Differential Enzyme Flexibility Probed Using Solid-State Nanopores

Utilizing solid-state nanopore sensing for high-efficiency and precise targeted localization in antiviral drug development

The efficient identification and validation of drug targets are paramount in drug discovery and development. Excessive costs, intricate procedures, and laborious sample handling frequently encumber contemporary methodologies. In this study, we introduce an innovative approach for the expeditious screening of drug targets utilizing solid-state nanopores. These nanopores provide a label-free, ultra-sensitive, and high-resolution platform for the real-time detection of biomolecular interactions. By observing the changes in relative ion currents over time after mixing different peptides with small molecule drugs, and supplementing this with noise analysis, we can pinpoint specific regions of drug action, thereby enhancing both the speed and cost-efficiency of drug development. This research offers novel insights into drug discovery, expands current perspectives, and lays the groundwork for formulating effective therapeutic strategies across a spectrum of diseases.

Bidirectional Peptide Translocation through Ultrasmall Solid-State Nanopores

It is important to obtain the configuration of polypeptides and the sequence information on amino acids for understanding various life processes and many biological applications. Nanopores, as a newly developed single-molecule detection technology, exhibit unique advantages in real-time dynamics detection. Here, we designed a special peptide chain with 10 arginine in the head and achieved successful single-molecule detection by ultrasmall solid-state nanopores (2-3 nm). Unique bidirectional translocation signals were observed and explained under the framework of charge distribution of the peptide and interaction with the nanopore wall. Two natural peptide chains, histatin-5 and angiopep-2, were also explored by nanopore experiments to confirm our conjecture. Our designed peptide chain could realize multiple detections of the same peptide chain, offering possibilities for high-resolution peptide detection and fingerprinting by solid-state nanopores in the future.

Angular-Inertia Regulated Stable and Nanoscale Sensing of Single Molecules Using Nanopore-In-A-Tube

Nanopore is commonly used for high-resolution, label-free sensing, and analysis of single molecules. However, controlling the speed and trajectory of molecular translocation in nanopores remains challenging, hampering sensing accuracy. Here, the study proposes a nanopore-in-a-tube (NIAT) device that enables decoupling of the current signal detection from molecular translocation and provides precise angular inertia-kinetic translocation of single molecules through a nanopore, thus ensuring stable signal readout with high signal-to-noise ratio (SNR). Specifically, the funnel-shaped silicon nanopore, fabricated at a 10-nm resolution, is placed into a centrifugal tube. A light-induced photovoltaic effect is utilized to achieve a counter-balanced state of electrokinetic effects in the nanopore. By controlling the inertial angle and centrifugation speed, the angular inertial force is harnessed effectively for regulating the translocation process with high precision. Consequently, the speed and trajectory of the molecules are able to be adjusted in and around the nanopore, enabling controllable and high SNR current signals. Numerical simulation reveals the decisive role of inertial angle in achieving uniform translocation trajectories and enhancing analyte-nanopore interactions. The performance of the device is validated by discriminating rigid Au nanoparticles with a 1.6-nm size difference and differentiating a 1.3-nm size difference and subtle stiffness variations in flexible polyethylene glycol molecules.

High-precision high-speed nanopore ping-pong control system based on field programmable gate array

"Molecular ping-pong," emerging as a control strategy in solid-state nanopore technology, presents a highly promising approach for repetitive measurements of single biomolecules, such as DNA. This paper introduces a high-precision, high-speed nanopore molecular ping-pong control system consisting of a home-built trans-impedance amplifier (TIA), a control system based on a Field Programmable Gate Array (FPGA), and a LabVIEW program operating on the host personal computer. Through feedback compensation and post-stage boosting, the TIA achieves a high bandwidth of about 200 kHz with a gain of 100 MΩ, along with low input-referred current noise of 1.6 × 10-4 pA2/Hz at 1 kHz and 1.1 × 10-3 pA2/Hz at 100 kHz. The FPGA-based control system demonstrates a minimum overall response time (tdelay) of 6.5 μs from the analog input current signal trigger to the subsequent reversal of the analog output drive voltage signal, with a control precision of 1 μs. Additionally, a LabVIEW program has been developed to facilitate rapid data exchange and communication with the FPGA program, enabling real-time signal monitoring, parameter adjustment, and data storage. Successful recapture of individual DNA molecules at various tdelay, resulting in an improvement in capture rate by up to 2 orders of magnitude, has been demonstrated. With unprecedented control precision and capture efficiency, this system provides robust technical support and opens novel research avenues for nanopore single-molecule sensing and manipulation.

In-tube micro-pyramidal silicon nanopore for inertial-kinetic sensing of single molecules

Electrokinetic force has been the major choice for driving the translocation of molecules through a nanopore. However, the use of this approach is limited by an uncontrollable translocation speed, resulting in non-uniform conductance signals with low conformational sensitivity, which hinders the accurate discrimination of the molecules. Here, we show the use of inertial-kinetic translocation induced by spinning an in-tube micro-pyramidal silicon nanopore fabricated using photovoltaic electrochemical etch-stop technique for biomolecular sensing. By adjusting the kinetic properties of a funnel-shaped centrifugal force field while maintaining a counter-balanced state of electrophoretic and electroosmotic effect in the nanopore, we achieved regulated translocation of proteins and obtained stable signals of long and adjustable dwell times and high conformational sensitivity. Moreover, we demonstrated instantaneous sensing and discrimination of molecular conformations and longitudinal monitoring of molecular reactions and conformation changes by wirelessly measuring characteristic features in current blockade readouts using the in-tube nanopore device.

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

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

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

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

Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown

Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.

Lithium Chloride Effects Field-Induced Protein Unfolding and the Transport Energetics Inside a Nanopipette

The tapered geometry of nanopipettes offers a unique perspective on protein transport through nanopores since both a gradual and fast confinement are possible depending on the translocation direction. The protein capture rate, unfolding, speed of translocation, and clogging probability are studied by toggling the LiCl concentration between 2 and 4 M. Interestingly, the proteins in this study could be transported with or against electrophoresis and offer vastly different attributes of sensing. Herein, a ruleset for studying proteins is developed that prevents irreversible pore clogging and yields upward of >100,000 events/nanopore. The extended duration of experiments further revealed that the capture rate takes ∼2 h to reach a steady state, emphasizing the importance of reaching equilibrated transport for studying the energetics and kinetics of protein transport (i.e., diffusion vs barrier-limited). Even in the equilibrated transport state, improper lowpass filtering was shown to distort the classification of diffusion-limited vs barrier-limited transport. Finally, electric-field-induced protein unfolding was found to be most prominent in electroosmotic-dominant transport, whereas electrophoretic-dominant events show no evidence of unfolding. Thus, our findings showcase the optimal conditions for protein translocations and the impact on studying protein unfolding, transporting energetics, and acquiring high bandwidth data.

Solid-State Nanopore Distinguishes Ferritin and Apo-Ferritin with Identical Exteriors through Amplified Flexibility at Single-Molecule Level

Protein identification and discrimination at the single-molecule level are big challenges. Solid-state nanopores as a sensitive biosensor have been used for protein analysis, although it is difficult to discriminate proteins with similar structures in the traditional discrimination method based on the current blockage fraction. Here, we select ferritin and apo-ferritin as the model proteins that exhibit identical exterior and different interior structures and verify the practicability of their discrimination with flexibility features by the strategy of gradually decreasing the nanopore size. We show that the larger nanopore (relative to the protein size) has no obvious effect on discriminating two proteins. Then, the comparable-sized nanopore plays a key role in discriminating two proteins based on the dwell time and fraction distribution, and the conformational changes of both proteins are also studied with this nanopore. Finally, in the smaller nanopore, the protein molecules are trapped rather than translocated, where two proteins are obviously discriminated through the current fluctuation caused by the vibration of proteins. This strategy has potential in the discrimination of other important similar proteins.

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.

Engineering Biological Nanopore Approaches toward Protein Sequencing

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.

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.

Solid-State Quad-Nanopore Array for High-Resolution Single-Molecule Analysis and Discrimination

The ability to detect and distinguish biomolecules at the single-molecule level is at the forefront of today's biomedicine and analytical chemistry research. Increasing the dwell time of individual biomolecules in the sensing spot can greatly enhance the sensitivity of single-molecule methods. This is particularly important in solid-state nanopore sensing, where the detection of small molecules is often limited by the transit dwell time and insufficient temporal resolution. Here, a quad-nanopore is introduced, a square array of four nanopores (with a space interval of 30-50 nm) to improve the detection sensitivity through electric field manipulation in the access region. It is shown that dwell times of short DNA strands (200 bp) are prolonged in quad-nanopores as compared to single nanopores of the same diameter. The dependence of dwell times on the quad-pore spacing is investigated and it is found that the "retarding effect" increases with decreasing space intervals. Furthermore, ultra-short DNA (50 bp) detection is demonstrated using a 10 nm diameter quad-nanopore array, which is hardly detected by a single nanopore. Finally, the general utility of quad-nanopores has been verified by successful discrimination of two kinds of small molecules, metal-organic cage and bovine serum albumin (BSA).

Discriminating Single Nucleotide Variations in Solid-State Nanopores by Evaluating the Combination Efficiency between DNA Polymerase and Its Substrate

A single nucleotide variant present between two otherwise identical nucleic acids will have unexpected functional consequences frequently. Here, a neoteric single nucleotide variation (SNV) detection assay that integrates two complementary nanotechnology systems, nanoassembly technology and an ingenious nanopore biosensing platform, has been applied to this research. Specifically, we set up a detection system to reflect the binding efficiency of the polymerase and nanoprobe through the difference of nanopore signals and then explore the effect of base mutation at the binding site. In addition, machine learning based on support vector machines is used to automatically classify characteristic events mapped by nanopore signals. Our system reliably discriminates single nucleotide variants at binding sites, even possessing the recognition among transitions, transversions, and hypoxanthine (base I). Our results demonstrate the potential of solid-state nanopore detection for SNV and provide some ideas for expanding solid-state nanopore detection platforms.

Wafer-Scale Fabrication of Uniform, Micrometer-Sized, Triangular Membranes on Sapphire for High-Speed Protein Sensing in a Nanopore

Ultra-low-noise solid-state nanopores are attractive for high-accuracy single-molecule sensing. A conventional silicon platform introduces acute capacitive noise to the system, which seriously limits the recording bandwidth. Recently, we have demonstrated the creation of thin triangular membranes on an insulating crystal sapphire wafer to eliminate the parasitic device capacitance. Uniquely different from the previous triangular etching window designs, here hexagonal windows were explored to produce triangular membranes by aligning to the sapphire crystal within a large tolerance of alignment angles (10-35°). Interestingly, sapphire facet competition serves to suppress the formation of more complex polygons but creates stable triangular membranes with their area insensitive to the facet alignment. Accordingly, a new strategy was successfully established on a 2 in. sapphire wafer to produce chips with an average membrane side length of 4.7 μm, an area of <30 μm² for 81% chips, or estimated calculated membrane capacitance as low as 0.06 pF. We finally demonstrated <4 μs high-speed and high-fidelity low-noise protein detection under 250 kHz high bandwidth.

Nanopore-based technologies beyond DNA sequencing

Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.

Metal-Organic Cage as Single-Molecule Carrier for Solid-State Nanopore Analysis

The ability to detect biomolecules at the single-molecule level is at the forefront of biological research, precision medicine, and early diagnosis. Recently, solid-state nanopore sensors have emerged as a promising technique for label-free and precise diagnosis assay. However, insufficient sensitivity and selectivity for small analytes are a great challenge for clinical diagnosis applications via solid-state nanopores. Here, for the first time, a metal-organic cage, PCC-57, is employed as a carrier to increase the sensitivity and selectivity of solid-state nanopores based on the intrinsic interaction of the nanocage with biomolecules. Firstly, it is found that the carrier itself is undetectable unless bound with the target analytes and used oligonucleotides as linkers to attach PCC-57 and target analytes. Secondly, two small analytes, oligonucleotide conjugated angiopep-2 and polyphosphoric acid, are successfully distinguished using the molecular carrier. Finally, selectivity of nanopore detection is achieved by attaching PCC-57 to oligonucleotide-tailed aptamers, and the human alpha-thrombin sample is successfully detected. It is believed that the highly designable metal-organic cage could serve as a rich carrier repository for a variety of biomolecules, facilitating single-molecule screening of clinically relevant biomolecules based on solid-state nanopores in the future.

Investigation of α-Synuclein and Amyloid-β(42)-E22Δ Oligomers Using SiN Nanopore Functionalized with L-Dopa

Solid-state nanopores are an emerging technology used as a high-throughput, label-free analytical method for the characterization of protein aggregation in an aqueous solution. In this work, we used Levodopamine to coat a silicon nitride nanopore surface that was fabricated through a dielectric breakdown in order to reduce the unspecific adsorption. The coating of inner nanopore wall by investigation of the translocation of heparin. The functionalized nanopore was used to investigate the aggregation of amyloid-β and α-synuclein, two biomarkers of degenerative diseases. In the first application, we demonstrate that the α-synuclein WT is more prone to form dimers than the variant A53T. In the second one, we show for the Aβ(42)-E22Δ (Osaka mutant) that the addition of Aβ(42)-WT monomers increases the polymorphism of oligomers, while the incubation with Aβ(42)-WT fibrils generates larger aggregates.

Enhanced Signal to Noise Ratio Enables High Bandwidth Nanopore Recordings and Molecular Weight Profiling of Proteins

Fast protein translocations often lead to bandwidth-limited amplitude-attenuated event signatures. In this study, we developed a protein- and electrolyte chemistry-centric pathway to construct a readily executable decision tree for the detection of non-attenuated protein translocations using conventional electronics. Each optimization encompasses increasing capture rate (C_R), signal-to-noise ratio (SNR), and minimizing irreversible analyte clogging to collect >10⁴ events/pipette spanning a host of electric fields. This was demonstrated using 11 proteins ranging from ∼12 kDa to ∼720 kDa. Moreover, both symmetric and asymmetric electrolyte conditions (cis and trans chamber electrolyte concentration ratios _<^> 1) were explored. As a result, asymmetric electrolyte conditions were favorable on the extreme ends of the size spectrum (i.e., larger, and smaller proteins) and while the remainder of proteins were best sensed under symmetric electrolyte conditions. Under these optimal conditions, only ≲10% of events were attenuated at 500 mV (≲ 5% for most proteins at 500 mV with only ≲1-5% of the population faster than ∼7 μs, which is the theoretical attenuation threshold for 100 kHz bandwidth). Finally, applied voltage (V_app), peak current drop (ΔI_p), electrolyte conductivity (K), and open-pore conductance (G₀) were used to generate a linear relationship to evaluate the molecular weight of the protein (M_w) using plots of (dΔI_p)/(dV_app) vs M_w/(G₀/K).

PlyAB Nanopores Detect Single Amino Acid Differences in Folded Haemoglobin from Blood

The real‐time identification of protein biomarkers is crucial for the development of point‐of‐care and portable devices. Here, we use a PlyAB biological nanopore to detect haemoglobin (Hb) variants. Adult haemoglobin (HbA) and sickle cell anaemia haemoglobin (HbS), which differ by just one amino acid, were distinguished in a mixture with more than 97 % accuracy based on individual blockades. Foetal Hb, which shows a larger sequence variation, was distinguished with near 100 % accuracy. Continuum and Brownian dynamics simulations revealed that Hb occupies two energy minima, one near the inner constriction and one at the trans entry of the nanopore. Thermal fluctuations, the charge of the protein, and the external bias influence the dynamics of Hb within the nanopore, which in turn generates the unique ionic current signal in the Hb variants. Finally, Hb was counted from blood samples, demonstrating that direct discrimination and quantification of Hb from blood using nanopores, is feasible.

Application of nanopore sensors for biomolecular interactions and drug discovery

Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.

Localized Nanopore Fabrication via Controlled Breakdown

Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.

Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores

Discrimination of nucleotides serves as the basis for DNA sequencing using solid-state nanopores. However, the translocation of DNA is usually too fast to be detected, not to mention nucleotide discrimination. Here, we utilized polyphenolic TA and Fe³⁺, an attractive metal-organic thin film, and achieved a fast and robust surface coating for silicon nitride nanopores. The hydrophilic coating layer can greatly reduce the low-frequency noise of an original unstable nanopore, and the nanopore size can be finely tuned in situ at the nanoscale by simply adjusting the relative ratio of Fe³⁺ and TA monomers. Moreover, the hydrogen bonding interaction formed between the hydroxyl groups provided by TA and the phosphate groups of DNAs significantly increases the residence time of a short double-strand (100 bp) DNA. More importantly, we take advantage of the different strengths of hydrogen bonding interactions between the hydroxyl groups provided by TA and the analytes to discriminate between two oligonucleotide samples (oligodeoxycytidine and oligodeoxyadenosine) with similar sizes and lengths, of which the current signal patterns are significantly different using the coated nanopore. The results shed light on expanding the biochemical functionality of surface coatings on solid-state nanopores for future biomedical applications.

β-Barrel Nanopores with an Acidic-Aromatic Sensing Region Identify Proteinogenic Peptides at Low pH

Biological nanopores are emerging as sensitive single-molecule sensors for proteins and peptides. The heterogeneous charge of a polypeptide chain, however, can complicate or prevent the capture and translocation of peptides and unfolded proteins across nanopores. Here, we show that two β-barrel nanopores, aerolysin and cytotoxin K, cannot efficiently detect proteinogenic peptides from a trypsinated protein under a wide range of conditions. However, the introduction of an acidic-aromatic sensing region in the β-barrel dramatically increased the dwell time and the discrimination of peptides in the nanopore at acidic pH. Surprisingly, despite the fact that the two β-barrel nanopores have a similar diameter and an acidic-aromatic construction, their capture mechanisms differ. The electro-osmotic flow played a dominant role for aerolysin, while the electrophoretic force dominated for cytotoxin K. Nonetheless, both β-barrel nanopores allowed the detection of mixtures of trypsinated peptides, with aerolysin nanopores showing a better resolution for larger peptides and cytotoxin K showing a better resolution for shorter peptides. Therefore, this work provides a generic strategy for modifying nanopores for peptide detection that will be most likely be applicable to other nanopore-forming toxins.

Fabrication of solid-state nanopores

Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.

Effects of off-axis translocation through nanopores on the determination of shape and volume estimates for individual particles

Resistive pulses generated by nanoparticles that translocate through a nanopore contain multi-parametric information about the physical properties of those particles. For example, non-spherical particles sample several different orientations during translocation, producing fluctuations in blockade current that relate to their shape. Due to the heterogenous distribution of electric field from the center to the wall of a nanopore while a particle travels through the pore, its radial position influences the blockade current, thereby affecting the quantification of parameters related to the particle's characteristics. Here, we investigate the influence of these off-axis effects on parameters estimated by performing finite element simulations of dielectric particles transiting a cylindrical nanopore. We varied the size, ellipsoidal shape, and radial position of individual particles, as well as the size of the nanopore. As expected, nanoparticles translocating near the nanopore wall produce increase current blockades, resulting in overestimates of particle volume. We demonstrated that off-axis effects also influence estimates of shape determined from resistive pulse analyses, sometimes producing a multiple-fold deviation in ellipsoidal length-to-diameter ratio between estimates and reference values. By using a nanopore with the minimum possible diameter that still allows the particle to rotate while translocating, off-axis effects on the determination of both volume and shape can be minimized. In addition, tethering the nanoparticles to a fluid coating on the nanopore wall makes it possible to determine an accurate particle shape with an overestimated volume. This work provides a framework to select optimal ratios of nanopore to nanoparticle size for experiments targeting free translocations.

Nanopore-Based Protein Identification

The implementation of a reliable, rapid, inexpensive, and simple method for whole-proteome identification would greatly benefit cell biology research and clinical medicine. Proteins are currently identified by cleaving them with proteases, detecting the polypeptide fragments with mass spectrometry, and mapping the latter to sequences in genomic/proteomic databases. Here, we demonstrate that the polypeptide fragments can instead be detected and classified at the single-molecule limit using a nanometer-scale pore formed by the protein aerolysin. Specifically, three different water-soluble proteins treated with the same protease, trypsin, produce different polypeptide fragments defined by the degree by which the latter reduce the nanopore's ionic current. The fragments identified with the aerolysin nanopore are consistent with the predicted fragments that trypsin could produce.

Solid-state nanopore analysis on the conformation change of DNA polymerase I induced by a DNA substrate

We studied the conformational changes between a Klenow fragment and its monomer complex with a DNA substrate using a SiN nanopore and found that the monomer complex has a tighter structure and transports slower.

Evaluation of the binding effect and cytotoxicity assay of 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione on calf thymus DNA: spectroscopic, calorimetric, and molecular dynamics approaches

With advances in new drug therapies, it is essential to understand the interactions between drugs and target molecules. In this study, we applied multiple spectroscopic techniques including absorbance, fluorescence, circular dichroism spectroscopy, viscosity, thermal melting, calorimetric, and molecular dynamics (MD) simulation to study the interaction between 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione (PPF) and calf thymus DNA (ct DNA) in the absence or presence of histone H1. PPF exhibits a high binding affinity towards ct DNA in binary and ternary systems. In addition, the result for the binding constant was observed within the range 10⁴  M^-1 achieved through fluorescence quenching data, while the values for enthalpy and entropy changes for ct DNA-PPF and (ct DNA-H1) PPF complexes were measured to be -72.54 kJ.mol^-1 , -161.14 J.mol^-1  K^-1 , -85.34 kJ.mol^-1 , and -19.023 J.mol^-1  K^-1 , respectively. Furthermore, in accordance with circular dichroism spectra, the inducement of ct DNA structural changes was observed during binding of PPF and H1 in binary and ternary system forms. The essential roles of hydrogen bonding and van der Waals forces throughout the interaction were suggested using thermodynamic parameters. According to the obtained data, the interaction mode of ct DNA-PPF and (ct DNA-H1) PPF complexes was intercalation binding. Suggested by the MD simulation study, the ct DNA-H1 complex caused a reduction in the stability of the DNA structure in the presence or absence of ligand, which demonstrated that PPF as an intercalating agent can further distort the structure. The information achieved from this study will be very helpful in understanding the effects of PPF on the conformational state of ct DNA in the absence or presence of the H1 molecule, which seems to be quite significant for clarifying the mechanisms of action and its pharmacokinetics.

Solid-state and polymer nanopores for protein sensing: A review

In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.

Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation

Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts, and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.

Allosteric Switching of Calmodulin in a Mycobacterium smegmatis porin A (MspA) Nanopore-Trap

Recent developments concerning large protein nanopores suggest a new approach to structure profiling of native folded proteins. In this work, the large vestibule of Mycobacterium smegmatis porin A (MspA) and calmodulin (CaM), a Ca²⁺ -binding protein, were used in the direct observation of the protein structure. Three conformers, including the Ca²⁺ -free, Ca²⁺ -bound, and target peptide-bound states of CaM, were unambiguously distinguished. A disease related mutant, CaM D129G was also discriminated by MspA, revealing how a single amino acid replacement can interfere with the Ca²⁺ -binding capacity of the whole protein. The binding capacity and aggregation effect of CaM induced by different ions (Mg²⁺ /Sr²⁺ /Ba²⁺ /Ca²⁺ /Pb²⁺ /Tb³⁺ ) were also investigated and the stability of MspA in extreme conditions was evaluated. This work demonstrates the most systematic single-molecule investigation of different allosteric conformers of CaM, acknowledging the high sensing resolution offered by the MspA nanopore trap.

In silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection

The identification of proteins at the single-molecule level would open exciting new venues in biological research and disease diagnostics. Previously, we proposed a nanopore-based method for protein identification called chop-n-drop fingerprinting, in which the fragmentation pattern induced and measured by a proteasome-nanopore construct is used to identify single proteins. In the simulation study presented here, we show that 97.1% of human proteome constituents are uniquely identified under close to ideal measuring circumstances, using a simple alignment-based classification method. We show that our method is robust against experimental error, as 69.4% can still be identified if the resolution is twice as low as currently attainable, and 10% of proteasome restriction sites and protein fragments are randomly ignored. Based on these results and our experimental proof of concept, we argue that chop-n-drop fingerprinting has the potential to make cost-effective single-molecule protein identification feasible in the near future.

Real-Time and Label-Free Measurement of Deubiquitinase Activity with a MspA Nanopore

Covalently attaching ubiquitin (Ub) to cellular proteins as a post-translational modification can result in altered function of modified proteins. Enzymes regulating Ub as a post-translational modification, such as ligases and deubiquitinases, are challenging to characterize in part due to the low throughput of in-vitro assays. Single-molecule nanopore based assays have the advantage of detecting proteins with high specificity and resolution, and in a label-free, real-time fashion. Here we demonstrate the use of a MspA nanopore for discriminating and quantifying Ub proteins. We further applied the MspA pore to measure the Ub-chain disassembly activity of UCH37, a proteasome associated deubiquitinase. The implementation of this MspA system into nanopore arrays could enable high throughput characterizations of unknown deubiquitinases as well as drug screening against disease related enzymes.

Discrimination of α-Thrombin and γ-Thrombin Using Aptamer-Functionalized Nanopore Sensing

Protein detection and identification at the single-molecule level are major challenges in many biotechnological fields. Solid-state nanopores have raised attention as label-free biosensors with high sensitivity. Here, we use solid-state nanopore sensing to discriminate two closely related proteins, α-thrombin and γ-thrombin. We show that aptamer functionalization improves protein discrimination thanks to a significant difference in the relative current blockade amplitude. To enhance discrimination, we postprocessed the signals using machine learning and training algorithms and we were able to reach an accuracy of 98.8% using seven features and ensemble methods.

The emerging landscape of single-molecule protein sequencing technologies

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

Translocation of a looped polymer threading through a nanopore

Recent experiments reported that the complicated translocation dynamics of a looped DNA chain through a nanopore can be detected by ionic current blockade profiles. Inspired by the experimental results, we systematically study the translocation dynamics of a looped polymer, formed by three building blocks of a loop in the middle and two tails of the same length connected with the loop, by using Langevin dynamics simulations. Based on two entering modes (tail-leading and loop-leading) and three translocation orders (loop-tail-tail, tail-loop-tail, and tail-tail-loop), the translocation of the looped polymer is classified into six translocation pathways, corresponding to different current blockade profiles. The probabilities of the six translocation pathways are dependent on the loop length, polymer length, and pore radius. Moreover, the translocation times of the entire polymer and the loop are investigated. We find that the two translocation times show different dependencies on the translocation pathways and on the lengths of the loop and the entire polymer.

Electrical unfolding of cytochrome c during translocation through a nanopore constriction

Many small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field-driven translocation behavior of cytochrome c (cyt c) through ultrathin silicon nitride (SiN_x) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5-nm-diameter pore, we find that, in a threshold electric-field regime of ∼30 to 100 MV/m, cyt c is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt c is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5- and 2.0-nm-diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (∼ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens avenues for exploring protein folding structures, internal contacts, and electric-field-induced deformability.

A nanofluidic device for ultrasensitive and label-free detection of tetracycline in association with γ-cyclodextrin and GO

Herein, an ultrasensitive and selective nanofluidic device for tetracycline (TC) was developed in association with γ-cyclodextrin and graphene oxide (GO). The assay was designed based on the change of the nanochannel surface charge due to the selective recognition ability of GO between aptamers and TC-aptamer complexes. And γ-cyclodextrin was utilized to eliminate the excess TC since the amine group molecules were inclined to be adsorbed onto the nanochannel surface and affected the adsorption efficiency of the nanochannel. In the presence of TC, TC specifically binded to the aptamer to form TC-aptamer and was separated from GO. The TC-aptamer complexes could be quantitated with conical nanochannels coated with polyethyleneimine (PEI)/Zr4+. The redundant TC was removed by γ-cyclodextrin. The detection limit of the nanofluidic device was as low as 2 ng L-1 (S/N = 3) and the linear range was 10 ng L-1 to 10 μg L-1. Moreover, the nanofluidic device provided high specificity and good recovery rates of 94.8-109.3% in natural river, tapwater and wastewater samples. The results revealed that our study provided a new rapid detection method for trace contaminant analysis.

Tuning Protein Discrimination Through Altering the Sampling Interface Formed between the Analyte and the OmpG Nanopore

Nanopore sensors capable of distinguishing homologous protein analytes are highly desirable tools for proteomics research and disease diagnostics. Recently, an engineered outer membrane protein G (OmpG) nanopore with a high-affinity ligand attached to a gating loop 6 showed specificity for distinguishing homologous proteins in complex mixtures. Here, we report the development of OmpG nanopores with the other six loops used as the anchoring point to host an affinity ligand for protein sensing. We investigated how the analyte binding to the affinity ligand located at different loops affects the detection sensitivity, selectivity, and specificity. Our results reveal that analytes weakly attracted to the OmpG nanopore surface are only detectable when the ligand is tethered to loop 6. In contrast, protein analytes that form a strong interaction with the OmpG surface via electrostatic attractions are distinguishable by all seven OmpG nanopore constructs. In addition, the same analyte can generate distinct binding signals with different OmpG nanopore constructs. The ability to exploit all seven OmpG loops will aid the design of a new generation of OmpG sensors with increased sensitivity, selectivity, and specificity for biomarker sensing.

Quantitative Measurements of Protein Volume and Concentration using Hydrogel-Backed Nanopores

Accurate identification and quantification of proteins in solution using nanopores is technically challenging in part because of the large fraction of missed translocation events due to short event times and limitations of conventional current amplifiers. Previously, we have shown that a nanopore interfaced with a poly(ethylene glycol)-dimethacrylate hydrogel with an average mesh size of 3.1 nm significantly enhances the protein residence time within the pore, reducing the number of missed events. We used hydrogel-backed nanopores to sense unlabeled proteins as small as 5.5 kDa in size and 10 fM in concentration. We show that the frequency of protein translocation events linearly scales with bulk concentration over a wide range of concentrations and that unknown protein concentrations can be determined from an interpolation of the frequency-concentration curve with less than 10% error. Further, we show an iterative method to determine a protein volume accurately from measurement data for proteins with a diameter comparable to a nanopore diameter. Our measurements and analysis also suggest several competing mechanisms for the detection enhancement enabled by the presence of the hydrogel.

Impact of surface state on polyethylene glycol conformation confined inside a nanopore

Solid-state nanopores are a promising platform for characterizing proteins. In order to improve their lifetime and prevent fouling, Polyethylene Glycol (PEG) grafting is one of the most efficient and low-cost solutions. Different models to calculate the PEG thickness do not consider their interaction with the nanopore inner surface nor the effect of confinement. Here, we investigate by molecular dynamic simulation the PEG conformation inside a nanopore in the case of hydrophobic and hydrophilic nanopores. Our results reveal that the nanopore inner surface plays a role in the PEG organization and, thus, in the speed of the salt constituent. The resulting pair interaction between PEG and its environment clearly shows a more important affinity for K⁺ compared to Li⁺ cations.

The translocation dynamics of the polymer through a conical pore: Non-stuck, weak-stuck, and strong-stuck modes

The external voltage-driven polymer translocation through a conical pore (with a large opening at the entry and a small tip at the exit) is studied by using the Langevin dynamics simulation in this paper. The entire translocation process is divided into an approaching stage and a threading stage. First, the approaching stage starts from the polymer entering the large opening and ends up at a terminal monomer reaching the pore tip. In this stage, the polymer will undergo the conformation adjustment to fit the narrowed cross-sectional area of the pore, leading to three approaching modes: the non-stuck mode with a terminal monomer arriving at the pore tip smoothly, the weak-stuck mode for the polymer stuck inside the pore for a short duration with minor conformational adjustments, and the strong-stuck mode with major conformational changes and a long duration. The approaching times (the duration of the approaching stage) of the three approaching modes show different behavior as a function of the pore apex angle. Second, the threading stage describes that the polymer threads through the pore tip with a linear fashion. In this stage, an increase in the apex angle causes the reduction of the threading time (the duration of the threading stage) due to the increase in the driving force with the apex angle at the tip. Moreover, we also find that with the increase in the apex angle or the polymer length, the polymer threading dynamics will change from the quasi-equilibrium state to the non-equilibrium state.

Snapshotting the transient conformations and tracing the multiple pathways of single peptide folding using a solid-state nanopore

A fundamental question relating to protein folding/unfolding is the time evolution of the folding of a protein into its precisely defined native structure. The proper identification of transition conformations is essential for accurately describing the dynamic protein folding/unfolding pathways. Owing to the rapid transitions and sub-nm conformation differences involved, the acquisition of the transient conformations and dynamics of proteins is difficult due to limited instrumental resolution. Using the electrochemical confinement effect of a solid-state nanopore, we were able to snapshot the transient conformations and trace the multiple transition pathways of a single peptide inside a nanopore. By combining the results with a Markov chain model, this new single-molecule technique is applied to clarify the transition pathways of the β-hairpin peptide, which shows nonequilibrium fluctuations among several blockage current stages. This method enables the high-throughput investigation of transition pathways experimentally to access previously obscure peptide dynamics, which is significant for understanding the folding/unfolding mechanisms and misfolding of peptides or proteins.

A solid-state nanopore based method is described for resolving protein-folding-related problems via snapshotting the folding intermediates and characterizing the kinetics of a single peptide.