Microscopic Kinetics of DNA Translocation through synthetic nanopores

Exploring ssDNA translocation through α-hemolysin using coarse-grained steered molecular dynamics

Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside nanopores. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies ssDNA translocation through α-hemolysin nanopores exploiting steered MD using the MARTINI CG force field. The impacts of the sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing the experimental properties of ssDNA translocation, including a wide distribution in translocation times per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by the conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of obtaining sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.

Asymmetric ion transport through "Janus" MoSSe sub-nanometer pores

We conduct all-atom molecular dynamics simulations to systematically investigate the underlying mechanisms governing ion transport through a sub-nanometer pore decorated with negative charges in a "Janus" MoSSe membrane. The charge imbalance between S and Se atoms on each side of the membrane induces different types of ion adsorption processes depending on the pore inner charge configuration, and the polarity of external biases, which leads to asymmetry in ionic I-V characteristics. Statistical analysis of the total translocation times including adsorption-desorption processes, and ion dwell times indicates that potassium ions predominantly remain adsorbed during their interaction with the membrane before undertaking a quick translocation through the pore. High applied biases suppress cation adsorption, which results in fast translocation with the current flow boosted by negative inner charges around the pore. We also show that in a membrane consisting of several "Janus" layers, the applied bias necessary to overcome the sub-nm pore barrier increases with the number of layers, providing control over the ionic current.

Importance of the electrophoresis and pulse energy for siRNA-mediated gene silencing by electroporation in differentiated primary human myotubes

BACKGROUND

Electrotransfection is based on application of high-voltage pulses that transiently increase membrane permeability, which enables delivery of DNA and RNA in vitro and in vivo. Its advantage in applications such as gene therapy and vaccination is that it does not use viral vectors. Skeletal muscles are among the most commonly used target tissues. While siRNA delivery into undifferentiated myoblasts is very efficient, electrotransfection of siRNA into differentiated myotubes presents a challenge. Our aim was to develop efficient protocol for electroporation-based siRNA delivery in cultured primary human myotubes and to identify crucial mechanisms and parameters that would enable faster optimization of electrotransfection in various cell lines.

RESULTS

We established optimal electroporation parameters for efficient siRNA delivery in cultured myotubes and achieved efficient knock-down of HIF-1α while preserving cells viability. The results show that electropermeabilization is a crucial step for siRNA electrotransfection in myotubes. Decrease in viability was observed for higher electric energy of the pulses, conversely lower pulse energy enabled higher electrotransfection silencing yield. Experimental data together with the theoretical analysis demonstrate that siRNA electrotransfer is a complex process where electropermeabilization, electrophoresis, siRNA translocation, and viability are all functions of pulsing parameters. However, despite this complexity, we demonstrated that pulse parameters for efficient delivery of small molecule such as PI, can be used as a starting point for optimization of electroporation parameters for siRNA delivery into cells in vitro if viability is preserved.

CONCLUSIONS

The optimized experimental protocol provides the basis for application of electrotransfer for silencing of various target genes in cultured human myotubes and more broadly for electrotransfection of various primary cell and cell lines. Together with the theoretical analysis our data offer new insights into mechanisms that underlie electroporation-based delivery of short RNA molecules, which can aid to faster optimisation of the pulse parameters in vitro and in vivo.

Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore

The nanopore sensing method holds the promise of delivering a single molecule technology for identification of biological proteins, direct detection of post-translational modifications, and perhaps de novo determination of a protein's amino acid sequence. The key quantity measured in such nanopore sensing experiments is the magnitude of the ionic current passing through a nanopore blocked by a polypeptide chain. Establishing a relationship between the amino acid sequence of a peptide fragment confined within a nanopore and the blockade current flowing through the nanopore remains a major challenge for realizing the nanopore protein sequencing. Using the results of all-atom molecular dynamics simulations, here we compare nanopore sequencing of DNA with nanopore sequencing of proteins. We then delineate the factors affecting the blockade current modulation by the peptide sequence, showing that the current can be determined by (i) the steric footprint of an amino acid, (ii) its interactions with the pore wall, (iii) the local stretching of a polypeptide chain, and (iv) the local enhancement of the ion concentration at the nanopore constriction. We conclude with a brief discussion of the prospects for purely computational prediction of the blockade currents.

Prediction and Control in DNA Nanotechnology

DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.

T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition

MOTIVATION

Nanopore sequencing is a new macromolecular recognition and perception technology that enables high-throughput sequencing of DNA, RNA, even protein molecules. The sequences generated by nanopore sequencing span a large time frame, and the labor and time costs incurred by traditional analysis methods are substantial. Recently, research on nanopore data analysis using machine learning algorithms has gained unceasing momentum, but there is often a significant gap between traditional and deep learning methods in terms of classification results. To analyze nanopore data using deep learning technologies, measures such as sequence completion and sequence transformation can be employed. However, these technologies do not preserve the local features of the sequences. To address this issue, we propose a sequence-to-image (S2I) module that transforms sequences of unequal length into images. Additionally, we propose the Transformer-based T-S2Inet model to capture the important information and improve the classification accuracy.

RESULTS

Quantitative and qualitative analysis shows that the experimental results have an improvement of around 2% in accuracy compared to previous methods. The proposed method is adaptable to other nanopore platforms, such as the Oxford nanopore. It is worth noting that the proposed method not only aims to achieve the most advanced performance, but also provides a general idea for the analysis of nanopore sequences of unequal length.

AVAILABILITY AND IMPLEMENTATION

The main program is available at https://github.com/guanxiaoyu11/S2Inet.

Ready-to-use nanopore platform for label-free small molecule quantification: Ethanolamine as first example

In recent decades, nanopores have become a promising diagnostic tool. Protein and solid-state nanopores are increasingly used for both RNA/DNA sequencing and small molecule detection. The latter is of great importance, as their detection is difficult or expensive using available methods such as HPLC or LC-MS. DNA aptamers are an excellent detection element for sensitive and specific detection of small molecules. Herein, a method for quantifying small molecules using a ready-to-use sequencing platform is described. Taking ethanolamine as an example, a strand displacement assay is developed in which the target-binding aptamer is displaced from the surface of magnetic particles by ethanolamine. Non-displaced aptamer and thus the ethanolamine concentration are detected by the nanopore system and can be quantified in the micromolar range using our in-house developed analysis software. This method is thus the first to describe a label-free approach for the detection of small molecules in a protein nanopore system.

DNA Barcodes Using a Dual Nanopore Device

We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.

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.

Nanopore sensors for single molecular protein detection: Research progress based on computer simulations

As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label-free and high-throughput protein sequencing. In recent years, nanopore-based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing.

DNA double helix, a tiny electromotor

Flowing fluid past chiral objects has been used for centuries to power rotary motion in man-made machines. By contrast, rotary motion in nanoscale biological or chemical systems is produced by biasing Brownian motion through cyclic chemical reactions. Here we show that a chiral biological molecule, a DNA or RNA duplex rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction being determined by the chirality of the duplex. The rotation is found to be powered by the drag force of the electro-osmotic flow, realizing the operating principle of a macroscopic turbine at the nanoscale. The resulting torques are sufficient to power rotation of nanoscale beads and rods, offering an engineering principle for constructing nanoscale systems powered by electric field.

A molecular dynamics investigation of Taq DNA polymerase and its complex with a DNA substrate using a solid-state nanopore biosensor

Proteins have a small volume difference by the diversity of amino acids, which make protein detection and identification a great challenge. Solid-state nanopore as label-free biosensors has attracted attention with high sensitivity. In this work, we investigated the Taq DNA polymerase before and after combining it with a DNA substrate on a solid-state nanopore through molecular dynamics. In simulation, we analyzed the contribution source of nanopore current blockage. In addition to considering the traditional physical exclusion volume model, the non-covalent interaction between the protein molecules and the pore wall also showed to affect the current blockage in the nanopore. When choosing pores of comparable size to protein molecules, the two states of Taq DNA polymerase produce differentiated non-covalent interactions with the pore wall, which enhanced the amplitude difference in current blockage. As a result, the two DNA polymerases can be distinguished through the distinct current blockage. However, when applying additional pulling force or increasing the pore size of the nanopore, the differences between the current blockages are not significant enough to distinguish. The introduction of the non-covalent interaction makes it clear to understand the current blockage differences, which guide the mechanism between molecules with similar structures or volumes.

Active learning for efficient analysis of high-throughput nanopore data

MOTIVATION

As the third-generation sequencing technology, nanopore sequencing has been used for high-throughput sequencing of DNA, RNA, and even proteins. Recently, many studies have begun to use machine learning technology to analyze the enormous data generated by nanopores. Unfortunately, the success of this technology is due to the extensive labeled data, which often suffer from enormous labor costs. Therefore, there is an urgent need for a novel technology that can not only rapidly analyze nanopore data with high-throughput, but also significantly reduce the cost of labeling. To achieve the above goals, we introduce active learning to alleviate the enormous labor costs by selecting the samples that need to be labeled. This work applies several advanced active learning technologies to the nanopore data, including the RNA classification dataset (RNA-CD) and the Oxford Nanopore Technologies barcode dataset (ONT-BD). Due to the complexity of the nanopore data (with noise sequence), the bias constraint is introduced to improve the sample selection strategy in active learning. Results: The experimental results show that for the same performance metric, 50% labeling amount can achieve the best baseline performance for ONT-BD, while only 15% labeling amount can achieve the best baseline performance for RNA-CD. Crucially, the experiments show that active learning technology can assist experts in labeling samples, and significantly reduce the labeling cost. Active learning can greatly reduce the dilemma of difficult labeling of high-capacity nanopore data. We hope active learning can be applied to other problems in nanopore sequence analysis.

AVAILABILITY AND IMPLEMENTATION

The main program is available at https://github.com/guanxiaoyu11/AL-for-nanopore.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

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.

Molecular Dynamics Simulation of a Single Carbon Chain through an Asymmetric Double-Layer Graphene Nanopore for Prolonging the Translocation Time

In recent years, sensing technology based on nanopores has become one of the trustworthy options for characterization and even identification of a single biomolecule. In nanopore based DNA sequencing technology, the DNA strand in the electrolyte solution passes through the nanopore under an applied bias electric field. Commonly, the ionic current signals carrying the sequence information are difficult to detect effectively due to the fast translocation speed of the DNA strand, so that slowing down the translocation speed is expected to make the signals easier to distinguish and improve the sequencing accuracy. Modifying the nanopore structure is one of the effective methods. Through all-atom molecular dynamics simulations, we designed an asymmetric double-layer graphene nanopore structure to regulate the translocation speed of a single carbon chain. The structure consists of two nanopores with different sizes located on two layers. The simulation results indicate that the asymmetric nanopore structure will affect the chain's translocation speed and the ionic current value. When the single carbon chain passes from the smaller pore to the larger pore, the translocation time is significantly prolonged, which is about three times as long as the chain passing from the larger pore to the smaller pore. These results provide a new idea for designing more accurate and effective single-molecule solid-state nanopore sensors.

Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study

A nanopore is a tool in single-molecule sensing biotechnology that offers label-free identification with high throughput. Nanopores have been successfully applied to sequence DNA and show potential in the study of proteins. Nevertheless, the task remains challenging due to the large variability in size, charges, and folds of proteins. Miniproteins have a small number of residues, limited secondary structure, and stable tertiary structure, which can offer a systematic way to reduce complexity. In this computational work, we theoretically evaluated sensing two miniproteins found in the human body using a silicon nitride nanopore. We employed molecular dynamics methods to compute occupied-pore ionic current magnitudes and electronic structure calculations to obtain interaction strengths between pore wall and miniprotein. From the interaction strength, we derived dwell times using a mix of combinatorics and numerical solutions. This latter approach circumvents typical computational demands needed to simulate translocation events using molecular dynamics. We focused on two miniproteins potentially difficult to distinguish owing to their isotropic geometry, similar number of residues, and overall comparable structure. We found that the occupied-pore current magnitudes not to vary significantly, but their dwell times differ by 1 order of magnitude. Together, these results suggest a successful identification protocol for similar miniproteins.

DNA sequencing based on electronic tunneling in a gold nanogap: a first-principles study

Deoxyribonucleic acid (DNA) sequencing has found wide applications in medicine including treatment of diseases, diagnosis and genetics studies. Rapid and cost-effective DNA sequencing has been achieved by measuring the transverse electronic conductance as a single-stranded DNA is driven through a nanojunction. With the aim of improving the accuracy and sensitivity of DNA sequencing, we investigate the electron transport properties of DNA nucleobases within gold nanogaps based on first-principles quantum transport simulations. Considering the fact that the DNA bases can rotate within the nanogap during measurements, different nucleobase orientations and their corresponding residence time within the nanogap are explicitly taken into account based on their energetics. This allows us to obtain an average current that can be compared directly to experimental measurements. Our results indicate that bare gold electrodes show low distinguishability among the four DNA nucleobases while the distinguishability can be substantially enhanced with sulfur atom decorated electrodes. We further optimized the size of the nanogap by maximizing the residence time of the desired orientation.

Multi-resolution simulation of DNA transport through large synthetic nanostructures

Modeling and simulation has become an invaluable partner in development of nanopore sensing systems. The key advantage of the nanopore sensing method - the ability to rapidly detect individual biomolecules as a transient reduction of the ionic current flowing through the nanopore - is also its key deficiency, as the current signal itself rarely provides direct information about the chemical structure of the biomolecule. Complementing experimental calibration of the nanopore sensor readout, coarse-grained and all-atom molecular dynamics simulations have been used extensively to characterize the nanopore translocation process and to connect the microscopic events taking place inside the nanopore to the experimentally measured ionic current blockades. Traditional coarse-grained simulations, however, lack the precision needed to predict ionic current blockades with atomic resolution whereas traditional all-atom simulations are limited by the length and time scales amenable to the method. Here, we describe a multi-resolution framework for modeling electric field-driven passage of DNA molecules and nanostructures through to-scale models of synthetic nanopore systems. We illustrate the method by simulating translocation of double-stranded DNA through a solid-state nanopore and a micron-scale slit, capture and translocation of single-stranded DNA in a double nanopore system, and modeling ionic current readout from a DNA origami nanostructure passage through a nanocapillary. We expect our multi-resolution simulation framework to aid development of the nanopore field by providing accurate, to-scale modeling capability to research laboratories that do not have access to leadership supercomputer facilities.

Dielectric Manipulation of Polymer Translocation Dynamics in Engineered Membrane Nanopores

The alteration of the dielectric membrane properties by membrane engineering techniques such as carbon nanotube (CNT) coating opens the way to novel molecular transport strategies for biosensing purposes. In this article, we predict a macromolecular transport mechanism enabling the dielectric manipulation of the polymer translocation dynamics in dielectric membrane pores confining mixed electrolytes. In the giant permittivity regime of these engineered membranes governed by attractive polarization forces, multivalent ions adsorbed by the membrane nanopore trigger a monovalent ion separation and set an electroosmotic counterion flow. The drag force exerted by this flow is sufficiently strong to suppress and invert the electrophoretic velocity of anionic polymers and also to generate the mobility of neutral polymers whose speed and direction can be solely adjusted by the charge and concentration of the added multivalent ions. These features identify the dielectrically generated transport mechanism as an efficient means to drive overall neutral or weakly charged analytes that cannot be controlled by an external voltage. We also reveal that, in anionic polymer translocation, multivalent cation addition into the monovalent salt solution amplifies the electric current signal by several factors. The signal amplification is caused by the electrostatic many-body interactions replacing the monovalent polymer counterions by the multivalent cations of higher electric mobility. The strength of this electrokinetic charge discrimination points out the potential of multivalent ions as current amplifiers capable of providing boosted resolution in nanopore-based biosensing techniques.

Li+ Selectivity of Carboxylate Graphene Nanopores Inspired by Electric Field and Nanoconfinement

The regulation of the ion selectivity by electric field and ion association on the Li⁺ selectivity of carboxyl functionalized graphene nanopores are investigated by molecular dynamics simulation. Carboxylate graphene nanopores of sub-2 nm exhibit excellent Li⁺ selectivity under the electric field of 1.0 V nm^-1 . The results show that ion association inspired by electric field may be a key factor affecting ion selectivity of sub-2 nm nanopores. The ion association of Mg²⁺ and Cl^- can be promoted obviously near the nanopores under the electric field of 1.0 V nm^-1 . The migrating of Mg²⁺ can be retarded by stable clusters of Mg²⁺ and Cl^- formed near nanopores. The degree of association of Li⁺ with Cl^- is relatively low and the disassociation of the Li⁺ cluster is easier so that Li⁺ can more easily pass through the nanopores. These results gain insight into the effect of ion association inspired by electric field and nanoconfinement of graphene nanopore on Mg²⁺ /Li⁺ separation, and provide helpful information for the application of nanoporous materials in extraction of Li⁺ ion from salt-lake brine.

Mass separation in an asymmetric channel

We present a mechanism to sort out particles of different masses in an asymmetric channel, where the entropic barriers arise naturally and control the diffusion of these particles. When particles are subjected to an oscillatory force, with the scaled amplitude a and frequency ω, the mean particle velocity exhibits a bell-shaped behavior as a function of the particle mass, indicating that particles with an optimal mass m_{op} drift faster than other particles. By tuning a and ω, we get an empirical relation to estimate m_{op}∼(aω^{2})^{-0.4}. An additional static bias, applied in the opposite direction of the rectified velocity, would push the particles of lighter mass to move in its direction while the others drift opposite to it. This study is useful to design lab-on-a-chip devices for separating particles of different masses.

Bioinspired Solid-State Nanochannel Sensors: From Ionic Current Signals, Current, and Fluorescence Dual Signals to Faraday Current Signals

Inspired from bioprotein channels of living organisms, constructing "abiotic" analogues, solid-state nanochannels, to achieve "smart" sensing towards various targets, is highly seductive. When encountered with certain stimuli, dynamic switch of terminal modified probes in terms of surface charge, conformation, fluorescence property, electric potential as well as wettability can be monitored via transmembrane ionic current, fluorescence intensity, faraday current signals of nanochannels and so on. Herein, the modification methodologies of nanochannels and targets-detecting application are summarized in ions, small molecules, as well as biomolecules, and systematically reviewed are the nanochannel-based detection means including 1) by transmembrane current signals; 2) by the coordination of current- and fluorescence-dual signals; 3) by faraday current signals from nanochannel-based electrode. The coordination of current and fluorescence dual signals offers great benefits for synchronous temporal and spatial monitoring. Faraday signals enable the nanoelectrode to monitor both redox and non-redox components. Notably, by incorporation with confined effect of tip region of a needle-like nanopipette, glorious in-vivo monitoring is conferred on the nanopipette detector at high temporal-spatial resolution. In addition, some outlooks for future application in reliable practical samples analysis and leading research endeavors in the related fantastic fields are provided.

Water molecules in CNT-Si3N4 membrane: Properties and the separation effect for water-alcohol solution

Water confined in carbon nanotubes (CNTs) has been intensively studied because of its unique properties and potential for various applications and is often embedded in silicon nitride (Si₃N₄) membranes. However, the understanding of the influence of Si₃N₄ on the properties of water in CNTs lacks clarity. In this study, we performed molecular dynamics simulations to investigate the effect of the Si₃N₄ membrane on water molecules inside CNTs. The internal electric field generated in the CNTs by the point charges of the Si₃N₄ membrane changes the structure and dynamical properties of water in the nanotubes, causing it to attain a disordered structure. The Si₃N₄ membrane decreases the diffusivity of water in the CNTs; this is because the Coulomb potential energy (i.e., electrostatic interaction) of water decreases owing to the presence of Si₃N₄, whereas the Lennard-Jones potential energy (i.e., van der Waals interaction) does not change significantly. Furthermore, electrostatic interactions make the water structure more stable in the CNTs. As a result, the Si₃N₄ membrane enhances the separation effect of the water-methanol mixture with CNTs in the presence of an external electric field. Furthermore, the threshold of the external electric field strength to induce water-methanol separation with CNTs is reduced owing to the presence of a silicon nitride membrane.

Overlimiting current near a nanochannel a new insight using molecular dynamics simulations

In this paper, we report for the first time overlimiting current near a nanochannel using all-atom molecular dynamics (MD) simulations. Here, the simulated system consists of a silicon nitride nanochannel integrated with two reservoirs. The reservoirs are filled with [Formula: see text] potassium chloride (KCl) solution. A total of [Formula: see text] million atoms are simulated with a total simulation time of [Formula: see text] over [Formula: see text] 30000 CPU hours using 128 core processors (Intel(R) E5-2670 2.6 GHz Processor). The origin of overlimiting current is found to be due to an increase in chloride ([Formula: see text]) ion concentration inside the nanochannel leading to an increase in ionic conductivity. Such effects are seen due to charge redistribution and focusing of the electric field near the interface of the nanochannel and source reservoir. Also, from the MD simulations, we observe that the earlier theoretical and experimental postulations of strong convective vortices resulting in overlimiting current are not the true origin for overlimiting current. Our study may open up new theories for the mechanism of overlimiting current near the nanochannel interconnect devices.

Field-Dependent Dehydration and Optimal Ionic Escape Paths for C2N Membranes

Most analytic theories describing electrostatically driven ion transport through water-filled nanopores assume that the corresponding permeation barriers are bias-independent. While this assumption may hold for sufficiently wide pores under infinitely small bias, transport through subnanometer pores under finite bias is difficult to interpret analytically. Given recent advances in subnanometer pore fabrication and the rapid progress in detailed computer simulations, it is important to identify and understand the specific field-induced phenomena arising during ion transport. Here we consider an atomistic model of electrostatically driven ion permeation through subnanoporous C2N membranes. We analyze probability distributions of ionic escape trajectories and show that the optimal escape path switches between two different configurations depending on the bias magnitude. We identify two distinct mechanisms contributing to field-induced changes in transport-opposing barriers: a weak one arising from field-induced ion dehydration and a strong one due to the field-induced asymmetry of the hydration shells. The simulated current-voltage characteristics are compared with the solution of the 1D Nernst-Planck model. Finally, we show that the deviation of simulated currents from analytic estimates for large fields is consistent with the field-induced barriers and the observed changes in the optimal ion escape path.

Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A

Folding of RNA can produce elaborate tertiary structures, corresponding to their diverse roles in the regulation of biological activities. Direct observation of RNA structures at high resolution in their native form however remains a challenge. The large vestibule and the narrow constriction of a Mycobacterium smegmatis porin A (MspA) suggests a sensing mode called nanopore trapping/translocation, which clearly distinguishes between microRNA, small interfering RNA (siRNA), transfer RNA (tRNA) and 5 S ribosomal RNA (rRNA). To further profit from the acquired event characteristics, a custom machine learning algorithm is developed. Events from measurements with a mixture of RNA analytes can be automatically classified, reporting a general accuracy of ~93.4%. tRNAs, which possess a unique tertiary structure, report a highly distinguishable sensing feature, different from all other RNA types tested in this study. With this strategy, tRNAs from different sources are measured and a high structural conservation across different species is observed in single molecule.

DNA Knot Malleability in Single-Digit Nanopores

Knots in long DNA molecules are prevalent in biological systems and serve as a model system for investigating static and dynamic properties of biopolymers. We explore the dynamics of knots in double-stranded DNA in a new regime of nanometer-scale confinement, large forces, and short time scales, using solid-state nanopores. We show that DNA knots undergo isomorphic translocation through a nanopore, retaining their equilibrium morphology by swiftly compressing in a lateral direction to fit the constriction. We observe no evidence of knot tightening or jamming, even for single-digit nanopores. We explain the observations as the malleability of DNA, characterized by sharp buckling of the DNA in nanopores, driven by the transient disruption of base pairing. Our molecular dynamics simulations support the model. These results are relevant not only for the understanding of DNA packing and manipulation in living cells but also for the polymer physics of DNA and the development of nanopore-based sequencing technologies.

Mapping the morphological identifiers of distinct conformations via the protein translocation current in nanopores

Conformational changes of proteins play a vital role in implementing their functions and revealing the underlying mechanisms in various biological processes. It is still challenging to monitor protein conformations with temporal fingerprints of current-resistance pulses in the nanopore technique. Here the low-resolution morphologies of different conformations of a typical integrin, α_xβ₂, were estimated via relative blockade currents simulated from all-atom molecular dynamics (MD). Distinct conformational states of α_xβ₂ were directly explained by the volume and shape identifiers. Protein modulation in ionic current was analyzed from the conductivity distribution inside the protein-blocked nanopore. Combining a discrete model with spheroidal approximation, a MD-based approach was developed to theoretically predict the volume and shape of the nanopore for sensing α_xβ₂. This method was also applicable in specifying morphological identifiers of six other proteins, and the theoretical predictions are in good agreement with the experimental measurements. These results potentiated the validity of this method for the conformational identification of proteins in nanopores.

DNA Detection with Single-Layer Ti3C2 MXene Nanopore

Nanopore based sequencing is an exciting alternative to the conventional sequencing methods as it allows for high-throughput sequencing with lower reagent costs and time requirements. Biological nanopores, such as α-hemolysin, are subject to breakdown under thermal, electrical, and mechanical stress after being used millions of times. On the contrary, two-dimensional (2D) nanomaterials have been explored as a solid-state platform for the sequencing of DNA. Their subnanometer thickness and outstanding mechanical properties have made possible the high-resolution and high-signal-to-noise ratio detection of DNA, but such a performance is dependent on the type of nanomaterial selected. Solid-state nanopores of graphene, Si₃N₄, and MoS₂ have been studied as potential candidates for DNA detection. However, it is important to understand the sensitivity and characterization of these solid-state materials for nanopore based detection. Recent developments in the synthesis of MXene have inspired our interest in its application as a nanopore based DNA detection membrane. Here, we simulate the metal carbide, MXene (Ti₃C₂), with single stranded DNA to understand its interactions and the efficiency of MXene as a putative material for the development of a nanopore based detection platform. Using molecular dynamics (MD) simulations, we present evidence that a MXene based nanopore is able to detect the different types of DNA bases. We have successfully identified features to differentiate the translocation of different types of DNA bases across the nanopore.

Light-Nucleotide versus Ion-Nucleotide Interactions for Single-Nucleotide Resolution

Several parallel reads of ionic currents through multiple CsgG nanopores provide information about ion-nucleotide interactions for sequencing single-stranded DNA (ss-DNA) using base-calling algorithms. However, the information in ion-nucleotide interactions seems insufficient for single-read nanopore DNA sequencing. Here we report discriminative light-nucleotide interactions calculated from density functional theory (DFT), which are compared with ionic currents obtained from molecular dynamics (MD) simulations. The MD simulations were performed on a system containing a transverse nanochannel and a longitudinal solid state nanopore. We show that both of the transverse and longitudinal ionic currents during the translocation of A₁₆, G₁₆, T₁₆, and C₁₆ through the nanopore, overlapped widely. On the other hand, the UV-vis and Raman spectra of different types of single nucleotides, nucleosides, and nucleobases show relatively higher resolution than the ionic currents. Light-nucleotide interactions provide better information for characterizing the nucleotides in comparison to ion-nucleotide interactions for nanopore DNA sequencing. This can be realized by using optical techniques including surface-enhanced Raman spectroscopy (SERS) or tip-enhanced Raman spectroscopy (TERS), while plasmon excitation can be used to localize light and control the rate of nucleotide flow.

High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System

Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing-an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores-could potentially improve single-molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate the potential utility of our double-nanopore system for DNA sequencing by simulating repeat back-and-forth motion-flossing-of a DNA strand through the double-nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.

Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores

As a type of biological macromolecule, the conformation of proteins dynamically changes in a solution, which often results in a change in their function. However, traditional biological assays have significant drawbacks in detecting the conformation properties of proteins. Alternatively, nanopores have potential advantages in this area, which can detect protein in high throughput and without labelling. Herein, we investigated the translocation of calmodulins through silicon nitride nanopores using molecular dynamics (MD) simulation. Initially, the calmodulins were fixed in the nanopore. Distinguished blocked ionic currents were obtained between the two forms of calmodulin. Next, in the translocation simulations, a prominent difference in time resolution was easily found between the two states of calmodulin by using the appropriate voltage and comparable size of pore to protein, r_p/r_g→ 1, 4.5 nm (where r_p is the protein radius and r_g is the gyration radius). These simulations on the nanoscale are helpful for developing Ca²⁺-sensitive ion channels and nanodevices.

Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5-HT3 Receptor Channel

In this study we examined the influence of a transmembrane voltage on the hydrophobic gating of nanopores using molecular dynamics simulations. We observed electric field induced wetting of a hydrophobic gate in a biologically inspired model nanopore based on the 5-HT3 receptor in its closed state, with a field of at least ∼100 mV nm-1 (corresponding to a supra-physiological potential difference of ∼0.85 V across the membrane) required to hydrate the pore. We also found an unequal distribution of charged residues can generate an electric field intrinsic to the nanopore which, depending on its orientation, can alter the effect of the external field, thus making the wetting response asymmetric. This wetting response could be described by a simple model based on water surface tension, the volumetric energy contribution of the electric field, and the influence of charged amino acids lining the pore. Finally, the electric field response was used to determine time constants characterizing the phase transitions of water confined within the nanopore, revealing liquid-vapor oscillations on a time scale of ∼5 ns. This time scale was largely independent of the water model employed and was similar for different sized pores representative of the open and closed states of the pore. Furthermore, our finding that the threshold voltage required for hydrating a hydrophobic gate depends on the orientation of the electric field provides an attractive perspective for the design of rectifying artificial nanopores.

Unzipping Mechanism of Free and Polyarginine-Conjugated DNA-PNA Duplexes, Preconfined Inside the α-Hemolysin Nanopore

In this work, comparative studies on DNA-PNA and polyarginine-conjugated DNA-PNA duplexes unzipping inside the α-hemolysin nanopore (α-HL) are presented. We identified significant differences in the blockade currents, as the applied voltage across the nanopore facilitated the duplex capture inside the nanopore's vestibule against the constriction region, subsequent cDNA strand insertion inside the nanopore's β-barrel past the constriction site, its complete unzip from the duplex, and translocation. We observed that inside the voltage-biased nanopore, polyarginine-conjugated DNA-PNA duplexes dehybridize faster than their DNA-PNA counterparts and proposed a model to describe the duplex unzipping. This study identifies key particularities of DNA-PNA duplex unzipping as it takes place inside the nanopore and being preceded by entrapment in the vestibule domain of the α-HL. Our results are a crucial step toward understanding the nucleic acids duplexes unzipping kinetics variability, in confined, variable geometries.

Computational investigation of geometrical effects in 2D boron nitride nanopores for DNA detection

Nanopore-based DNA detection and analysis have been intensively pursued theoretically and experimentally over the past decade. Owing to their nanometer thickness, 2D nanopores, such as boron nitride nanopores, show great potential for achieving DNA detection at base resolution. Although 2D nanopore devices hold great promise for next-generation DNA detection, efficiently and reliably detecting different DNA sequences is still a challenging problem. To date, most of the investigated nanopores adopt circular shapes. Because of the successful fabrication of triangular nanopores, investigating the shape effect of nanopores for DNA detection has become more and more important. In this study, boron nitride nanopores with circular, hexagonal, quadrangular and triangular shapes were modeled at various sizes. The translocation of homogeneous dsDNA through these nanopores was investigated by all-atom molecular dynamic simulations. The ionic conductivity of these nanopores was characterized and formulas for the total resistance based on the pore and access resistance were derived. The ionic current, dwell time and conductance blockade of homogeneous dsDNA were compared for nanopores with different shapes. We demonstrate that the charge distribution at the pore mouth plays an important role in the transportation of ions and DNA molecules. Our findings may shed light on the design of 2D nanopores and can facilitate the development of fast, low-cost and reliable nanopore-based DNA detection.

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all known platforms suffer from high cost, read-write latency and error-rates that render them noncompetitive with modern storage devices. One means to avoid the above problems is using readily available native DNA. As the sequence content of native DNA is fixed, one can modify the topology instead to encode information. Here, we introduce DNA punch cards, a macromolecular storage mechanism in which data is written in the form of nicks at predetermined positions on the backbone of native double-stranded DNA. The platform accommodates parallel nicking on orthogonal DNA fragments and enzymatic toehold creation that enables single-bit random-access and in-memory computations. We use Pyrococcus furiosus Argonaute to punch files into the PCR products of Escherichia coli genomic DNA and accurately reconstruct the encoded data through high-throughput sequencing and read alignment.

Current synthetic DNA-based data storage systems have high recording costs, read-write latency and error-rates that make them uncompetitive compared to traditional digital storage. The authors use nicks in native DNA to encode data in parallel and create access sites for in-memory computations.

Molecular Insights into Distinct Detection Properties of α-Hemolysin, MspA, CsgG, and Aerolysin Nanopore Sensors

Protein nanopores have been widely used as single-molecule sensors for the detection and characterization of biological polymers such as DNA, RNA, and polypeptides. A variety of protein nanopores with various geometries have been exploited for this purpose, which usually exhibit distinct sensing capabilities, but the underlying molecular mechanism remains elusive. Here, we systematically characterize the molecular transport properties of four widely studied protein nanopores, α-hemolysin, MspA, CsgG, and aerolysin, by extensive molecular dynamics simulations. It is found that a sudden drop in electrostatic potentials occurs at the sole constriction in MspA and CsgG nanopores in contrast to the gradual potential change inside α-hemolysin and aerolysin pores, indicating the crucial role of pore geometry in ionic and molecular transport. We further demonstrate that these protein nanopores exhibit open-pore currents and ssDNA-induced current blockades both in the order MspA > α-hemolysin > CsgG > aerolysin, but an equivalent blockade percentage around 80%. In addition, the substitution of key amino acids at the pore constriction, especially by charged ones, provides an efficient way to modulate the pore electrostatic potential and ionic current. This work sheds new light on the search for high-performance nanopores, engineering of protein nanopores, and design of bioinspired solid-state nanopores.

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.

Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study

The MARTINI coarse-grained (CG) force field is used to test the ability of CG models to simulate ionic transport through protein nanopores. The ionic conductivity of CG ions in solution was computed and compared with experimental results. Next, we studied the electrostatic behavior of a solvated CG lipid bilayer in salt solution under an external electric field. We showed this approach correctly describes the experimental conditions under a potential bias. Finally, we performed CG molecular dynamics simulations of the ionic transport through a protein nanopore (α-hemolysin) inserted in a lipid bilayer, under different electric fields, for 2-3 microseconds. The resulting I - V curve is qualitatively consistent with experiments, although the computed current is one order of magnitude smaller. Current saturation was observed for potential biases over ±350 mV. We also discuss the time to reach a stationary regime and the role of the protein flexibility in our CG simulations.

Computational modeling of ionic currents through difform graphene nanopores with consistent cross-sectional areas

Unveiling the mystery of ion transport behavior in nanopores with consistent cross-sectional areas shows that this behavior is highly related to the geometry and hydrophobicity of the nanopores.

Effects of solvent quality and non-equilibrium conformations on polymer translocation

The conformation and its relaxation of a single polymer depend on solvent quality in a polymer solution: a polymer collapses into a globule in a poor solvent, while the polymer swells in a good solvent. When one translocates a polymer through a narrow pore, a drastic conformational change occurs such that the kinetics of the translocation is expected to depend on the solvent quality. However, the effects of solvent quality on the translocation kinetics have been controversial. In this study, we employ a coarse-grained model for a polymer and perform Langevin dynamics simulations for the driven translocation of a polymer in various types of solvents. We estimate the free energy of polymer translocation using steered molecular dynamics simulations and Jarzynski's equality and find that the free energy barrier for the translocation increases as the solvent quality becomes poorer. The conformational entropy contributes most to the free energy barrier of the translocation in a good solvent, while a balance between entropy and energy matters in a poor solvent. Interestingly, contrary to what is expected from the free energy profile, the translocation kinetics is a non-monotonic function of the solvent quality. We find that for any type of solvent, the polymer conformation stays far away from the equilibrium conformation during translocation due to an external force and tension propagation. However, the degree of tension propagation differs depending on the solvent quality as well as the magnitude of the external force: the tension propagation is more significant in a good solvent than in a poor solvent. We illustrate that such differences in tension propagation and non-equilibrium conformations between good and poor solvents are responsible for the complicated non-monotonic effects of solvent quality on the translocation kinetics.

Controllable and reversible DNA translocation through a single-layer molybdenum disulfide nanopore

A challenge that remains to be solved in the high-throughput and low-cost nanopore DNA sequencing is that DNA translocates through the nanopore too quickly to be sequenced with enough accuracy. Here, we present a proof of principle study of slowing down DNA translocation across the molybdenum disulfide nanopore and even reversing its translocation direction by adjusting the proportion of molybdenum atoms to sulfur atoms at the nanopore boundary. When the proportion is smaller than 0.17, the electro-osmotic flow moves in the opposite direction to the electric force exerted on the DNA molecule and the more sulfur atoms at the nanopore boundary, the stronger the electro-osmotic flow is. For the nanopore with the proportion equal to 0.17, the electro-osmotic force exerted on DNA is smaller than the electrophoretic force, DNA can be captured and its translocation speed was found to be almost three times smaller than the speed through nanopores with the proportion larger than 0.27. However, for nanopores with the proportion smaller than 0.08, DNA would even be pushed away and prevented from entering the nanopore so that its translocation direction would be reversed. The theoretical study performed here provides a new means for controlling DNA transport dynamics in both translocation velocity and direction, which would facilitate better and cheaper nanopore DNA sequencing in the future.

Water-Compression Gating of Nanopore Transport

Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.

Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing

Nanopores have emerged as helpful research tools for single molecule detection. Through continuum modeling, we investigated the effects of membrane thickness, nanopore size, and pore shape on current signal characteristics of DNA. The simulation results showed that, when reducing the pore diameter, the amplitudes of current signals of DNA increase. Moreover, we found that, compared to cylindrically shaped nanopores, conical-shaped nanopores produce greater signal amplitudes from biomolecules translocation. Finally, we demonstrated that continuum model simulations for the discrimination of DNA and RNA yield current characteristics approximately consistent with experimental measurements and that A-T and G-C base pairs can be distinguished using thin conical solid-state nanopores. Our study not only suggests that computational approaches in this work can be used to guide the designs of nanopore for single molecule detection, but it also provides several possible ways to improve the current amplitudes of nanopores for better resolution.