Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes

Ion Transport in Multi-Nanochannels Regulated by pH and Ion Concentration

Nanochannels are a powerful technique for detecting a wide range of biomolecules without labeling. The ion transport phenomena in nanochannel arrays differ from those in single nanochannels and are caused by interchannel communication. This study uses a fully coupled Poisson-Nernst-Planck (PNP) and Navier-Stokes model to investigate ion transport in nanochannel arrays. Instead of being set at a constant value, the surface charge density used in this study is established by the protonation and deprotonation of the silanol groups that are present on the walls of the silicon-based nanochannels. The surface charge density of the nanochannel walls varies with the number of nanochannels, the channel lateral distance, and the background solution properties, which consequently influence the ionic concentration distribution, flow velocity, and electric field strength. For example, in different numbers of nanochannel systems, the ion concentration in nanochannels is not much different, but it is different in reservoirs, especially near the openings of nanochannels. The number of nanochannels and the distance between nanochannels can also affect the formation of electro-convective vortex zones under certain conditions. These findings can aid in optimizing the nanochannel array design by regulating the number and distance of nanochannels and facilitating the construction of solid-state nanochannel arrays with any desired nanochannel dimensions.

A DNA turbine powered by a transmembrane potential across a nanopore

Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24-27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s-1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.

Label-Free Imaging of DNA Interactions with 2D Materials

Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.

2D materials towards energy conversion processes in nanofluidics

Hierarchically assembled 2D material membranes are extremely promising platforms for energy conversion processes in nanofluidics. In this perspective, we discuss recent advances in the production of smart 2D material membranes that come close to mimicking biological energy conversion processes and how these efforts translate into the design of water purification systems, artificial photosynthesis, and solar energy conversion devices. As we depict here, 2D material membranes synergistically modulate the intrinsic active sites (nanopores), electron transport, mass transfer, and mechanical and chemical stability aiming at cost-effective and highly efficient smart membranes.

Nanopore fingerprinting of supramolecular DNA nanostructures

DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.

Drilling accurate nanopores for biosensors by energetic multi-wall carbon nanotubes: a molecular dynamics investigation

Drilling precise nanopores in thin layers is in rapid demand for biosensing applications. We demonstrate that an energetic multi-wall carbon nanotube (MWCNT) can be a good candidate to fabricate nanopores on graphene from molecular dynamics simulations with a bond-order potential. High-quality nanopores with expected size and smooth margins could be created by an incident nanotube at chosen size and energy. Besides, a nanotube is in advantage of absorbing and translocating many biological macromolecules due to its strong adsorption capacity. It implies a feasible way to drill nanopores and carry big molecules through the fabricated nanopores in one step for fast biosensing applications.

Localized Nanopore Fabrication via Controlled Breakdown

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

Pillar-structured 3D inlets fabricated by dose-modulated e-beam lithography and nanoimprinting for DNA analysis in passive, clogging-free, nanofluidic devices

We present the fabrication of three-dimensional inlets with gradually decreasing widths and depths and with nanopillars on the slope, all defined in just one lithography step. In addition, as an application, we show how these micro- and nanostructures can be used for micro- and nanofluidics and lab-on-a-chip devices to facilitate the flow and analyze single molecules of DNA. For the fabrication of 3D inlets in a single layer process, dose-modulated electron beam lithography was used, producing depths between 750 nm and 50 nm along a 30 μm long inlet, which is additionally structured with nanometer-scale pillars randomly distributed on top, as a result of incomplete exposure and underdevelopment of the resist. The fabrication conditions affect the slope of the inlet, the nanopillar density and coverage. The key parameters are the dose used for the electron beam exposure and the development conditions, like the developer's dilution, stirring and development time. The 3D inlets with nanostructured pillars were integrated into fluidic devices, acting as a transition between micro and nanofluidic structures for pre-stretching and unfolding DNA molecules, avoiding the intrusion of folded molecules and clogging the analysis channel. After patterning these structures in silicon, they can be replicated in polymer by UV nanoimprinting. We show here how the inlets with pillars slow down the molecules before they enter the nanochannels, resulting in a 3-fold decrease in speed, which would translate to an improvement in the resolution for DNA optical mapping.

Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control

We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.

Optical Nanopore Sensors for Quantitative Analysis

Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.

Detecting Single Molecule Deoxyribonucleic Acid in a Cell Using a Three-Dimensionally Integrated Nanopore

Amplification-free genome analysis can revolutionize biology and medicine by uncovering genetic variations among individuals. Here, the authors report on a 3D-integrated nanopore for electrolysis to in situ detection of single-molecule DNA in a cell by ionic current measurements. It consists of a SiO₂ multipore sheet and a SiN_x nanopore membrane stacked vertically on a Si wafer. Single cell lysis is demonstrated by 10⁶  V m^-1 -level electrostatic field focused at the multinanopore. The intracellular molecules are then directly detected as they move through a sensing zone, wherein the authors find telegraphic current signatures reflecting folding degrees of freedom of the millimeter-long polynucleotides threaded through the SiN_x nanopore. The present device concept may enable on-chip single-molecule sequencing to multi-omics analyses at a single-cell level.

Simultaneous detection of multiple proteases using a non-array nanopore platform

Multiplexing methods which are capable of measurement of multiple analytes in a single assay are of great importance in many fields. The conventional strategy for simultaneous detection of multiple species is to construct a sensor array. Herein, we report an innovative multiplex multi-analyte detection platform in a non-array format for protease measurement. By monitoring protease degradation of a single peptide substrate containing two cleavage sites for a disintegrin and metalloproteinase 10 (ADAM10) and a disintegrin and metalloproteinase 10 (ADAM17) in a single nanopore, simultaneous detection and quantification of these two model proteases in mixture samples could satisfactorily be accomplished. Our developed multiplexing sensing platform has the potential to be coupled with the traditional sensor array to further improve the multiplexing capability of the sensor, which may find useful applications in clinical diagnosis and prognosis.

Lithographic Processes for the Scalable Fabrication of Micro- and Nanostructures for Biochips and Biosensors

Since the early 2000s, extensive research has been performed to address numerous challenges in biochip and biosensor fabrication in order to use them for various biomedical applications. These biochips and biosensor devices either integrate biological elements (e.g., DNA, proteins or cells) in the fabrication processes or experience post fabrication of biofunctionalization for different downstream applications, including sensing, diagnostics, drug screening, and therapy. Scalable lithographic techniques that are well established in the semiconductor industry are now being harnessed for large-scale production of such devices, with additional development to meet the demand of precise deposition of various biological elements on device substrates with retained biological activities and precisely specified topography. In this review, the lithographic methods that are capable of large-scale and mass fabrication of biochips and biosensors will be discussed. In particular, those allowing patterning of large areas from 10 cm² to m², maintaining cost effectiveness, high throughput (>100 cm² h^-1), high resolution (from micrometer down to nanometer scale), accuracy, and reproducibility. This review will compare various fabrication technologies and comment on their resolution limit and throughput, and how they can be related to the device performance, including sensitivity, detection limit, reproducibility, and robustness.

In situ solid-state nanopore fabrication

Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.

Prospects of Observing Ionic Coulomb Blockade in Artificial Ion Confinements

Nanofluidics encompasses a wide range of advanced approaches to study charge and mass transport at the nanoscale. Modern technologies allow us to develop and improve artificial nanofluidic platforms that confine ions in a way similar to single-ion channels in living cells. Therefore, nanofluidic platforms show great potential to act as a test field for theoretical models. This review aims to highlight ionic Coulomb blockade (ICB)-an effect that is proposed to be the key player of ion channel selectivity, which is based upon electrostatic exclusion limiting ion transport. Thus, in this perspective, we focus on the most promising approaches that have been reported on the subject. We consider ion confinements of various dimensionalities and highlight the most recent advancements in the field. Furthermore, we concentrate on the most critical obstacles associated with these studies and suggest possible solutions to advance the field further.

Tunable Nanopore Arrays as the Basis for Ionic Circuits

There has been considerable interest in preparing ionic circuits capable of manipulating ionic and molecular transport in a solution. This direction of research is inspired by biological systems where multiple pores with different functionalities embedded in a cell membrane transmit external signals and underlie all physiological processes. In this manuscript, we describe the modeling of ion transport through small arrays of nanopores consisting of 3, 6, and 9 nanopores and an integrated gate electrode placed on the membrane surface next to one pore opening. We show that by tuning the gate voltage and strategically placing nanopores with nonlinear current-voltage characteristics, the local signal at the gate affects ionic transport through all nanopores in the array. Conditions were identified when the same gate voltage induced opposite rectification properties of neighboring nanopores. We also demonstrate that an ionic diode embedded in a nanopore array can modulate transport properties of neighboring pores even without a gate voltage. The results are explained by the role of concentration polarization and overlapping depletion zones on one side of the membrane. The modeling presented here is intended to become an inspiration to future experiments to create nanopore arrays that can transduce signals in space and time.

Stochastic Ionic Transport in Single Atomic Zero-Dimensional Pores

We report on single atomic zero-dimensional (0D) pores fabricated using aberration-corrected scanning transmission electron microscopy (AC-STEM) in monolayer MoS₂. Pores are comprised of a few atoms missing in the two-dimensional (2D) lattice (1-5 Mo atoms) of characteristic sizes from ∼0.5 to 1.2 nm, and pore edges directly probed by AC-STEM to map the atomic structure. We categorize them into ∼30 geometrically possible zigzag, armchair, and mixed configurations. While theoretical studies predict that transport properties of 2D pores in this size range depend strongly on pore size and their atomic configuration, 0D pores show an average conductance in the range from ∼0.6-1 nS (bias up to 0.1 V), similar to biological pores. In some devices, the current was immeasurably small and/or pores could not be wet. Furthermore, current-voltage (I-V) characteristics are largely independent of bulk molarity (10 mM to 3 M KCl) and the type of cation (K⁺, Li⁺, Mg²⁺). This work lays the experimental foundation for understanding of the confinement effects possible in atomic-scale 2D material pores and the realization of solid-state analogues of ion channels in biology.

Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements

Nanopores are promising for many applications including DNA sequencing and molecular filtration. Solid-state nanopores are preferable over their biological counterparts for applications requiring durability and operation under a wider range of external parameters, yet few studies have focused on optimizing their robustness. We report the lifetime and durability of pores and porous arrays in 10 to 100 nm-thick, low-stress silicon nitride (SiN_x) membranes. Pores are fabricated using a transmission electron microscope (TEM) and/or electron beam lithography (EBL) and reactive ion etching (RIE), with diameters from 2 to 80 nm. We store them in various electrolyte solutions (KCl, LiCl, MgCl₂) and record open pore conductance over months to quantify pore stability. Pore diameters increase with time, and diameter etch rate increases with electrolyte concentration from Δd/Δt ∼ 0.2 to ∼ 3 nm/day for 0.01 to 3 M KCl, respectively. TEM confirms the range of diameter etch rates from ionic measurements. Using electron energy loss spectroscopy (EELS), we observe a N-deficient region around the edges of TEM-drilled pores. Pore expansion is caused by etching of the Si/SiO₂ pore walls, which resembles the dissolution of silicon found in minerals such as silica (SiO₂) in salty ocean water. The etching process occurs where the membrane was exposed to the electron beam and can result in pore formation. However, coating pores with a conformal 1 nm-thick hafnium oxide layer prevents expansion in 1 M KCl, in stark contrast to bare SiN_x pores (∼ 1.7 nm/day). EELS data reveal the atomic composition of bare and HfO₂-coated pores.

Single-molecule analysis of nucleic acid biomarkers - A review

Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.

Comparing Current Noise in Biological and Solid-State Nanopores

Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.

FPGA-Accelerated 3rd Generation DNA Sequencing

DNA measurement machines are undergoing an orders-of-magnitude size and power reduction. As a result, the analysis of genetic molecules is increasingly appropriate for mobile platforms. However, sequencing these measurements (converting to the molecule's A-C-G-T text equivalent) requires intense computing resources, a problem for potential realizations as mobile devices. This paper proposes a step towards addressing this issue, the design and implementation of a low-power real-time FPGA hardware accelerator for the basecalling task of nanopore-based DNA measurements. Key basecalling computations are identified and ported to a custom FPGA which operates in tandem with a CPU across a high-speed serial link and a simple API. A measured speed-up over CPU-only basecalling in excess of 100X is realized with an energy efficiency improvement of three orders of magnitude.

Beyond mass spectrometry, the next step in proteomics

Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.

A novel shaped-controlled fabrication of nanopore and its applications in quantum electronics

High-intensity (10⁷–10⁸ A m⁻²) electron beams can be used to fabricate nanoscale pores. This approach enables real-time observation of nanopore drilling and precise control of the diameter of the nanopore. Nevertheless, it is not suitable for tuning the nanopore’s sidewall shape. In this study, we demonstrate the use of low-intensity electron beams to fabricate nanopores on a silicon nitride (SiN_x) membrane. This technique allows the precise adjustment of the nanopore dimension and the shaping of its three-dimensional (3D) nanostructure. The 3D structures of the nanopore were evaluated by electron tomography, and series of oblique images were used in reconstructing the 3D images of nanopores using a weighted back-projection method. The sidewall shape of the nanopore was observed at different electron-beam conditions, and the formation mechanism was elucidated based on these results. The nanopore fabricated with this technique can be used as a template to develop electronics at the nanoscale based on which a quantum-dot device can be prepared with a simple evaporation process. The measured results show that the device can resolve well-defined electronic states that are characteristic for the behaviors of the quantum-dot device.

Optical properties of plasmonic nanopore arrays prepared by electron beam and colloidal lithography

Solid state nanopores are central structures for many applications. To date, much effort has been spent on controlled fabrication of single nanopores, while relatively little work has focused on large scale fabrication of arrays of nanopores. In this work we show wafer-scale fabrication of plasmonic nanopores in 50 nm thick silicon nitride membranes with one or two 30 nm gold films, using electron beam lithography with a negative resist or a new version of colloidal lithography. Both approaches offer good control of pore diameter (even below 100 nm) and with high yield (>90%) of intact membranes. Colloidal lithography has the advantage of parallel patterning without expensive equipment. Despite its serial nature, electron beam lithography provides high throughput and can make arbitrary array patterns. Importantly, both methods prevent metal from ending up on the membrane pore sidewalls. The new fabrication methods make it possible to compare the optical properties of structurally identical plasmonic nanopore arrays with either long-range order (e-beam) or short-range order (colloidal). The resonance features in the extinction spectrum are very similar for both structures when the pitch is the same as the characteristic spacing in the self-assembled colloidal pattern. Long-range ordering slightly enhances the magnitude of the extinction maximum and blueshift the transmission maximum by tens of nm. Upon reducing the diameter in long-range ordered arrays, the resonance is reduced in magnitude and the transmission maximum is further blue shifted, just like for short-range ordered arrays. These effects are well explained by interpreting the spectra as Fano interference between the grating-type excitation of propagating surface plasmons and the broad transmission via individual pores in the metal film. Furthermore, we find that only the short-range ordered arrays scatter light, which we attribute to the highly limited effective period in the short-range ordered system and the corresponding lack of coherent suppression of scattering by interference effects.

Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection

Plasmonic and nanopore sensors have separately received much attention for achieving single-molecule precision. A plasmonic "hotspot" confines and enhances optical excitation at the nanometer length scale sufficient to optically detect surface-analyte interactions. A nanopore biosensor actively funnels and threads analytes through a molecular-scale aperture, wherein they are interrogated by electrical or optical means. Recently, solid-state plasmonic and nanopore structures have been integrated within monolithic devices that address fundamental challenges in each of the individual sensing methods and offer complimentary improvements in overall single-molecule sensitivity, detection rates, dwell time and scalability. Here, the physical phenomena and sensing principles of plasmonic and nanopore sensing are summarized to highlight the novel complementarity in dovetailing these techniques for vastly improved single-molecule sensing. A literature review of recent plasmonic nanopore devices is then presented to delineate methods for solid-state fabrication of a range of hybrid device formats, evaluate the progress and challenges in the detection of unlabeled and labeled analyte, and assess the impact and utility of localized plasmonic heating. Finally, future directions and applications inspired by the present state of the art are discussed.

Porous Zero-Mode Waveguides for Picogram-Level DNA Capture

We have recently shown that nanopore zero-mode waveguides are effective tools for capturing picogram levels of long DNA fragments for single-molecule DNA sequencing. Despite these key advantages, the manufacturing of large arrays is not practical due to the need for serial nanopore fabrication. To overcome this challenge, we have developed an approach for the wafer-scale fabrication of waveguide arrays on low-cost porous membranes, which are deposited using molecular-layer deposition. The membrane at each waveguide base contains a network of serpentine pores that allows for efficient electrophoretic DNA capture at picogram levels while eliminating the need for prohibitive serial pore milling. Here, we show that the loading efficiency of these porous waveguides is up to 2 orders of magnitude greater than their nanopore predecessors. This new device facilitates the scaling-up of the process, greatly reducing the cost and effort of manufacturing. Furthermore, the porous zero-mode waveguides can be used for applications that benefit from low-input single-molecule real-time sequencing.

Conformation-induced separation of 3-chloropropene from 1-chloropropane through nanoporous monolayer graphenes

Conformation-induced separation shows that C₃H₅ twisting to the pore preferred cis-conformation with a lower energy penalty than C₃H₇ can cross the nanopore.

Salt-Mediated Nanopore Detection of ADAM-17

ADAM-17 (a disintegrin and metalloproteinase 17) plays an important role in various physiological and pathophysiological processes. Overexpression/underexpression of ADAM-17 could lead to various diseases. In this work, by taking advantage of ionic strength and salt gradient, and monitoring the cleavage of a substrate peptide by ADAM-17 in a nanopore, we developed a label-free sensor for the rapid detection of ADAM-17. The sensor was highly sensitive and selective: picomolar concentrations of ADAM-17 could be detected within minutes, while structure similar proteases such as ADAM-9 and MMP-9 did not interfere with its detection. Our developed nanopore sensing strategy should find useful applications in the development of nanopore sensors for other proteases of biological, pharmaceutical, and medical importance.

Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores

Solid-state nanopores have emerged as promising platforms for biosensing including diagnostics for disease detection. Here we show nanopore experiments that detect CRISPR-dCas9, a sequence-specific RNA-guided protein system that specifically binds to a target DNA sequence. While CRISPR-Cas9 is acclaimed for its gene editing potential, the CRISPR-dCas9 variant employed here does not cut DNA but instead remains tightly bound at a user-defined binding site, thus providing an excellent target for biosensing. In our nanopore experiments, we observe the CRISPR-dCas9 proteins as local spikes that appear on top of the ionic current blockade signal of DNA molecules that translocate through the nanopore. The proteins exhibit a pronounced blockade signal that allows for facile identification of the targeted sequence. Even at the high salt conditions (1 M LiCl) required for nanopore experiments, dCas9 proteins are found to remain stably bound. The binding position of the target sequence can be read from the spike position along the DNA signal. We anticipate applications of this nanopore-based CRISPR-dCas9 biosensing approach in DNA-typing based diagnostics such as quick disease-strain identification, antibiotic-resistance detection, and genome typing.