Syn) is an intrinsically disordered protein whose aggregation in the brain has been significantly implicated in Parkinson's disease (PD). Beyond the brain, oligomers of α-Synuclein are also found in cerebrospinal fluid (CSF) and blood, where the analysis of these aggregates may provide diagnostic routes and enable a better understanding of disease mechanisms. However, detecting α-Syn in CSF and blood is challenging due to its heterogeneous protein size and shape, and low abundance in clinical samples. Nanopore technology offers a promising route for the detection of single proteins in solution; however, the method often lacks the necessary selectivity in complex biofluids, where multiple background biomolecules are present. We address these limitations by developing a strategy that combines nanopore-based sensing with molecular carriers that can specifically capture α-Syn oligomers with sizes of less than 20 nm. We demonstrate that α-Synuclein oligomers can be detected directly in clinical samples, with minimal sample processing, by their ion current characteristics and successfully utilize this technology to differentiate cohorts of PD patients from healthy controls. The measurements indicate that detecting α-Syn oligomers present in CSF may potentially provide valuable insights into the progression and monitoring of Parkinson's disease.

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.

Combining iontronic, chromatography and nanopipette for Aβ42 aggregates detection and separation

In this work, we aim to capture, detect and analysis at single molecule level Aβ42 aggregates. To this end, two strategies of track-etched nanopore membranes functionalization were investigated. The first one uses an aptamer and requires only three steps, whereas the second strategy uses Lecanemab antibodies and requires six steps. Out of the two presented strategies, the second one was found to be the most suitable to detect Aβ42 aggregates using a quick current-voltage readout. The resulting single nanopore was then upscale to multipore membranes to capture the Aβ42 aggregates before analysis through them through a single-molecule approach. By comparing the species present in the retentate and filtrate, we confirmed the membrane's affinity for the larger Aβ42 aggregates present in the sample. We found that chromatographic membranes combined with an ionic diode for binary on/off readout are powerful tools for detecting rare biomarkers before single molecule analysis.

Aβ42 fibril and non-fibril oligomers characterization using a nanopipette

The Aβ42 aggregates with different structures and morphology was investigated through a single molecule label-free technique. To this end, the quartz nanopipettes were functionalized with polyethylene glycol. The set of Aβ42- epigallocatechin-3-gallate fibrils with length (from 85 nm to 250 nm) obtained by sonication was detected. The comparison of experimental and computed value of the amplitude of relative current blockade using a geometrical model show that for fibrils longer than 80 nm, the discriminating parameter is their diameter. Then, non-fibril oligomers obtain from Aβ42(Osaka) aggregation at different time seed was investigated. The analysis of the amplitude of relative current blockade shows that detected oligomers are smaller than 30 nm regardless the aggregation time. In addition, the wide distributions of the dwell time suggests the polymorph character of the sample.

Ultrasensitive Detection of Aβ42 Seeds in Cerebrospinal Fluid with a Nanopipette-Based Real-Time Fast Amyloid Seeding and Translocation Assay

In this work, early-stage Aβ42 aggregates were detected using a real-time fast amyloid seeding and translocation (RT-FAST) assay. Specifically, Aβ42 monomers were incubated in buffer solution with and without preformed Aβ42 seeds in a quartz nanopipette coated with L-DOPA. Then, formed Aβ42 aggregates were analyzed on flyby resistive pulse sensing at various incubation time points. Aβ42 aggregates were detected only in the sample with Aβ42 seeds after 180 min of incubation, giving an on/off readout of the presence of preformed seeds. Moreover, this RT-FAST assay could detect preformed seeds spiked in 4% cerebrospinal fluid/buffer solution. However, in this condition, the time to detect the first aggregates was increased. Analysis of Cy3-labeled Aβ42 monomer adsorption on a quartz substrate after L-DOPA coating by confocal fluorescence spectroscopy and molecular dynamics simulation showed the huge influence of Aβ42 adsorption on the aggregation process.

Stochastic Sensing of Dynamic Interactions and Chemical Reactions with Nanopores/Nanochannels

Nanopore sensing technology is an emerging analysis method with the advantages of simple operation, high sensitivity, fast output and being label free, and it is widely used in protein analysis, gene sequencing, biomarker detection, and other fields. The confined space of the nanopore provides a place for dynamic interactions and chemical reactions between substances. The use of nanopore sensing technology to track these processes in real time is helpful to understand the interaction/reaction mechanism at the single-molecule level. According to nanopore materials, we summarize the development of biological nanopores and solid-state nanopores/nanochannels in the stochastic sensing of dynamic interactions and chemical reactions. The goal of this paper is to stimulate the interest of researchers and promote the development of this field.

Multifold improvement in allergen detection capability of dipstick-type immunosensors via macromolecular crowding

Dipstick-type lateral flow immunosensors are used widely for on-site detection of food allergens. The weakness of the immunosensors of this type, however, is their low sensitivity. Contrary to current methods, that focus on improving detection capability through the introduction of novel labels or multistep protocols, this work exploits macromolecular crowding to modify and regulate the microenvironment of the immunoassay, thus promoting the interactions that are responsible for allergen recognition and signal generation. The effect of 14 macromolecular crowding agents was explored using, as a model, commercially available and widely applied dipstick immunosensors, which are already optimized in terms of reagents and conditions for peanut allergen detection. An about 10-fold improvement in detection capability was achieved by using polyvinylpyrrolidone, Mr 29,000, as a macromolecular crowder without compromising simplicity and practicality. The proposed approach is complementary to other methods of improving the sensitivity by using novel labels. Because biomacromolecular interactions have a fundamental role in all types of biosensors, we foresee that the proposed strategy will also find applications in other biosensors and analytical devices.

The Modification and Applications of Nanopipettes in Electrochemical Analysis

Nanopipette, which is fabricated by glasses and possesses a nanoscale pore in the tip, has been proven to be immensely useful in electrochemical analysis. Numerous nanopipette-based sensors have emerged with improved sensitivity, selectivity, ease of use, and miniaturization. In this minireview, we provide an overview of the recent developments of nanopipette-based electrochemical sensors based on different types of nanopipettes, including single-nanopipettes, self-referenced nanopipettes, dual-nanopipettes, and double-barrel nanopipettes. Several important modification materials for nanopipette functionalization are highlighted, such as conductive materials, macromolecular materials, and functional molecules. These materials can improve the sensing performance and targeting specificities of nanopipettes. We also discuss examples of related applications and the future development of nanopipette-based strategies.

Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores

Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing. A clear molecular-level understanding of how the presence of PEGs offers such desirable outcomes in nanopore sensing is still missing. In this work, we present a new theoretical approach to probe the effect of PEG crowders on DNA capture and translocation through the αHL nanopore. We develop an exactly solvable discrete-state stochastic model based on the cooperative partitioning of individual polycationic PEGs within the cavity of the αHL nanopore. It is argued that the apparent electrostatic interactions between the DNA and PEGs control all of the dynamic processes. Our analytical predictions find excellent agreements with existing experiments, thereby strongly supporting our theory.

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.

Mechanistic Study of the Conductance and Enhanced Single-Molecule Detection in a Polymer-Electrolyte Nanopore

Solid-state nanopores have been widely employed in the detection of biomolecules, but low signal-to-noise ratios still represent a major obstacle in the discrimination of nucleic acid and protein sequences substantially smaller than the nanopore diameter. The addition of 50% poly(ethylene) glycol (PEG) to the external solution is a simple way to enhance the detection of such biomolecules. Here, we demonstrate with finite-element modeling and experiments that the addition of PEG to the external solution introduces a strong imbalance in the transport properties of cations and anions, drastically affecting the current response of the nanopore. We further show that the strong asymmetric current response is due to a polarity-dependent ion distribution and transport at the nanopipette tip region, leading to either ion depletion or enrichment for few tens of nanometers across its aperture. We provide evidence that a combination of the decreased/increased diffusion coefficients of cations/anions in the bath outside the nanopore and the interaction between a translocating molecule and the nanopore-bath interface is responsible for the increase in the translocation signals. We expect this new mechanism to contribute to further developments in nanopore sensing by suggesting that tuning the diffusion coefficients of ions could enhance the sensitivity of the system.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection

A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a G-nanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.

Portable nanopore-sequencing technology: Trends in development and applications

Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.