Solid-state nanopore channels with DNA selectivity

DNA Origami Incorporated into Solid-State Nanopores Enables Enhanced Sensitivity for Precise Analysis of Protein Translocations

The rapidly advancing field of nanotechnology is driving the development of precise sensing methods at the nanoscale, with solid-state nanopores emerging as promising tools for biomolecular sensing. This study investigates the increased sensitivity of solid-state nanopores achieved by integrating DNA origami structures, leading to the improved analysis of protein translocations. Using holo human serum transferrin (holo-hSTf) as a model protein, we compared hybrid nanopores incorporating DNA origami with open solid-state nanopores. Results show a significant enhancement in holo-hSTf detection sensitivity with DNA origami integration, suggesting a unique role of DNA interactions beyond confinement. This approach holds potential for ultrasensitive protein detection in biosensing applications, offering advancements in biomedical research and diagnostic tool development for diseases with low-abundance protein biomarkers. Further exploration of origami designs and nanopore configurations promises even greater sensitivity and versatility in the detection of a wider range of proteins, paving the way for advanced biosensing technologies.

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.

Advancement of Next-Generation DNA Sequencing through Ionic Blockade and Transverse Tunneling Current Methods

DNA sequencing is transforming the field of medical diagnostics and personalized medicine development by providing a pool of genetic information. Recent advancements have propelled solid-state material-based sequencing into the forefront as a promising next-generation sequencing (NGS) technology, offering amplification-free, cost-effective, and high-throughput DNA analysis. Consequently, a comprehensive framework for diverse sequencing methodologies and a cross-sectional understanding with meticulous documentation of the latest advancements is of timely need. This review explores a broad spectrum of progress and accomplishments in the field of DNA sequencing, focusing mainly on electrical detection methods. The review delves deep into both the theoretical and experimental demonstrations of the ionic blockade and transverse tunneling current methods across a broad range of device architectures, nanopore, nanogap, nanochannel, and hybrid/heterostructures. Additionally, various aspects of each architecture are explored along with their strengths and weaknesses, scrutinizing their potential applications for ultrafast DNA sequencing. Finally, an overview of existing challenges and future directions is provided to expedite the emergence of high-precision and ultrafast DNA sequencing with ionic and transverse current approaches.

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.

Ion-Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores

DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.

Nanopore Identification of N-Acetylation by Hydroxylamine Deacetylation (NINAHD)

N-Acetyl modification, a chemical modification commonly found on biomacromolecules, plays a crucial role in the regulation of cell activities and is related to a variety of diseases. However, due to the instability of N-acetyl modification, accurate and rapid identification of N-acetyl modification with a low measurement cost is still technically challenging. Here, based on hydroxylamine deacetylation and nanopore single molecule chemistry, a universal sensing strategy for N-acetyl modification has been developed. Acetohydroxamic acid (AHA), which is produced by the hydroxylamine deacetylation reaction and serves as a reporter for N-acetylation identification, is specifically sensed by a phenylboronic acid (PBA)-modified Mycobacterium smegmatis porin A (MspA). With this strategy, N-acetyl modifications on RNA, DNA, proteins, and glycans were identified, demonstrating its generality. Specifically, histones can be treated with hydroxylamine deacetylation, from which the generated AHA can represent the amount of N-acetyl modification detected by a nanopore sensor. The unique event features of AHA also demonstrate the robustness of sensing against other interfering analytes in the environment.

Enhancing ion selectivity by tuning solvation abilities of covalent-organic-framework membranes

Understanding the molecular-level mechanisms involved in transmembrane ion selectivity is essential for optimizing membrane separation performance. In this study, we reveal our observations regarding the transmembrane behavior of Li+ and Mg2+ ions as a response to the changing pore solvation abilities of the covalent-organic-framework (COF) membranes. These abilities were manipulated by adjusting the lengths of the oligoether segments attached to the pore channels. Through comparative experiments, we were able to unravel the relationships between pore solvation ability and various ion transport properties, such as partitioning, conduction, and selectivity. We also emphasize the significance of the competition between Li+ and Mg2+ with the solvating segments in modulating selectivity. We found that increasing the length of the oligoether chain facilitated ion transport; however, it was the COF membrane with oligoether chains containing two ethylene oxide units that exhibited the most pronounced discrepancy in transmembrane energy barrier between Li+ and Mg2+, resulting in the highest separation factor among all the evaluated membranes. Remarkably, under electro-driven binary-salt conditions, this specific COF membrane achieved an exceptional Li+/Mg2+ selectivity of up to 1352, making it one of the most effective membranes available for Li+/Mg2+ separation. The insights gained from this study significantly contribute to advancing our understanding of selective ion transport within confined nanospaces and provide valuable design principles for developing highly selective COF membranes.

Solid-State Nanopore/Nanochannel Sensors with Enhanced Selectivity through Pore-in Modification

Nanopore sensing technology, as an emerging analytical method, has the advantages of simple operation, fast output, and label-free and has been widely used in fields such as protein analysis, gene sequencing, and biomarker detection. Inspired by biological ion channels, scientists have prepared various artificial solid-state nanopores/nanochannels. Biological ion channels have extremely high ion transport selectivity, while solid-state nanopores/nanochannels have poor selectivity. The selectivity of solid-state nanopores and nanochannels can be enhanced by modifying channel charge, varying pore size, incorporating specific chemical functionality, and adjusting operating (or solution) conditions. This Perspective highlights pore-in modification strategies for enhancing the selectivity of solid-state nanopore/nanochannel sensors by summarizing the articles published in the last 10 years. The future development prospects and challenges of pore-in modification in solid-state nanopore and nanochannel sensors are discussed. This Perspective helps readers better understand nanopore sensing technology, especially the importance of detection selectivity. We believe that solid-state nanopore/nanochannel sensors will soon enter our homes after various challenges.

Deciphering DNA nucleotide sequences and their rotation dynamics with interpretable machine learning integrated C3N nanopores

A solid-state nanopore combined with the quantum transport method has garnered substantial attention and intrigue for DNA sequencing due to its potential for providing rapid and accurate sequencing results, which could have numerous applications in disease diagnosis and personalized medicine. However, the intricate and multifaceted nature of the experimental protocol poses a formidable challenge in attaining precise single nucleotide analysis. Here, we report a machine learning (ML) framework combined with the quantum transport method to accelerate high-throughput single nucleotide recognition with C3N nanopores. The optimized eXtreme Gradient Boosting Regression (XGBR) algorithm has predicted the fingerprint transmission of each unknown nucleotide and their rotation dynamics with root mean square error scores as low as 0.07. Interpretability of ML black box models with the game theory-based SHapley Additive exPlanation method has provided a quasi-explanation for the model working principle and the complex relationship between electrode-nucleotide coupling and transmission. Moreover, a comprehensive ML classification of nucleotides based on binary, ternary, and quaternary combinations shows maximum accuracy and F1 scores of 100%. The results suggest that ML in tandem with a nanopore device can potentially alleviate the experimental hurdles associated with quantum tunneling and facilitate fast and high-precision DNA sequencing.

Nano-injection molding with resin mold inserts for prototyping of nanofluidic devices for single molecular detection

While injection molding is becoming the fabrication modality of choice for high-scale production of microfluidic devices, especially those used for in vitro diagnostics, its translation into the growing area of nanofluidics (structures with at least one dimension <100 nm) has not been well established. Another prevailing issue with injection molding is the high startup costs and the relatively long time between device iterations making it in many cases impractical for device prototyping. We report, for the first time, functional nanofluidic devices with dimensions of critical structures below 30 nm fabricated by injection molding for the manipulation, identification, and detection of single molecules. UV-resin molds replicated from Si masters served as mold inserts, negating the need for generating Ni-mold inserts via electroplating. Using assembled devices with a cover plate via hybrid thermal fusion bonding, we demonstrated two functional thermoplastic nanofluidic devices. The first device consisted of dual in-plane nanopores placed at either end of a nanochannel and was used to detect and identify single ribonucleotide monophosphate molecules via resistive pulse sensing and obtain the effective mobility of the molecule through nanoscale electrophoresis to allow its identification. The second device demonstrated selective binding of a single RNA molecule to a solid phase bioreactor decorated with a processive exoribonuclease, XRN1. Our results provide a simple path towards the use of injection molding for device prototyping in the development stage of any nanofluidic or even microfluidic application, through which rapid scale-up is made possible by transitioning from prototyping to high throughput production using conventional Ni mold inserts.

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.

Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks

DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.

Functional Nanopores Enabled with DNA

Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.

Multi-physics simulations and experimental comparisons for the optical and electrical forces acting on a silica nanoparticle trapped by a double-nanohole plasmonic nanopore sensor

Bimodal optical-electrical data generated when a 20 nm diameter silica (SiO2) nanoparticle was trapped by a plasmonic nanopore sensor were simulated using Multiphysics COMSOL and compared with sensor measurements for closely matching experimental parameters. The nanosensor, employed self-induced back action (SIBA) to optically trap nanoparticles in the center of a double nanohole (DNH) structure on top a solid-state nanopores (ssNP). This SIBA actuated nanopore electrophoresis (SANE) sensor enables simultaneous capture of optical and electrical data generated by several underlying forces acting on the trapped SiO2 nanoparticle: plasmonic optical trapping, electroosmosis, electrophoresis, viscous drag, and heat conduction forces. The Multiphysics simulations enabled dissecting the relative contributions of those forces acting on the nanoparticle as a function of its location above and through the sensor's ssNP. Comparisons between simulations and experiments demonstrated qualitative similarities in the optical and electrical time-series data generated as the nanoparticle entered and exited from the SANE sensor. These experimental parameter-matched simulations indicated that the competition between optical and electrical forces shifted the trapping equilibrium position close to the top opening of the ssNP, relative to the optical trapping force maximum that was located several nm above. The experimentally estimated minimum for the optical force needed to trap a SiO2 nanoparticle was consistent with corresponding simulation predictions of optical-electrical force balance. The comparison of Multiphysics simulations with experiments improves our understanding of the interplay between optical and electrical forces as a function of nanoparticle position across this plasmonic nanopore sensor.

Solid-state nanopore: chemical modifications, interactions, and functionalities

Nanopore technology is a burgeoning detection technology for single-molecular sensing and ion rectification. Solid-state nanopores have attracted more and more attention because of their higher stability and tunability than biological nanopores. However, solid-state nanopores still suffer the drawbacks of low signal-to-noise ratio and low resolution, which hinders their practical applications. Thus, developing operatical and useful methods to overcome the shortages of solid-state nanopores is urgently needed. Here, we summarize the recent research on nanopore modification to achieve this goal. Modifying solid-state nanopores with different coating molecules can improve the selectivity, sensitivity, and stability of nanopores. The modified molecules can introduce different functions into the nanopores, greatly expanding the applications of this novel detection technology. We hope that this review of nanopore modification will provide new ideas for this field.

Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing

Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.

Recent advance in solid state nanopores modification and characterization

Nanopore, due to its advantages of modifiable, controllability and sensitivity, has made a splash in recent years in the fields of biomolecular sequencing, small molecule detection, salt differential power generation, and biomimetic ion channels, etc. In these applications, the role of chemical or biological modification is indispensable. Compared with small molecules, the modification of polymers is more difficult and the methods are more diverse. Choosing appropriate modification method directly determines the success or not of the research, therefore, it is necessary to summarize the polymer modification methods toward nanopores. In addition, it is also important to provide clear and convincing evidence that the nanopore modification is successful, the corresponding characterization methods are also indispensable. Therefore, this review will summarize the methods of polymer modification of nanopores and efficient characterization methods. And we hope that this review will provide some reference value for like-minded researchers.

A nanofluidic system based on cylindrical polymer brushes: how to control the size of nanodroplets

In molecular dynamics simulations we investigate the self-organized formation of droplets from a continuous flow of incoming nanoparticles. This transformation is facilitated by a cylindrical channel that is decorated with a polymer brush in a marginally poor solvent. We analyze droplet formation and propagation by means of simple scaling arguments which are tested in the simulations. Polymer brushes in marginally poor solvents serve as a pressure feedback system, exhibit a collapse transition under the moderate pressure of the incident flow, without the need for additional external stimuli, and finally close spontaneously after droplet passage. Our results qualitatively demonstrate the control of polymer brushes over continuous fluids and droplet formation, and its effectiveness as a means of fluid control can be used to design nanofluidic rectification devices that operate reliably under moderate pressure.

Mechanisms of Enzymatic Transduction in Nanochannel Biosensors

The immobilization of enzymes in solid-state nanochannels is a new avenue for the design of biosensors with outstanding selectivity and sensitivity. This work reports the first theoretical model of an enzymatic nanochannel biosensor. The model is applied to the system previously experimentally studied by Lin, et al. (Anal. Chem. 2014, 86, 10546): a hourglass nanochannel modified by glucose oxidase for the detection of glucose. Our predictions are in good agreement with experimental observations as a function of the applied potential, pH and glucose concentration. The sensing mechanism results from the combination of three processes: i) the establishment of a steady-state proton concentration gradient due to a reaction-diffusion mechanism, ii) the effect of that gradient on the charge of the adsorbed enzymes and native surface groups, and iii) the effect of the resulting surface charge on the ionic current. Strategies to improve the sensor performance based on this mechanism are identified and discussed.

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.

Lifetime of glass nanopores in a PDMS chip for single-molecule sensing

Nanopore sensing is an emerging technology that has many biosensing applications ranging from DNA sequencing using biological pores to biomolecular analysis using solid-state pores. Solid-state nanopores that are more stable are an attractive choice for biosensing applications. Still, biomolecule interactions with the nanopore surface reduce nanopore stability and increase usage costs. In this study, we investigated the biosensing capability for 102 quartz glass nanopores with a diameter of 11–18 nm that were fabricated using laser-assisted capillary pulling. Nanopores were assembled into multiple microfluidic chips that were repeatedly used for up to 19 weeks. We find that using vacuum storage combined with minimal washing steps improved the number of use cycles for nanopores. The single-molecule biosensing capability over repeated use cycles was demonstrated by quantitative analysis of a DNA carrier designed for detection of short single-stranded DNA oligonucleotides.

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Maintaining low noise and linear current-voltage relation is crucial for biosensing

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Multiple nanopores embedded in a chip can make more than 90 different measurements

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Nanopores can be reused weekly over 19 weeks

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Nanopore failure can be attributed to contaminant accumulation and dissolution

Functionalised nanopores: chemical and biological modifications

Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information can be elucidated. Early studies utilised nanopore technology for sensing applications, and subsequent developments have diversified its remit. Nanopores can be synthetic, solid-state, or biological in origin, but recent work has seen these boundaries blurred as hybrid functionalised pores emerge. The modification of existing pores and the construction of novel synthetic pores has been an enticing goal for creating systems with tailored properties and functionality. Here, we explore chemically functionalised biological pores and the bio-inspired functionalisation of solid-state pores, highlighting how the convergence of these domains provides enhanced functionality.

The convergence of chemistry, biology, and solid-state approaches enables the construction hybrid nanopores with enhanced single-molecule applications.

Bio-inspired Track-Etched Polymeric Nanochannels: Steady-State Biosensors for Detection of Analytes

Bio-inspired polymeric nanochannel (also referred as nanopore)-based biosensors have attracted considerable attention on account of their controllable channel size and shape, multi-functional surface chemistry, unique ionic transport properties, and good robustness for applications. There are already very informative reviews on the latest developments in solid-state artificial nanochannel-based biosensors, however, which concentrated on the resistive-pulse sensing-based sensors for practical applications. The steady-state sensing-based nanochannel biosensors, in principle, have significant advantages over their counterparts in term of high sensitivity, fast response, target analytes with no size limit, and extensive suitable range. Furthermore, among the diverse materials, nanochannels based on polymeric materials perform outstandingly, due to flexible fabrication and wide application. This compressive Review summarizes the recent advances in bio-inspired polymeric nanochannels as sensing platforms for detection of important analytes in living organisms, to meet the high demand for high-performance biosensors for analysis of target analytes, and the potential for development of smart sensing devices. In the future, research efforts can be focused on transport mechanisms in the field of steady-state or resistive-pulse nanochannel-based sensors and on developing precisely size-controlled, robust, miniature and reusable, multi-functional, and high-throughput biosensors for practical applications. Future efforts should aim at a deeper understanding of the principles at the molecular level and incorporating these diverse pore architectures into homogeneous and defect-free multi-channel membrane systems. With the rapid advancement of nanoscience and biotechnology, we believe that many more achievements in nanochannel-based biosensors could be achieved in the near future, serving people in a better way.

Regional and functional division of functional elements of solid-state nanochannels for enhanced sensitivity and specificity of biosensing in complex matrices

Solid-state nanochannels (SSNs) provide a promising approach for biosensing due to the confinement of molecules inside, their great mechanical strength and diversified surface chemical properties; however, until now, their sensitivity and specificity have not satisfied the practical requirements of sensing applications, especially in complex matrices, i.e., media of diverse constitutions. Here, we report a protocol to achieve explicit regional and functional division of functional elements at the outer surface (FE_OS) and inner wall (FE_IW) of SSNs, which offers a nanochannel-based sensing platform with enhanced specificity and sensitivity. The protocol starts with the fabrication and characterization of the distribution of FE_OS and FE_IW. Then, the evaluation of the contributions of FE_OS and FE_IW to ionic gating is described; the FE_IW mainly regulate ionic gating, and the FE_OS can produce a synergistic effect. Finally, hydrophobic or highly charged FE_OS are applied to ward off interference molecules, non-target molecules that may affect the ionic signal of nanochannels, which decreases false signals and helps to achieve the highly specific ionic output in complex matrices. Compared with other methods currently available, this method will contribute to the fundamental understanding of substance transport in SSNs and provide high specificity and sensitivity in SSN-based analyses. The procedure takes 3-6 d to complete.

Detection of single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of Phi29 DNA packaging motor

Protein post-translational modification (PTM) is crucial to modulate protein interactions and activity in various biological processes. Emerging evidence has revealed PTM patterns participate in the pathology onset and progression of various diseases. Current PTM identification relies mainly on mass spectrometry-based approaches that limit the assessment to the entire protein population in question. Here we report a label-free method for the detection of the single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of phi29 DNA packaging motor, which bears the deletion of 25-amino acids (AA) at the C-terminus or 17-AA at the internal loop of the channel. The mutant channels were used to detect propionylation modification via single-molecule fingerprinting in either the traditional patch-clamp or the portable MinION™ platform of Oxford Nanopore Technologies. Up to 2000 channels are available in the MinION™ Flow Cells. The current signatures and dwell time of individual channels were identified. Peptides with only one propionylation were differentiated. Excitingly, identification of single or multiple modifications on the MinION™ system was achieved. The successful application of PTM differentiation on the MinION™ system represents a significant advance towards developing a label-free and high-throughput detection platform utilizing nanopores for clinical diagnosis based on PTM.

Single-Entity Detection With TEM-Fabricated Nanopores

Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.

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.

Measurement of Alcohol-Dependent Physiological Changes in Red Blood Cells Using Resistive Pulse Sensing

Alcohol exposure has been postulated to adversely affect the physiology and function of the red blood cells (RBCs). The global pervasiveness of alcohol abuse, causing health issues and social problems, makes it imperative to resolve the physiological effects of alcohol on RBC physiology. Alcohol consumed recreationally or otherwise almost immediately alters cell physiology in ways that is subtle and still unresolved. In this paper, we introduce a high-resolution device for quantitative electrofluidic measurement of changes in RBC volume upon alcohol exposure. We present an exhaustive calibration of our device using model cells to measure and resolve volume changes down to 0.6 fL. We find an RBC shrinkage of 5.3% at 0.125% ethanol (the legal limit in the United States) and a shrinkage of 18.5% at 0.5% ethanol (the lethal limit) exposure. Further, we also measure the time dependence of cell volume shrinkage (upon alcohol exposure) and then recovery (upon alcohol removal) to quantify shrinkage and recovery of RBC volumes. This work presents the first direct quantification of temporal and concentration-dependent changes in red blood cell volume upon ethanol exposure. Our device presents a universally applicable high-resolution and high-throughput platform to measure changes in cell physiology under native and diseased conditions.

Rational design of DNA nanostructures for single molecule biosensing

The ability to detect low concentrations of biomarkers in patient samples is one of the cornerstones of modern healthcare. In general, biosensing approaches are based on measuring signals resulting from the interaction of a large ensemble of molecules with the sensor. Here, we report a biosensor platform using DNA origami featuring a central cavity with a target-specific DNA aptamer coupled with a nanopore read-out to enable individual biomarker detection. We show that the modulation of the ion current through the nanopore upon the DNA origami translocation strongly depends on the presence of the biomarker in the cavity. We exploit this to generate a biosensing platform with a limit of detection of 3 nM and capable of the detection of human C-reactive protein (CRP) in clinically relevant fluids. Future development of this approach may enable multiplexed biomarker detection by using ribbons of DNA origami with integrated barcoding.

Sensing with Nanopores and Aptamers: A Way Forward

In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.

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

Nanopore analysis of nucleic acid is now routine, but detection of proteins remains challenging. Here, we report the systematic characterization of the effect of macromolecular crowding on the detection sensitivity of a solid-state nanopore for circular and linearized DNA plasmids, globular proteins (β-galactosidase), and filamentous proteins (α-synuclein amyloid fibrils). We observe a remarkable ca. 1000-fold increase in the molecule count for the globular protein β-galactosidase and a 6-fold increase in peak amplitude for plasmid DNA under crowded conditions. We also demonstrate that macromolecular crowding facilitates the study of the topology of DNA plasmids and the characterization of amyloid fibril preparations with different length distributions. A remarkable feature of this method is its ease of use; it simply requires the addition of a macromolecular crowding agent to the electrolyte. We therefore envision that macromolecular crowding can be applied to many applications in the analysis of biomolecules by solid-state nanopores.

Sequence-Specific Recognition of HIV-1 DNA with Solid-State CRISPR-Cas12a-Assisted Nanopores (SCAN)

Nucleic acid detection methods are crucial for many fields such as pathogen detection and genotyping. Solid-state nanopore sensors represent a promising platform for nucleic acid detection due to its unique single molecule sensitivity and label-free electronic sensing. Here, we demonstrated the use of the glass nanopore for highly sensitive quantification of single-stranded circular DNAs (reporters), which could be degraded under the trans-cleavage activity of the target-specific CRISPR-Cas12a. We developed and optimized the Cas12a assay for HIV-1 analysis. We validated the concept of the solid-state CRISPR-Cas12a-assisted nanopores (SCAN) to specifically detect the HIV-1 DNAs. We showed that the glass nanopore sensor is effective in monitoring the cleavage activity of the target DNA-activated Cas12a. We developed a model to predict the total experimental time needed for making a statistically confident positive/negative call in a qualitative test. The SCAN concept combines the much-needed specificity and sensitivity into a single platform, and we anticipate that the SCAN would provide a compact, rapid, and low-cost method for nucleic acid detection at the point of care.

Measuring temperature effects on nanobubble nucleation via a solid-state nanopore

In this study, we designed SiN_X solid-state nanopores to detect the temperature effect on the hydrogen nanobubble formation. Here, we integrated a temperature controller with the highly sensitive nanopore. As the temperature decreases from 25 °C to 5 °C, the occurrence of the nanobubble nucleation inside a 12.3 nm SiN_X nanopore confined space decreased from 102 s^-1 to 23 s^-1, and the life-time of nanobubbles increased from 1.16 ms to 4.78 ms. The results further gave the activation energy for nanobubble nucleation which was 8.1 × 10^-20 J with a 12.3 nm SiN_X nanopore. Our method provides an efficient analytical tool for revealing the temperature-dependent nanobubble nucleation, which further benefits the fundamental understanding of nanobubble nucleation.

Durable, Stable, and Functional Nanopores Decorated by Self-Assembled Dipeptides

Nanopores have become an important tool for the detection and analysis of molecules at the single-molecule level. Surface modification of solid-state nanopores can improve their durability and efficiency. Peptides are ideal for surface modifications as they allow tailoring of multiple properties by a rational design of their sequence. Here, silicon nitride nanopores were coated by a dipeptide layer where a l-3,4-dihydroxyphenylalanine (DOPA) residue is the anchoring element and the other amino acid moiety is the functional element. DOPA binds tightly to many types of surfaces and allows a one-step functionalization of surfaces by simple immersion. As a result, the lifetime of coated nanopores increased from hours to months and the current-stability has significantly improved with respect to uncoated pores. This improvement is achieved by controlling the surface wettability and charge. Peptide-coated nanopores can be utilized as sensitive sensors that can be adjusted based on the choice of the functional moiety of the coated peptide. In addition, the coating slows down dsDNA translocation because of the DNA interaction with the pore coating.

Mechanism and Kinetics of Lipid Bilayer Formation in Solid-State Nanopores

Solid-state nanopores provide a highly versatile platform for rapid electrical detection and analysis of single molecules. Lipid bilayer coating of the nanopores can reduce nonspecific analyte adsorption to the nanopore sidewalls and increase the sensing selectivity by providing possibilities for tethering specific ligands in a cell-membrane mimicking environment. However, the mechanism and kinetics of lipid bilayer formation from vesicles remain unclear in the presence of nanopores. In this work, we used a silicon-based, truncated pyramidal nanopore array as the support for lipid bilayer formation. Lipid bilayer formation in the nanopores was monitored in real time by the change in ionic current through the nanopores. Statistical analysis revealed that a lipid bilayer is formed from the instantaneous rupture of individual vesicle upon adsorption in the nanopores, differing from the generally agreed mechanism that lipid bilayer forms at a high vesicle surface coverage on a planar support. The dependence of the lipid bilayer formation process on the applied bias, vesicle size, and concentration was systematically studied. In addition, the nonfouling properties of the lipid bilayer coated nanopores were demonstrated during long single-stranded DNA translocation through the nanopore array. The findings indicate that the lipid bilayer formation process can be modulated by introducing nanocavities intentionally on the planar surface to create active sites or changing the vesicle size and concentration.

Tailoring Dielectric Surface Charge via Atomic Layer Thickness

Channel surface property is a crucial factor that affects capture-to-translocation dynamics of single-particles in solid-state pores. Here, we show that atomically-thin dielectrics can be used to finely tune the pore wall surface potential. We isotopically coated alumina of atomically controlled thickness on a Si₃N₄ micropore. The surface zeta-potential in a buffer was found to decrease sharply by 1 nm thick deposition that served as a water-permeable ultra-thin sheet to modulate the effective charge density of the Al₂O₃/Si₃N₄ multilayer structure. Further thickening of the atomic layer enabled to control the zeta potential with a thickness at 3.4 mV/nm resolution. Accordingly, we observed concomitant enhancement in the capture rate and the translocation speed of negatively charged polymeric particles by virtue of the mitigated electroosmotic back flow in the functionalized pore channel. This simple method is widely applicable for tailoring the surface charge properties of essentially any sensors and devices working in aqueous media.

Revealing the mechanism of DNA passing through graphene and boron nitride nanopores

Nanopores on 2D materials have great potential for DNA sequencing, which is attributed to their high sequencing speed and reduced cost. However, identifying DNA bases at such a high speed with nanometer precision has remained a big challenge. Here, we implemented theoretical calculations to show the translocation of single-stranded DNA (ssDNA) through solid-state nanopores on a 2D hexagonal boron nitride (h-BN) and graphene sheet. A base-specific ssDNA sequencing technique was devised, based on the individual differences in the ion current responses for the (polyA)₁₆, (polyG)₁₆, (polyC)₁₆, and (polyT)₁₆ bases of ssDNA. Our sequential procedure for sequencing is built on a comparative approach between the current signals obtained from the nanopores to achieve base-specific detection. Our results indicate that at higher voltages (1.0, 1.2, 1.4, 1.6, 1.8 and 2.0 V nm^-1), DNA translocation is tracked though the 1.5 and 2.0 nm nanopores, and at the 1.5 nm pore size, folded ssDNA close to the nanopore accounts for 93% and 81% of events for graphene and h-BN. Our calculations indicate charge transfer from the graphene to ssDNA, while the reverse happens in the case of the h-BN membrane. These results provide critical insights into our understanding of single molecule sequencing through solid-state nanopore research.

Surface coatings for solid-state nanopores

Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.

Loop-Mediated Isothermal Amplification-Coupled Glass Nanopore Counting Toward Sensitive and Specific Nucleic Acid Testing

Solid-state nanopores have shown great promise and achieved tremendous success in label-free single-molecule analysis. However, there are three common challenges in solid-state nanopore sensors, including the nanopore size variations from batch to batch that makes the interpretation of the sensing results difficult, the incorporation of sensor specificity, and the impractical analysis time at low analyte concentration due to diffusion-limited mass transport. Here, we demonstrate a novel loop-mediated isothermal amplification (LAMP)-coupled glass nanopore counting strategy that could effectively address these challenges. By using the glass nanopore in the counting mode (versus the sizing mode), the device fabrication challenge is considerably eased since it allows a certain degree of pore size variations and no surface functionalization is needed. The specific molecule replication effectively breaks the diffusion-limited mass transport thanks to the exponential growth of the target molecules. We show the LAMP-coupled glass nanopore counting has the potential to be used in a qualitative test as well as in a quantitative nucleic acid test. This approach lends itself to most amplification strategies as long as the target template is specifically replicated in numbers. The highly sensitive and specific sensing strategy would open a new avenue for solid-state nanopore sensors toward a new form of compact, rapid, low-cost nucleic acid testing at the point of care.

Rectification of protein translocation in truncated pyramidal nanopores

Solid-state nanopore technology presents an emerging single-molecule-based analytical tool for the separation and analysis of nanoparticles. Different approaches have been pursued to attain the anticipated detection performance. Here, we report the rectification behaviour of protein translocation through silicon-based truncated pyramidal nanopores. When the size of translocating proteins is comparable to the smallest physical constriction of the nanopore, the frequency of translocation events observed is lower for proteins that travel from the larger to the small opening of the nanopore than for those that travel in the reverse direction. When the proteins are appreciably smaller than the nanopore, an opposite rectification in the frequency of translocation events is evident. The maximum rectification factor achieved is around ten. Numerical simulations reveal the formation of an electro-osmotic vortex in such asymmetric nanopores. The vortex-protein interaction is found to play a decisive role in rectifying the translocation in terms of polarity and amplitude. The reported phenomenon can be potentially exploitable for the discrimination of various nanoparticles.

Polarization Induced Electro-Functionalization of Pore Walls: A Contactless Technology

This review summarizes recent advances in micro- and nanopore technologies with a focus on the functionalization of pores using a promising method named contactless electro-functionalization (CLEF). CLEF enables the localized grafting of electroactive entities onto the inner wall of a micro- or nano-sized pore in a solid-state silicon/silicon oxide membrane. A voltage or electrical current applied across the pore induces the surface functionalization by electroactive entities exclusively on the inside pore wall, which is a significant improvement over existing methods. CLEF's mechanism is based on the polarization of a sandwich-like silicon/silicon oxide membrane, creating electronic pathways between the core silicon and the electrolyte. Correlation between numerical simulations and experiments have validated this hypothesis. CLEF-induced micro- and nanopores functionalized with antibodies or oligonucleotides were successfully used for the detection and identification of cells and are promising sensitive biosensors. This technology could soon be successfully applied to planar configurations of pores, such as restrictions in microfluidic channels.

Dynamical transitions during the collapse of inertial holes

At the center of a collapsing hole lies a singularity, a point of infinite curvature where the governing equations break down. It is a topic of fundamental physical interest to clarify the dynamics of fluids approaching such singularities. Here, we use scaling arguments supported by high-fidelity simulations to analyze the dynamics of an axisymmetric hole undergoing capillary collapse in a fluid sheet of small viscosity. We characterize the transitions between the different dynamical regimes —from the initial inviscid dynamics that dominate the collapse at early times to the final Stokes dynamics that dominate near the singularity— and demonstrate that the crossover hole radii for these transitions are related to the fluid viscosity by power-law relationships. The findings have practical implications for the integrity of perforated fluid films, such as bubble films and biological membranes, as well as fundamental implications for the physics of fluids converging to a singularity.

A numerical study of the selectivity of an isolated cylindrical or conical nanopore to a charged macro-ion

The selectivity of a single nanopore in a uniformly charged solid membrane to a charged analyte ion is studied using numerical simulation. A continuum model is used where the ions are regarded as point particles and characterized by a continuously varying number density. The problem is described by the coupled equations for the electrostatic potential, ion-transport, and hydrodynamic flow, which are solved under appropriate boundary conditions using a finite volume method. The nanopore geometry is considered conical, the cylindrical pore being a special case where the cone angle is zero. The selectivity is characterized by a dimensionless parameter: the pore selectivity index. Results are presented showing how the pore selectivity index varies with the membrane surface charge and other parameters of the problem. The role of hydrodynamic flow on transport properties is examined and found to be consistent with theoretical results on electroosmotic flow through nanopores.

Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers

In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: first, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Fourth, they offer a method for tuning nanopore diameters by choice of the length of the lipid's acyl chains. The work presented here compares four properties of various lipid compositions with regard to their suitability as nanopore coatings for protein sensing experiments: (1) electrical noise during current recordings through solid-state nanopores before and after lipid coating, (2) long-term stability of the recorded current baseline and, by inference, of the coating, (3) viscosity of the coating as quantified by the lateral diffusion coefficient of lipids in the coating, and (4) the success rate of generating a suitable coating for quantitative nanopore-based resistive pulse recordings. We surveyed lipid coatings prepared from bolaamphiphilic, monolayer-forming lipids inspired by extremophile archaea and compared them to typical bilayer-forming phosphatidylcholine lipids containing various fractions of curvature-inducing lipids or cholesterol. We found that coatings from archaea-inspired lipids provide several advantages compared to conventional phospholipids; the stable, low noise baseline qualities and high viscosity make these membranes especially suitable for analysis that estimates physical protein parameters such as the net charge of proteins as they enable translocation events with sufficiently long duration to time-resolve dwell time distributions completely. The work presented here reveals that the ease or difficulty of coating a nanopore with lipid membranes did not depend significantly on the composition of the lipid mixture, but rather on the geometry and surface chemistry of the nanopore in the solid state substrate. In particular, annealing substrates containing the nanopore increased the success rate of generating stable lipid coatings.

Silicon nitride nanopore created by dielectric breakdown with a divalent cation: deceleration of translocation speed and identification of single nucleotides

Nanopore DNA sequencing with a solid-state nanopore requires deceleration of the ultrafast translocation speed of single-stranded DNA (ssDNA). We report an unexpected phenomenon: controlled dielectric breakdown (CBD) with a divalent metal cation, especially Ca2+, provides a silicon nitride nanopore with the ability to decelerate ssDNA speed to 100 μs per base even after solution replacement. This speed is two orders of magnitude slower than that for CBD with a conventional monovalent metal cation. Temperature dependence experiments revealed that the enthalpic barrier for a nanopore created via CBD with Ca2+ is 25-30kBT, comparable to that of a biological nanopore. The slowing effect originates from the strong interaction between ssDNA and divalent cations, which were coated on the sidewall of the nanopore during the CBD process. In addition, we found that the nanopore created via CBD with Ca2+ can decelerate the speed of even single-nucleotide monomers, dNMPs, to 0.1-10 ms per base. The four single nucleotides could be statistically identified according to their blockade currents. Our approach is simple and practical because it simultaneously allows nanopore fabrication, ssDNA deceleration and the identification of nucleotide monomers.