Unraveling single-stranded DNA in a solid-state nanopore

Label-free and amplification-free viral RNA quantification from primate biofluids using a trapping-assisted optofluidic nanopore platform

Viral outbreaks can cause widespread disruption, creating the need for diagnostic tools that provide high performance and sample versatility at the point of use with moderate complexity. Current gold standards such as PCR and rapid antigen tests fall short in one or more of these aspects. Here, we report a label-free and amplification-free nanopore sensor platform that overcomes these challenges via direct detection and quantification of viral RNA in clinical samples from a variety of biological fluids. The assay uses an optofluidic chip that combines optical waveguides with a fluidic channel and integrates a solid-state nanopore for sensing of individual biomolecules upon translocation through the pore. High specificity and low limit of detection are ensured by capturing RNA targets on microbeads and collecting them by optical trapping at the nanopore location where targets are released and rapidly detected. We use this device for longitudinal studies of the viral load progression for Zika and Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections in marmoset and baboon animal models, respectively. The up to million-fold trapping-based target concentration enhancement enables amplification-free RNA quantification across the clinically relevant concentration range down to the assay limit of RT-qPCR as well as cases in which PCR failed. The assay operates across all relevant biofluids, including semen, urine, and whole blood for Zika and nasopharyngeal and throat swab, rectal swab, and bronchoalveolar lavage for SARS-CoV-2. The versatility, performance, simplicity, and potential for full microfluidic integration of the amplification-free nanopore assay points toward a unique approach to molecular diagnostics for nucleic acids, proteins, and other targets.

Translocation of Proteins through Solid-State Nanopores Using DNA Polyhedral Carriers

The detection of biomolecules at the single molecule level has important applications in the fields of biosensing and biomedical diagnosis. The solid-state nanopore (SS nanopore) is a sensitive tool for detecting single molecules because of its unique label-free and low sample consumption properties. SS nanopore translocation of small biomolecules is typically driven by an electronic field force and is thus influenced by the charge, shape, and size of the target molecules. Therefore, it remains challenging to control the translocation of biomolecules through SS nanopores, particularly for different proteins with complex conformations and unique charges. Toward this problem, a DNA polyhedral carrier coating strategy to assist protein translocation through SS nanopores is developed, which facilitates target protein detection. The current signal-to-noise ratios are improved significantly using this DNA carrier loading strategy. The proposed method should aid the detection of proteins, which are difficult to translocate through nanopores. This coating-assisted method offers a wide range of applications for SS nanopore detection and promotes the development of single-molecule detection.

Synthesis of length-tunable DNA carriers for nanopore sensing

Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise hard-to-detect molecules such as small, weakly-charged proteins. However, existing carrier designs can often introduce drawbacks to nanopore experiments including higher levels of cost/complexity and carrier-pore interactions that lead to ambiguous signals and elevated clogging rates. In this work, we present a simple method of carrier production based on sticky-ended DNA molecules that emphasizes ease-of-synthesis and compatibility with nanopore sensing and analysis. In particular, our method incorporates the ability to flexibly control the length of the DNA carriers produced, enhancing the multiplexing potential of this carrier system through the separable nanopore signals they could generate for distinct targets. A proof-of-concept nanopore experiment is also presented, involving carriers produced by our method with multiple lengths and attached to DNA nanostructure targets, in order to validate the capabilities of the system. As the breadth of applications for nanopore sensors continues to expand, the availability of tools such as those presented here to help translate the outcomes of these applications into robust nanopore signals will be of major importance.

Which 2D Material is Better for DNA Detection: Graphene, MoS2, or MXene?

Despite much research on characterizing 2D materials for DNA detection with nanopore technology, a thorough comparison between the performance of different 2D materials is currently lacking. In this work, using extensive molecular dynamics simulations, we compare nanoporous graphene, MoS₂ and titanium carbide MXene (Ti₃C₂) for their DNA detection performance and sensitivity. The ionic current and residence time of DNA are characterized in each nanoporous materials by performing hundreds of simulations. We devised two statistical measures including the Kolmogorov-Smirnov test and the absolute pairwise difference to compare the performance of nanopores. We found that graphene nanopore is the most sensitive membrane for distinguishing DNA bases. The MoS₂ is capable of distinguishing the A and T bases from the C and G bases better than graphene and MXene. Physisorption and the orientation of DNA in nanopores are further investigated to provide molecular insight into the performance characteristics of different nanopores.

Numerical Study to Enhance the Sensitivity of a Surface Plasmon Resonance Sensor with BlueP/WS2-Covered Al2O3-Nickel Nanofilms

In the traditional surface plasmon resonance sensor, the sensitivity is calculated by the usage of angular interrogation. The proposed surface plasmon resonance (SPR) sensor uses a diamagnetic material (Al₂O₃), nickel (Ni), and two-dimensional (2D) BlueP/WS₂ (blue phosphorous-tungsten di-sulfide). The Al₂O₃ sheet is sandwiched between silver (Ag) and nickel (Ni) films in the Kretschmann configuration. A mathematical simulation is performed to improve the sensitivity of an SPR sensor in the visible region at a frequency of 633 nm. The simulation results show that an upgraded sensitivity of 332°/RIU is achieved for the metallic arrangement consisting of 17 nm of Al₂O₃ and 4 nm of Ni in thickness for analyte refractive indices ranging from 1.330 to 1.335. The thickness variation of the layers plays a curial role in enhancing the performance of the SPR sensor. The thickness variation of the proposed configuration containing 20 nm of Al₂O₃ and 1 nm of Ni with a monolayer of 2D material BlueP/WS₂ enhances the sensitivity to as high as 374°/RIU. Furthermore, it is found that the sensitivity can be altered and managed by means of altering the film portions of Ni and Al₂O₃

Understanding and modelling the magnitude of the change in current of nanopore sensors

Nanopores are promising sensing devices that can be used for the detection of analytes at the single molecule level. It is of importance to understand and model the current response of a nanopore sensor for improving the sensitivity of the sensor, a better interpretation of the behaviours of different analytes in confined nanoscale spaces, and quantitative analysis of the properties of the targets. The current response of a nanopore sensor, usually called a resistive pulse, results from the change in nanopore resistance when an analyte translocates through the nanopore. This article reviews the theoretical models used for the calculation of the resistance of the nanopore, and the corresponding change in nanopore resistance due to a translocation event. Models focus on the resistance of the pore cavity region and the access region of the nanopore. The influence of the sizes, shapes and surface charges of the translocating species and the nanopore, as well as the trajectory that the analyte follows are also discussed. This review aims to give a general guidance to the audience for understanding the current response of a nanopore sensor and the application of this class of sensor to a broad range of species with the theoretical models.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Shaped DNA origami carrier nanopore translocation influenced by aptamer based surface modification

DNA origami is widely used as a translocation carrier to assist solid-state nanopore analysis, e.g., soft linear origami carrier and special-shaped origami structures. In the linear origami carriers based nanopore sensing, molecular modifications induced tiny structural and charge changes, can result in significant variations on translocation signals to facilitating single-molecule sensing. However, an understanding on the influences of surface modifications on special-shaped DNA origami structures during solid-state (SS) nanopores translocation is still far elusive. Herein, we reported a surface modification strategy using aptamer/target-binding to influence the translocation of the shaped origami ribbon carrier through SS-nanopore. Our measurements indicate that the translocation signal variations can respond to ATP/aptamer binding on the carrier surface, even to the surface modifications induced by spatial distributions and enzyme catalysis. Meanwhile, the results also suggest a possibility to identify small spatial and electronic changes on DNA origami by using SS-nanopore. We envision that the surface aptamer-binding influenced origami translocation strategy could find more applications in origami carrier assisted SS-nanopore sensing and detection.

Silicon Nitride-BP-Based Surface Plasmon Resonance Highly Sensitive Biosensor for Virus SARS-CoV-2 Detection

In this study, we propose a surface plasmon resonance (SPR)-based biosensor using silicon nitride (Si₃N₄), black phosphorous (BP), and thiol-tethered DNA as a ligand for fast detection of the SARS-CoV-2 virus. In the proposed biosensor, we have deposited silver (Ag), Si₃N₄, and BP on the base of the BK-7 prism and investigated the performance parameters on the probe in different combinations of the mentioned materials. Herein, three (Ag, Si₃N₄, and BP) different configurations are introduced and compared for the detection of SARS-CoV-2. Furthermore, with the help of the transfer matrix method (TMM), all the three configurations have been analyzed. Notably, the combination of Ag, Si₃N₄, and BP shows better sensitivity (154°/RIU) when compared with other configurations for the detection of SARS-CoV-2. This work may facilitate a new sensing device to detect SARS-CoV-2, based on the hybrid materials.

Optical trapping assisted label-free and amplification-free detection of SARS-CoV-2 RNAs with an optofluidic nanopore sensor

Ultrasensitive, versatile sensors for molecular biomarkers are a critical component of disease diagnostics and personalized medicine as the COVID-19 pandemic has revealed in dramatic fashion. Integrated electrical nanopore sensors can fill this need via label-free, direct detection of individual biomolecules, but a fully functional device for clinical sample analysis has yet to be developed. Here, we report amplification-free detection of SARS-CoV-2 RNAs with single molecule sensitivity from clinical nasopharyngeal swab samples on an electro-optofluidic chip. The device relies on optically assisted delivery of target carrying microbeads to the nanopore for single RNA detection after release. A sensing rate enhancement of over 2,000x with favorable scaling towards lower concentrations is demonstrated. The combination of target specificity, chip-scale integration and rapid detection ensures the practicality of this approach for COVID-19 diagnosis over the entire clinically relevant concentration range from 10⁴-10⁹ copies/mL.

Performance Enhancement of a Novel Surface Plasmon Resonance Biosensor using Thallium Bromide

In this paper, we present the performance enhancement of the SPR biosensor using a novel dielectric material of thallium bromide (TIBr). The proposed structure comprised of six layers, including BK7 prism, silver (Ag), aluminum arsenide (AlAs), TIBr, black phosphorus (BP), and a sensing layer. In this investigation, we have considered four structures using the above-defined layers for the performance comparison and heightened the impact of TIBr in the proposed SPR sensor. The performance analysis is studied numerically at 633nm wavelength by considering the angular interrogation method and it endorsed with the wavelength variation method as well as the electric field intensity performance, employing the transfer matrix method and the FDTD solutions. The proposed structure is referred to as structure-IV is achieved the sensitivity of 475°/RIU compared to structures- III, II, I that have the sensitivities of 155, 120, 105°/RIU, respectively, at the minimal unit changes in the refractive index of the biomolecules. In addition, the proposed structure facilitates a quality factor of 80.37 and a figure of merit of 79.72. This investigation is introduced the performance of combined sensitive factor (CSF) of 77.9, which shows the SPR's overall performance. In order to observe the wavelength resolution, the sensor's sensitivity is investigated for different wavelengths at different metal thicknesses. Finally, the proposed structure's performance is compared with the existing works, demonstrating that the proposed SPR sensor can be established as a new platform for researchers in the field of bio-sensing applications.

Recent advances in integrated solid-state nanopore sensors

The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.

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

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

Single-molecule, hybridization-based strategies for short nucleic acids detection and recognition with nanopores

DNA nanotechnology has seen large developments over the last 30 years through the combination of detection and discovery of DNAs, and solid phase synthesis to increase the chemical functionalities on nucleic acids, leading to the emergence of novel and sophisticated in features, nucleic acids-based biopolymers. Arguably, nanopores developed for fast and direct detection of a large variety of molecules, are part of a revolutionary technological evolution which led to cheaper, smaller and considerably easier to use devices enabling DNA detection and sequencing at the single-molecule level. Through their versatility, the nanopore-based tools proved useful biomedicine, nanoscale chemistry, biology and physics, as well as other disciplines spanning materials science to ecology and anthropology. This mini-review discusses the progress of nanopore- and hybridization-based DNA detection, and explores a range of state-of-the-art applications afforded through the combination of certain synthetically-derived polymers mimicking nucleic acids and nanopores, for the single-molecule biophysics on short DNA structures.

Structure-flexible DNA origami translocation through a solid-state nanopore

Nanopore detection is a label-free detection method designed to analyze single molecules by comparing specific translocation events with high signal-to-noise ratios. However, it is still challenging to understand the influences of structural flexibility of 100 nm DNA origami on nanopore translocations. Here, we used solid-state nanopores to characterize the translocation of “nunchaku” origami structures, the flexibility of which can be regulated by introducing specific DNA strands and streptavidin protein. The structural changes can result in significant variations in the translocation signals and distributions. It is anticipated that such a method of the flexible DNA origami translocation through a solid-state nanopore will find further applications in molecular detection as well as biosensing.

Using a solid-state nanopore to characterize the translocation of “nunchaku” origami with tunable-structures.

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.

Deformation-Mediated Translocation of DNA Origami Nanoplates through a Narrow Solid-State Nanopore

With the development in DNA self-assembly technology, DNA origami nanostructures have been widely applied in biomedical research. Solid-state nanopores represent an emerging single-molecule sensing platform for studying nanostructures with arbitrary dimensions and physical characteristics, including DNA origami. Here, we employed relatively narrow silicon nitride nanopores to detect the deformation and translocation of DNA origami nanoplates with dimensions of approximately 60 × 54 nm. We performed translocation experiments using three nanopore diameters that are all smaller than the plat dimensions. Analysis of current blockade signals and the representative events reveals three types of translocation orientations for the nanoplates. Furthermore, by studying the electrical signal characteristics (current change and dwell time) for the different diameter pores, we obtained information about the translocation behaviors for the DNA nanoplates through different constrictions. Our investigation provides an approach to analyze the deformation and translocation of DNA origami structures.

Label-free detection of early oligomerization of α-synuclein and its mutants A30P/E46K through solid-state nanopores

A30P and E46K are two mutants of α-synuclein (α-Syn) associated with familial early-onset Parkinson's disease (PD), and amyloid fibrils of α-Syn are the hallmarks of this disease. Detecting the heterogeneous system in the oligomerization stage of α-Syn is crucial for understanding the fibril formation and in vivo toxicity of α-Syn oligomers. Over the last two decades, solid-state nanopore technology has been developed into a reliable and versatile method in single-molecule studies. In this work, we study the time-dependent kinetics of early oligomerization of wild-type α-Syn, A30P, and E46K mutants through silicon nitride solid-state nanopores. By testing A30P, E46K, and wild-type α-Syn samples with different incubation times-from 3 to 15 days-we identify three typical types of oligomers formed in the oligomerization stage and confirm that A30P and E46K mutants aggregate faster than wild-type α-Syn. The results imply that the distinct aggregation pathways and kinetics featured by wild-type α-Syn and mutations may account for their distinct cytotoxicity and pathology in PD-related studies.

Reduction of DNA Folding by Ionic Liquids and Its Effects on the Analysis of DNA-Protein Interaction Using Solid-State Nanopore

DNA folding is not desirable for solid-state nanopore techniques when analyzing the interaction of a biomolecule with its specific binding sites on DNA since the signal derived from the binding site could be buried by a large signal from the folding of DNA nearby. To resolve the problems associated with DNA folding, ionic liquids (ILs), which are known to interact with DNA through charge-charge and hydrophobic interactions are employed. 1-n-butyl-3-methylimidazolium chloride (C4 mim) is found to be the most effective in lowering the incident of DNA folding during its translocation through solid-state nanopores (4-5 nm diameter). The rate of folding signals from the translocation of DNA-C4 mim is decreased by half in comparison to that from the control bare DNA. The conformational changes of DNA upon complexation with C4 mim are further examined using atomic force microscopy, showing that the entanglement of DNA which is common in bare DNA is not observed when treated with C4 mim. The stretching effect of C4 mim on DNA strands improves the detection accuracy of nanopore for identifying the location of zinc finger protein bound to its specific binding site in DNA by lowering the incident of DNA folding.

Controllable Shrinking of Glass Capillary Nanopores Down to sub-10 nm by Wet-Chemical Silanization for Signal-Enhanced DNA Translocation

Diameter is a major concern for nanopore based sensing. However, directly pulling glass capillary nanopore with diameter down to sub-10 nm is very difficult. So, post treatment is sometimes necessary. Herein, we demonstrate a facile and effective wet-chemical method to shrink the diameter of glass capillary nanopore from several tens of nanometers to sub-10 nm by disodium silicate hydrolysis. Its benefits for DNA translocation are investigated. The shrinking of glass capillary nanopore not only slows down DNA translocation, but also enhances DNA translocation signal and signal-to-noise ratio significantly (102.9 for 6.4 nm glass nanopore, superior than 15 for a 3 nm silicon nitride nanopore). It also affects DNA translocation behaviors, making the approach and glass capillary nanopore platform promising for DNA translocation studies.

Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores

Biological nanopores are nanoscale sensors employed for high-throughput, low-cost, and long read-length DNA sequencing applications. The analysis and sequencing of proteins, however, is complicated by their folded structure and non-uniform charge. Here we show that an electro-osmotic flow through Fragaceatoxin C (FraC) nanopores can be engineered to allow the entry of polypeptides at a fixed potential regardless of the charge composition of the polypeptide. We further use the nanopore currents to discriminate peptide and protein biomarkers from 25 kDa down to 1.2 kDa including polypeptides differing by one amino acid. On the road to nanopore proteomics, our findings represent a rationale for amino-acid analysis of folded and unfolded polypeptides with nanopores.

Biological nanopore–based protein sequencing and recognition is challenging due to the folded structure or non-uniform charge of peptides. Here the authors show that engineered FraC nanopores can overcome these problems and recognize biomarkers in the form of oligopeptides, polypeptides and folded proteins.

Graphene Oxide-Polycarbonate Track-Etched Nanosieve Platform for Sensitive Detection of Human Immunodeficiency Virus Envelope Glycoprotein

Solid-state nanopores within graphene-based materials are on the brink of fundamentally changing the sensing of desired bioanalytes through ion trafficking across nanoporous membranes. Here, we report on a two-electrode electrochemical biosensor comprised of a graphene oxide-polycarbonate track-etched nanosieve platform for the rapid and sensitive detection of the Human Immunodeficiency Virus Type 1 (HIV-1) envelope glycoprotein ectodomain (gp140_MS). We have covalently linked an engineered high-affinity one-domain soluble CD4 fused to a human domain targeting HIV-1 coreceptor binding site and ferrocene (Fc) (2Dm2m) to the nanosieve platform. An exponential decrease in the ionic current resulted from a partial blockade of the nanosieve due to the specific interactions of gp140_MS with the 2Dm2m protein, which was immobilized on the nanosieve platform by biolinkage as a function of applied voltages of 0.1-2.0 V. There was no change in current when a nonspecific antigen bovine serum albumin was tested under identical conditions. This platform had high sensitivity, and when the receptor-binding phenomenon was tested to identify the minimum concentration of target analyte, the lowest detection limit was as short as 8.3 fM and with sensitivity and response times of 0.87 mA mM^-1 cm^-1 and 12 s, respectively. In addition to this remarkable sensitivity, our nanobiorecognition platform has the advantage of superior stability due to the few layered graphene oxide laminates. It also exhibits exceptional biomolecule binding and higher reusability, sustainability, and ease of fabrication in a soft mechanism. Real samples of HIV positive and negative patients were successfully tested to confirm the virus by the developed platform. To the best of our knowledge, this is the first time prosperous pervious remembrance surface has been employed in a nanobiosensing application. In light of the recent great trend of using graphene-based nanopore surfaces created by sophisticated ion-beam methods in sensing and sequencing, this hybrid-surface nanolayer fabricated by the simple vacuum filtration of a few layered graphene oxide laminates may serve as a good alternative in terms of ease of fabrication without expensive instrumental prerequisites.

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.

Discrimination of three types of homopolymers in single-stranded DNA with solid-state nanopores through external control of the DNA motion

To achieve DNA sequencing with solid-state nanopores, the speed of the DNA in the nanopore must be controlled to obtain sequence-specific signals. In this study, we fabricated a nanopore-sensing system equipped with a DNA motion controller. DNA strands were immobilized on a Si probe, and approach of this probe to the nanopore vicinity could be controlled using a piezo actuator and stepper motor. The area of the Si probe was larger than the area of the membrane, which meant that the immobilized DNA could enter the nanopore without the need for the probe to scan to determine the location of the nanopore in the membrane. We demonstrated that a single-stranded DNA could be inserted into and removed from a nanopore in our experimental system. The number of different ionic-current levels observed while DNA remained in the nanopore corresponded to the number of different types of homopolymers in the DNA.

Slowing the translocation of single-stranded DNA by using nano-cylindrical passage self-assembled by amphiphilic block copolymers

We report a novel approach to slow the translocation of single-stranded DNA (ssDNA) by employing polyethylene oxide (PEO) filled nano-cylindrical domains as transportation channels. DNA strands were demonstrated to electrophoretically translocate through PEO filled cylindrical domains with diameters of 2 and 9 nm, which were self-assembled by amphiphilic liquid crystalline block copolymers. The average translocation rate of ssDNA strands was effectively reduced to an order of 10 μs per nucleotide, which was 1-2 orders slower than that attained by utilizing conventional solid-state nanopore devices.

Protein patterning by a DNA origami framework

A spatial arrangement of proteins provides structural and functional advantages in vast technological applications as well as fundamental research. Most protein patterning procedures employ complicated, time consuming and very costly nanofabrication techniques. As an alternative route, we developed a fully biomolecular self-assembly method using DNA Origami Frames (DOF) as a template for both small and large scale protein patterning. We employed a triangular DOF (tDOF) to arrange the Bovine Serum Albumin (BSA) protein. Our in situ protein patterning strategy provides a novel, fully organic platform using a fast and low-cost surface approach with possible utilization in fundamental science and technological applications.

Slowing DNA Translocation in a Nanofluidic Field-Effect Transistor

Here, we present an experimental demonstration of slowing DNA translocation across a nanochannel by modulating the channel surface charge through an externally applied gate bias. The experiments were performed on a nanofluidic field-effect transistor, which is a monolithic integrated platform featuring a 50 nm-diameter in-plane alumina nanocapillary whose entire length is surrounded by a gate electrode. The field-effect transistor behavior was validated on the gating of ionic conductance and protein transport. The gating of DNA translocation was subsequently studied by measuring discrete current dips associated with single λ-DNA translocation events under a source-to-drain bias of 1 V. The translocation speeds under various gate bias conditions were extracted by fitting event histograms of the measured translocation time to the first passage time distributions obtained from a simple 1D biased diffusion model. A positive gate bias was observed to slow the translocation of single λ-DNA chains markedly; the translocation speed was reduced by an order of magnitude from 18.4 mm/s obtained under a floating gate down to 1.33 mm/s under a positive gate bias of 9 V. Therefore, a dynamic and flexible regulation of the DNA translocation speed, which is vital for single-molecule sequencing, can be achieved on this device by simply tuning the gate bias. The device is realized in a conventional semiconductor microfabrication process without the requirement of advanced lithography, and can be potentially further developed into a compact electronic single-molecule sequencer.

Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA

Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.

Deceleration of single-stranded DNA passing through a nanopore using a nanometre-sized bead structure

DNA sequencing with a solid-state nanopore requires a reduction of the translocation speeds of single-stranded DNA (ssDNA) over 10 μs/base. In this study, we report that a nanometre-sized bead structure constructed around a nanopore can reduce the moving speed of ssDNA to 270 μs/base by adjusting the diameter of the bead and its surface chemical group. This decelerating effect originates from the strong interaction between ssDNA and the chemical group on the surface of the bead. This nanostructure was simply prepared by dip coating in which a substrate with a nanopore was immersed in a silica bead solution and then dried in an oven. As compared with conventional approaches, our novel method is less laborious, simpler to perform and more effective in reducing ssDNA translocation speed.

Self-assembled Messenger RNA Nanoparticles (mRNA-NPs) for Efficient Gene Expression

Although mRNA has several advantages over plasmid DNA when delivered into cells for gene expression, mRNA transfection is a very rare occurrence in gene delivery. This is mainly because of the labile nature of RNA, resulting in a low expression level of the desired protein. In this study, self-assembled mRNA nanoparticles (mRNA-NPs) packed with multiple repeats of mRNA were synthesized to achieve efficient gene expression. This approach required only a one-step process to synthesize particles with a minimal amount of plasmid DNA to produce the RNA transcripts via rolling circle transcription. Moreover, there are no concerns for cytotoxicity which can be caused by chemical condensates because mRNA-NPs are made entirely of mRNA. An examination of the cells transfected with the mRNA-NPs encoding the green fluorescence protein (GFP) confirmed that the mRNA-NPs can be used as a novel platform for effective gene delivery.

Nanopore Analysis of Single-Stranded Binding Protein Interactions with DNA

We study the binding of E. coli single-stranded binding protein (SSB) to single-stranded DNA (ssDNA) using a solid-state nanopore assay. We find that saturated nucleoprotein complexes can be distinguished easily from free SSB, ssDNA, or double-stranded DNA individually and demonstrate that the high affinity of SSB for ssDNA can be exploited to achieve high-fidelity differentiation from duplex molecules in a mixture. We then study nucleoprotein filament formation by systematically varying the amount of SSB relative to ssDNA. We observe a concomitant shift in the mean amplitude of electrical events that is consistent with weakly cooperative binding. Finally, we compare circular and linearized ssDNA saturated with SSB and use the results to infer structural details of the nucleoprotein complex.

Electro-optical detection of single λ-DNA

Single λ-DNA molecules are detected on a nanopore-gated optofluidic chip electrically and optically. Statistical variations in the single particle trajectories are used to predict the intensity distribution of the fluorescence signals.

Using a Péclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions

Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavor to match any particular set of experimental conditions. In this manuscript, we use the concept of a Péclet number for translocation, P(t), to compare the drift-diffusion balance in a typical experiment vs a typical simulation. We find that the standard coarse-grained approach overestimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using double stranded DNA (dsDNA). By defining a Péclet control parameter, λ, we are able to correct this and tune the simulations to replicate the experimental P(t) (for dsDNA and other scenarios). To show the effect that a particular P(t) can have on the dynamics of translocation, we perform simulations across a wide range of P(t) values for two different types of driving forces: a force applied in the pore and a pulling force applied to the end of the polymer. As P(t) brings the system from a diffusion dominated to a drift dominated regime, a variety of effects are observed including a non-monotonic dependence of the translocation time τ on P(t) and a steep rise in the probability of translocating. Comparing the two force cases illustrates the impact of the crowding effects that occur on the trans side: a non-monotonic dependence of the width of the τ distributions is obtained for the in-pore force but not for the pulling force.

Fine tuning of nanopipettes using atomic layer deposition for single molecule sensing

ALD modified pipettes provides a quick and efficient method for fine-tuning the nanopore diameter which can be used for a broad range of applications including the detection of small biomolecules at the single molecule level.

Surface modification of solid-state nanopores for sticky-free translocation of single-stranded DNA

Nanopore technology is one of the most promising approaches for fast and low-cost DNA sequencing application. Single-stranded DNA detection is primary objective in such device, while solid-state nanopores remain less explored than their biological counterparts due to bio-molecule clogging issue caused by surface interaction between DNA and nanopore wall. By surface coating a layer of polyethylene glycol (PEG), solid-state nanopore can achieve long lifetime for single-stranded DNA sticky-free translocation at pH 11.5. Associated with elimination of non-specific binding of molecule, PEG coated nanopore presents new surface characteristic as less hydrophility, lower 1/f noise, and passivated surface charge responsiveness on pH. Meanwhile, conductance blockage of single-stranded DNA is found to be deeper than double-stranded DNA, which can be well described by a string of blobs model for a quasi-equilibrium state polymer in constraint space.

SSB binding to single-stranded DNA probed using solid-state nanopore sensors

Single-stranded DNA (ssDNA) binding protein plays an important role in the DNA replication process in a wide range of organisms. It binds to ssDNA to prevent premature reannealing and to protect it from degradation. Current understanding of SSB/ssDNA interaction points to a complex mechanism, including SSB motion along the DNA strand. We report on the first characterization of this interaction at the single-molecule level using solid-state nanopore sensors, namely without any labeling or surface immobilization. Our results show that the presence of SSB on the ssDNA can control the speed of nanopore translocation, presumably due to strong interactions between SSB and the nanopore surface. This enables nanopore-based detection of ssDNA fragments as short as 37 nt, which is normally very difficult with solid-state nanopore sensors, due to constraints in noise and bandwidth. Notably, this fragment is considerably shorter than the 65 nt binding motif, typically required for SSB binding at high salt concentrations. The nonspecificity of SSB binding to ssDNA further suggests that this approach could be used for fragment sizing of short ssDNA.

Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter

To slow the translocation of single-stranded DNA (ssDNA) through a solid-state nanopore, a nanopore was narrowed, and the effect of the narrowing on the DNA translocation speed was investigated. In order to accurately measure the speed, long (5.3 kb) ssDNA (namely, ss-poly(dA)) with uniform length (±0.4 kb) was synthesized. The diameters of nanopores fabricated by a transmission electron microscope were controlled by atomic-layer deposition. Reducing the nanopore diameter from 4.5 to 2.3 nm slowed down the translocation of ssDNA by more than 16 times (to 0.18 μs base(-1)) when 300 mV was applied across the nanopore. It is speculated that the interaction between the nanopore and the ssDNA dominates the translocation speed. Unexpectedly, the translocation speed of ssDNA through the 4.5 nm nanopore is more than two orders of magnitude higher than that of double-stranded DNA (dsDNA) through a nanopore of almost the same size. The cause of such a faster translocation of ssDNA can be explained by the weaker drag force inside the nanopore. Moreover, the measured translocation speeds of ssDNA and dsDNA agree well with those calculated by molecular-dynamics (MD) simulation. The MD simulation predicted that reducing the nanopore diameter to almost the same as that of ssDNA (i.e. 1.4 nm) decreases the translocation speed (to 1.4 μs base(-1)). Narrowing the nanopore is thus an effective approach for accomplishing nanopore DNA sequencing.

Ultrathin suspended nanopores with surface plasmon resonance fabricated by combined colloidal lithography and film transfer

Suspended plasmonic nanopores in ultrathin film layers were fabricated through a simple and widely applicable method combining colloidal lithography and thin film transfer, which allows mass production of short-range ordered nanopore arrays on a large scale. By this combined method, mechanically stable and flexible free-standing nanopore membranes with a thickness down to 15-30 nm were produced. The plasmon resonances of the ultrathin plasmonic nanopores fabricated in AlN/Au/AlN trilayer and single layer Au membranes were tuned to lie in the vis-NIR wavelength range by properly designing their dimensions. The optical responses to the refractive index changes were tested and applied to adlayer sensing. The trilayer nanopore membrane showed a unique property to support water only on one side of the membrane, which was confirmed by the resonance shift and comparison with numerical simulation. Pore size reduction down to 10 nm can be achieved through additional material deposition. The filtering function of such pore-size-reduced conical shaped nanofunnels has also been demonstrated. The presented nanopore fabrication method offers new platforms for ultrathin nanopore sensing or filtering devices with controlled pore-size and optical properties. The film transfer technique employed in this work would enable the transformation of any substrate-based nanostructures to free-standing membrane based devices without complicated multiple etching processes.

Stabilization of graphene nanopore

Graphene is an ultrathin, impervious membrane. The controlled introduction of nanoscale pores in graphene would lead to applications that involve water purification, chemical separation, and DNA sequencing. However, graphene nanopores are unstable against filling by carbon adatoms. Here, using aberration-corrected scanning transmission electron microscopy and density-functional calculations, we report that Si atoms stabilize graphene nanopores by bridging the dangling bonds around the perimeter of the hole. Si-passivated pores remain intact even under intense electron beam irradiation, and they were observed several months after the sample fabrication, demonstrating that these structures are intrinsically robust and stable against carbon filling. Theoretical calculations reveal the underlying mechanism for this stabilization effect: Si atoms bond strongly to the graphene edge, and their preference for tetrahedral coordination forces C adatoms to form dendrites sticking out of the graphene plane, instead of filling the nanopore. Our results provide a novel way to develop stable nanopores, which is a major step toward reliable graphene-based molecular translocation devices.

A nanopore machine promotes the vectorial transport of DNA across membranes

The transport of nucleic acids through membrane pores is a fundamental biological process that occurs in all living organisms. It occurs, for example, during the import of viral DNA into the host cell or during the nuclear pore complex-mediated transport of mRNA in and out the cell nucleus and has implications in nucleic acid drug delivery and gene therapy. Here we describe an engineered DNA transporter that is able to recognize and chaperone a specific DNA molecule across a biological membrane under a fixed transmembrane potential. The transported DNA strand is then released by a simple mechanism based on DNA strand displacement. This nanopore machine might be used to separate or concentrate nucleic acids or to transport genetic information across biological membranes.

Ionic permeability and mechanical properties of DNA origami nanoplates on solid-state nanopores

While DNA origami is a popular and versatile platform, its structural properties are still poorly understood. In this study we use solid-state nanopores to investigate the ionic permeability and mechanical properties of DNA origami nanoplates. DNA origami nanoplates of various designs are docked onto solid-state nanopores where we subsequently measure their ionic conductance. The ionic permeability is found to be high for all origami nanoplates. We observe the conductance of docked nanoplates, relative to the bare nanopore conductance, to increase as a function of pore diameter, as well as to increase upon lowering the ionic strength. The honeycomb lattice nanoplate is found to have slightly better overall performance over other plate designs. After docking, we often observe spontaneous discrete jumps in the current, a process which can be attributed to mechanical buckling. All nanoplates show a nonlinear current-voltage dependence with a lower conductance at higher applied voltages, which we attribute to a physical bending deformation of the nanoplates under the applied force. At sufficiently high voltage (force), the nanoplates are strongly deformed and can be pulled through the nanopore. These data show that DNA origami nanoplates are typically very permeable to ions and exhibit a number of unexpected mechanical properties, which are interesting in their own right, but also need to be considered in the future design of DNA origami nanostructures.

Biomimetic nanopore for sensitive and selective detection of Hg(ii) in conjunction with single-walled carbon nanotubes

Through SWNTs, duplex DNA derived from folding of single-stranded DNA can be quantitated with Zr⁴⁺–PEI coated cone-shaped nanopore. With Hg²⁺ detection, sensitivity and selectivity based on this paradigm is guaranteed without probe immobilization.

Detection of long and short DNA using nanopores with graphitic polyhedral edges

Graphene is a unique material with a thickness as low as a single atom, high in-plane conductivity and a robust lattice that is self-supporting over large length scales. Schematically, graphene is an ideal solid-state material for tuning the properties of a nanopore because self-supported sheets, ranging from single to multiple atomic layers, can create pores with near-arbitrary dimensions which can provide exquisite control of the electric field drop within the pore. In this study, we characterize the drilling kinetics of nanopores using a thermionic electron source and various electron beam fluxes to minimize secondary hole formation. Once established, we investigated the use of multilayer graphene to create highly tailored nanostructures including nanopores with graphite polyhedral crystals formed around the nanopore edge. Finally, we report on the translocation of double stranded and single stranded DNA through such graphene pores and show that the single stranded DNA translocates much slower allowing detection of extremely short fragments (25 nucleotides in length). Our findings suggest that the kinetic and controllable properties of graphene nanopores under sculpting conditions can be used to further enhance the detection of DNA analytes.

Hydrodynamic flow in the vicinity of a nanopore induced by an applied voltage

Continuum simulation is employed to study ion transport and fluid flow through a nanopore in a solid-state membrane under an applied potential drop. The results show the existence of concentration polarization layers on the surfaces of the membrane. The nonuniformity of the ionic distribution gives rise to an electric pressure that drives vortical motion in the fluid. There is also a net hydrodynamic flow through the nanopore due to an asymmetry induced by the membrane surface charge. The qualitative behavior is similar to that observed in a previous study using molecular dynamic simulations. The current-voltage characteristics show some nonlinear features but are not greatly affected by the hydrodynamic flow in the parameter regime studied. In the limit of thin Debye layers, the electric resistance of the system can be characterized using an equivalent circuit with lumped parameters. Generation of vorticity can be understood qualitatively from elementary considerations of the Maxwell stresses. However, the flow strength is a strongly nonlinear function of the applied field. Combination of electrophoretic and hydrodynamic effects can lead to ion selectivity in terms of valences and this could have some practical applications in separations.

Translocating kilobase RNA through the Staphylococcal α-hemolysin nanopore

The electrophoretic translocation of polynucleotides through nanopores may permit direct single-molecule nucleic acid sequencing. Here we describe the translocation of ssRNA heteropolymers (91-6083 bases) through the α-hemolysin nanopore. Translocation of these long ssRNAs is characterized by surprisingly long, almost complete ionic current blockades with durations averaging milliseconds per base (at +180 mV). The event durations decrease exponentially with increased transmembrane potential but are largely unaffected by the presence of urea. When the ssRNA is coupled at the 3' end to streptavidin, which cannot translocate through the pore, permanent blockades are observed, supporting our conclusion that the transient blockades arise from ssRNA translocation.