Large Scale Parallel DNA Detection by Two-Dimensional Solid-State Multipore Systems

Enhanced Discriminability of Viral Vectors in Viscous Nanopores

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

Nanopore-based sensors for DNA sequencing: a review

Nanopore sensors, owing to their distinctive structural properties, can be used to detect biomolecular translocation events. These sensors operate by monitoring variations in electric current amplitude and duration, thereby enabling the calibration and distinction of various biomolecules. As a result, nanopores emerge as a potentially powerful tool in the field of deoxyribonucleic acid (DNA) sequencing. However, the interplay between testing bandwidth and noise often leads to the loss of part of the critical translocation signals, presenting a substantial challenge for the precise measurement of biomolecules. In this context, innovative detection mechanisms have been developed, including optical detection, tunneling current detection, and nanopore field-effect transistor (FET) detection. These novel detection methods are based on but beyond traditional nanopore techniques and each of them has unique advantages. Notably, nanopore FET sensors stand out for their high signal-to-noise ratio (SNR) and high bandwidth measurement capabilities, overcoming the limitations typically associated with traditional solid-state nanopore (SSN) technologies and thus paving the way for new avenues to biomolecule detection. This review begins by elucidating the fundamental detection principles, development history, applications, and fabrication methods for traditional SSNs. It then introduces three novel detection mechanisms, with a particular emphasis on nanopore FET detection. Finally, a comprehensive analysis of the advantages and challenges associated with both SSNs and nanopore FET sensors is performed, and then insights into the future development trajectories for nanopore FET sensors in DNA sequencing are provided. This review has two main purposes: firstly, to provide researchers with a preliminary understanding of advancements in the nanopore field, and secondly, to offer a comprehensive analysis of the fabrication techniques, transverse current detection principles, challenges, and future development trends in the field of nanopore FET sensors. This comprehensive analysis aims to help give researchers in-depth insights into cutting-edge advancements in the field of nanopore FET sensors.

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.

Selective Capture and Manipulation of DNA through Double Charged Nanopores

In the past few decades, nanometer-scale pores have been employed as powerful tools for sensing biological molecules. Owing to its unique structure and properties, solid-state nanopores provide interesting opportunities for the development of DNA sequencing technology. Controlling DNA translocation in nanopores is an important means of improving the accuracy of sequencing. Here we present a proof of principle study of accelerating DNA captured across targeted graphene nanopores using surface charge density and find the intrinsic mechanism of the combination of electroosmotic flow induced by charges of nanopore and electrostatic attraction/repulsion between the nanopore and ssDNA. The theoretical study performed here provides a new means for controlling DNA transport dynamics and makes better and cheaper application of graphene in molecular sequencing.

Ion Trapping and Thermionic Emission across Sub-nm Pores

Ionic transport through a graphene biomimetic subnanometer (sub-nm) pore of arbitrary shape and realistically decorated by intrinsic negatively charged sites is investigated by all-atom molecular dynamics (MD) simulations. In the presence of external electric fields, cation trapping-assisted translocation occurs in the vicinity of the 2D subnanometer pore, while the anion current is blocked by the negative charges. The adsorbed cations in such asymmetrically charged nanopores are located on the top of the nanopore instead of blocking the pore, as suggested previously in highly symmetric pores such as crown ethers. Our analysis of the different types of energy involved in ion translocations indicates that electrostatics is the dominant factor controlling ion transfer across these sub-nm pores. A physical model based on the thermionic emission formalism to account for the free energy barriers to ion flow reproduces the I-V characteristics.

Ion Density-Dependent Dynamic Conductance Switching in Biomimetic Graphene Nanopores

Gating in ion transport is at the center of many vital living-substance transmission processes, and understanding how gating works at an atomic level is essential but intricate. However, our understanding and finite experimental findings of subcontinuum ion transport in subnanometer nanopores are still limited, which is out of reach of the classical continuum nanofluidics. Moreover, the influence of ion density on subcontinuum ion transport is poorly understood. Here we report the ion density-dependent dynamic conductance switching process in biomimetic graphene nanopores and explain the phenomenon by a reversible ion absorption mechanism. Our molecular dynamics simulations demonstrate that the cations near the graphene nanopore can interact with the surface charges on the nanopore, thereby realizing the switching of high- and low-conductance states. This work has deepened the understanding of gating in ion transport.

Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing

Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.

3D DNA Walker-Assisted CRISPR/Cas12a Trans-Cleavage for Ultrasensitive Electrochemiluminescence Detection of miRNA-141

In this study, a CRISPR/Cas12a (LbCpf1)-mediated electrochemiluminescence (ECL) paper-based platform on the basis of a three-dimensional (3D) DNA walker was proposed for the ultrasensitive detection of miRNA-141. Initially, 3D-rGO with a tremendous loading space was modified on the paper working electrode (PWE) to construct an excellent conductive substrate and facilitate the growth of AuPd nanoparticles (NPs). Afterward, the AuPd NPs were introduced as the coreaction emitter medium of the 3D-rGO/PWE to provide convenience for the transformation between S₂O₈^2- and SO₄^2-, amplifying the ECL emission of g-C₃N₄ nanosheets (NSs). Meanwhile, with the help of Nt.BsmAI nicking endonuclease, a 3D DNA walker signal amplifier was designed to convert and magnify the target miRNA-141 into a particular trigger sequence, which could act as activator DNA to motivate the trans-acting deoxyribonuclease activity of CRISPR/Cas12a to further achieve efficient annihilation of the ECL signal. Furthermore, the proposed multimechanism-driven biosensor exhibited excellent sensitivity and specificity, with a relatively low detection limit at 0.331 fM (S/N = 3) in the concentration range between 1 fM and 10 nM. Consequently, the designed strategy not only extended the application scope of CRISPR/Cas12a but also devoted a new approach for the clinical diagnosis of modern medicine.

High-throughput single nanoparticle detection using a feed-through channel-integrated nanopore

The outstanding sensitivity of solid-state nanopore sensors comes at a price of low detection efficiency due to the lack of active means to transfer objects into the nanoscale sensing zone. Here we report on a key technology for high-throughput single-nanoparticle detection which exploits mutual effects of microfluidics control and multipore electrophoresis in nanopore-in-channel units integrated on a thin Si₃N₄ membrane. Using this novel nanostructure, we demonstrated a proof-of-concept for influenza viruses via hydropressure regulation of mass transport in the fluidic channel for continuous feeding of biosamples into the effective electric field extending out from the nanopores, wherein the feed-through mechanism allowed us to selectively detect charged objects in physiological media such as human saliva. With the versatility of nanopore sensing technologies applicable to analytes of virtually any size from cells to polynucleotides, the present integration strategy may open new avenues for practical ultrasensitive bioanalytical tools.

Particle Capture in Solid-State Multipores

Utilization of multiple-channel structure is a promising way of accomplishing high-throughput detections of analytes in solid-state pore sensors. Here we report on systematic investigation of particle capture efficiency in Si₃N₄ multipore systems of various array configurations. We demonstrated enhanced detection throughput with increasing numbers of pore channels in a membrane. Meanwhile, we also observed significant contributions of the interchannel crosstalk in closely integrated multipores that tended to deteriorate throughput performance by causing shrinkage of the absorption zone via the interference-derived weakening of the electric field around the pore orifice. At the same time, the interference-derived electric field distributions were also found to diminish the electroosmotic contributions to the particle capture efficiency. The present findings can be useful in designing pore arrays with optimal throughput performance.

Selective detections of single-viruses using solid-state nanopores

Rapid diagnosis of flu before symptom onsets can revolutionize our health through diminishing a risk for serious complication as well as preventing infectious disease outbreak. Sensor sensitivity and selectivity are key to accomplish this goal as the number of virus is quite small at the early stage of infection. Here we report on label-free electrical diagnostics of influenza based on nanopore analytics that distinguishes individual virions by their distinct physical features. We accomplish selective resistive-pulse sensing of single flu virus having negative surface charges in a physiological media by exploiting electroosmotic flow to filter contaminants at the Si₃N₄ pore orifice. We demonstrate identifications of allotypes with 68% accuracy at the single-virus level via pattern classifications of the ionic current signatures. We also show that this discriminability becomes >95% under a binomial distribution theorem by ensembling the pulse data of >20 virions. This simple mechanism is versatile for point-of-care tests of a wide range of flu types.

Classification of Epigenetic Biomarkers with Atomically Thin Nanopores

We use the electronic properties of 2D solid-state nanopore materials to propose a versatile and generally applicable biosensor technology by using a combination of molecular dynamics, nanoscale device simulations, and statistical signal processing algorithms. As a case study, we explore the classification of three epigenetic biomarkers, the methyl-CpG binding domain 1 (MBD-1), MeCP2, and γ-cyclodextrin, attached to double-stranded DNA to identify regions of hyper- or hypomethylations by utilizing a matched filter. We assess the sensing ability of the nanopore device to identify the biomarkers based on their characteristic electronic current signatures. Such a matched filter-based classifier enables real-time identification of the biomarkers that can be easily implemented on chip. This integration of a sensor with signal processing architectures could pave the way toward the development of a multipurpose technology for early disease detection.