High-throughput optical sensing of nucleic acids in a nanopore array

Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction

Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.

Ion transport through short nanopores modulated by charged exterior surfaces

Short nanopores find extensive applications, capitalizing on their high throughput and detection resolution. Ionic behaviors through long nanopores are mainly determined by charged inner-pore walls. When pore lengths decrease to sub-200 nm, charged exterior surfaces provide considerable modulation to ion current. We find that the charge status of inner-pore walls affects the modulation of ion current from charged exterior surfaces. For 50-nm-long nanopores with neutral inner-pore walls, the charged exterior surfaces on the voltage (surfaceV) and ground (surfaceG) sides enhance and inhibit the ion transport by forming ion enrichment and depletion zones inside nanopores, respectively. For nanopores with both charged inner-pore and exterior surfaces, continuous electric double layers enhance the ion transport through nanopores significantly. The charged surfaceV results in higher ion current by simultaneously weakening the ion depletion at pore entrances and enhancing the intra-pore ion enrichment. The charged surfaceG expedites the exit of ions from nanopores, resulting in a decrease in ion enrichment at pore exits. Through adjustment in the width of charged-ring regions near pore boundaries, the effective charged width of the charged exterior is explored at ∼20 nm. Our results may provide a theoretical guide for further optimizing the performance of nanopore-based applications, such as seawater desalination, biosensing, and osmotic energy conversion.

Selective Single-Molecule Nanopore Detection of mpox A29 Protein Directly in Biofluids

Single-molecule antigen detection using nanopores offers a promising alternative for accurate virus testing to contain their transmission. However, the selective and efficient identification of small viral proteins directly in human biofluids remains a challenge. Here, we report a nanopore sensing strategy based on a customized DNA molecular probe that combines an aptamer and an antibody to enhance the single-molecule detection of mpox virus (MPXV) A29 protein, a small protein with an M.W. of ca. 14 kDa. The formation of the aptamer-target-antibody sandwich structures enables efficient identification of targets when translocating through the nanopore. This technique can accurately detect A29 protein with a limit of detection of ∼11 fM and can distinguish the MPXV A29 from vaccinia virus A27 protein (a difference of only four amino acids) and Varicella Zoster Virus (VZV) protein directly in biofluids. The simplicity, high selectivity, and sensitivity of this approach have the potential to contribute to the diagnosis of viruses in point-of-care settings.

Confirming Silent Translocation through Nanopores with Simultaneous Single-Molecule Fluorescence and Single-Channel Electrical Recordings

Most of what is known concerning the luminal passage of materials through nanopores arises from electrical measurements. Whether nanopores are biological, solid-state, synthetic, hybrid, glass-capillary-based, or protein ion channels in cells and tissues, characteristic signatures embedded in the flow of ionic current are foundational to understanding functional behavior. In contrast, this work describes passage through a nanopore that occurs without producing an electrical signature. We refer to the phenomenon as "silent translocation." By definition, silent translocations are invisible to the standard tools of electrophysiology and fundamentally require a simultaneous ancillary measurement technique for positive identification. As a result, this phenomenon has been largely unexplored in the literature. Here, we report on a derivative of Cyanine 5 (sCy5a) that passes through the α-hemolysin (αHL) nanopore silently. Simultaneously acquired single-molecule fluorescence and single-channel electrical recordings from bilayers formed over a closed microcavity demonstrate that translocation does indeed take place, albeit infrequently. We report observations of silent translocation as a function of time, dye concentration, and nanopore population in the bilayer. Lastly, measurement of the translocation rate as a function of applied potential permits estimation of an effective energy barrier for transport through the pore as well as the effective charge on the dye, all in the absence of an information-containing electrical signature.

Evidence of Cytolysin A nanopore incorporation in mammalian cells assessed by a graphical user interface

Technologies capable of assessing cellular metabolites with high precision and temporal resolution are currently limited. Recent developments in the field of nanopore sensors allow the non-stochastic quantification of metabolites, where a nanopore is acting as an electrical transducer for selective substrate binding proteins (SBPs). Here we show that incorporation of the pore-forming toxin Cytolysin A (ClyA) into the plasma membrane of Chinese hamster ovary cells (CHO-K1) results in the appearance of single-channel conductance amenable to multiplexed automated patch-clamp (APC) electrophysiology. In CHO-K1 cells, SBPs modify the ionic current flowing though ClyA nanopores, thus demonstrating its potential for metabolite sensing of living cells. Moreover, we developed a graphical user interface for the analysis of the complex signals resulting from multiplexed APC recordings. This system lays the foundation to bridge the gap between recent advances in the nanopore field (e.g., proteomic and transcriptomic) and potential cellular applications.

Single-Nanoparticle-Based Nanomachining for Fabrication of a Uniform Nanochannel Sensor

The structure of nanomaterials and nanodevices determines their functionality and applications. A single uniform nanochannel with a high aspect ratio is an attractive structure due to its unique rigid structures, easy preparation, and diverse pore structures and it holds significant promising importance in fields such as nanopore sensing and nanomanufacturing. Although the metal-nanoparticle-assistant silicon etching technique can produce uniform nanochannels, however, the fabrication of single through nanochannels remains a challenge thus far. A simple and versatile strategy is developed that allows for the retention of individual gold nanoparticle on a substrate, enabling single-nanoparticle nanomachining. This method involves three steps: the formation of a carbon protective layer on individual nanoparticles via electron-beam irradiation, selective removal of unprotected nanoparticles using a corrosive agent, and subsequent elimination of the carbon layer. This enables the fabrication of a single submillimeter-long uniform through nanochannel in the silicon wafer, which can be employed for nanopore sensing and shape-based nanoparticle distinguishing. The developed method can also facilitate single-nanoparticle studies and nanomachining for a broad application in materials science, electronics, micro/nano-optics, and catalysis.

Stochastic Sensing of Dynamic Interactions and Chemical Reactions with Nanopores/Nanochannels

Nanopore sensing technology is an emerging analysis method with the advantages of simple operation, high sensitivity, fast output and being label free, and it is widely used in protein analysis, gene sequencing, biomarker detection, and other fields. The confined space of the nanopore provides a place for dynamic interactions and chemical reactions between substances. The use of nanopore sensing technology to track these processes in real time is helpful to understand the interaction/reaction mechanism at the single-molecule level. According to nanopore materials, we summarize the development of biological nanopores and solid-state nanopores/nanochannels in the stochastic sensing of dynamic interactions and chemical reactions. The goal of this paper is to stimulate the interest of researchers and promote the development of this field.

The ER calcium channel Csg2 integrates sphingolipid metabolism with autophagy

Sphingolipids are ubiquitous components of membranes and function as bioactive lipid signaling molecules. Here, through genetic screening and lipidomics analyses, we find that the endoplasmic reticulum (ER) calcium channel Csg2 integrates sphingolipid metabolism with autophagy by regulating ER calcium homeostasis in the yeast Saccharomyces cerevisiae. Csg2 functions as a calcium release channel and maintains calcium homeostasis in the ER, which enables normal functioning of the essential sphingolipid synthase Aur1. Under starvation conditions, deletion of Csg2 causes increases in calcium levels in the ER and then disturbs Aur1 stability, leading to accumulation of the bioactive sphingolipid phytosphingosine, which specifically and completely blocks autophagy and induces loss of starvation resistance in cells. Our findings indicate that calcium homeostasis in the ER mediated by the channel Csg2 translates sphingolipid metabolism into autophagy regulation, further supporting the role of the ER as a signaling hub for calcium homeostasis, sphingolipid metabolism and autophagy.

Electrochemical Shot Noise of a Redox Monolayer

Redox monolayers are the base for a wide variety of devices including high-frequency molecular diodes or biomolecular sensors. We introduce a formalism to describe the electrochemical shot noise of such a monolayer, confirmed experimentally at room temperature in liquid. The proposed method, carried out at equilibrium, avoids parasitic capacitance, increases the sensitivity, and allows us to obtain quantitative information such as the electronic coupling (or standard electron transfer rates), its dispersion, and the number of molecules. Unlike in solid-state physics, the homogeneity in energy levels and transfer rates in the monolayer yields a Lorentzian spectrum. This first step for shot noise studies in molecular electrochemical systems opens perspectives for quantum transport studies in a liquid environment at room temperature as well as highly sensitive measurements for bioelectrochemical sensors.

High-resolution discrimination of homologous and isomeric proteinogenic amino acids in nanopore sensors with ultrashort single-walled carbon nanotubes

The hollow and tubular structure of single-walled carbon nanotubes (SWCNTs) makes them ideal candidates for making nanopores. However, the heterogeneity of SWCNTs hinders the fabrication of robust and reproducible carbon-based nanopore sensors. Here we develop a modified density gradient ultracentrifugation approach to separate ultrashort (≈5-10 nm) SWCNTs with a narrow conductance range and construct high-resolution nanopore sensors with those tubes inserted in lipid bilayers. By conducting ionic current recordings and fluorescent imaging of Ca2+ flux through different nanopores, we prove that the ion mobilities in SWCNT nanopores are 3-5 times higher than the bulk mobility. Furthermore, we employ SWCNT nanopores to discriminate homologue or isomeric proteinogenic amino acids, which are challenging tasks for other nanopore sensors. These successes, coupled with the building of SWCNT nanopore arrays, may constitute a crucial part of the recently burgeoning protein sequencing technologies.

Digital and Absolute Assays for Low Abundance Molecular Biomarkers

There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.

An Engineered OmpG Nanopore with Displayed Peptide Motifs for Single-Molecule Multiplex Protein Detection

Molecular detection via nanopore, achieved by monitoring changes in ionic current arising from analyte interaction with the sensor pore, is a promising technology for multiplex sensing development. Outer Membrane Protein G (OmpG), a monomeric porin possessing seven functionalizable loops, has been reported as an effective sensing platform for selective protein detection. Using flow cytometry to screen unfavorable constructs, we identified two OmpG nanopores with unique peptide motifs displayed in either loop 3 or 6, which also exhibited distinct analyte signals in single-channel current recordings. We exploited these motif-displaying loops concurrently to facilitate single-molecule multiplex protein detection in a mixture. We additionally report a strategy to increase sensor sensitivity via avidity motif display. These sensing schemes may be expanded to more sophisticated designs utilizing additional loops to increase multiplicity and sensitivity.

Single-molecule tracking of perfringolysin O assembly and membrane insertion uncoupling

We exploit single-molecule tracking and optical single channel recording in droplet interface bilayers to resolve the assembly pathway and pore formation of the archetypical cholesterol-dependent cytolysin nanopore, Perfringolysin O. We follow the stoichiometry and diffusion of Perfringolysin O complexes during assembly with 60 ms temporal resolution and 20 nm spatial precision. Our results suggest individual nascent complexes can insert into the lipid membrane where they continue active assembly. Overall, these data support a model of stepwise irreversible assembly dominated by monomer addition, but with infrequent assembly from larger partial complexes.

Multiplexed Organelles Portrait Barcodes for Subcellular MicroRNA Array Detection in Living Cells

Multiplexed profiling of microRNAs' subcellular expression and distribution is essential to understand their spatiotemporal function information, but it remains a crucial challenge. Herein, we report an encoding approach that leverages combinational fluorescent dye barcodes, organelle targeting elements, and an independent quantification signal, termed Multiplexed Organelles Portrait Barcodes (MOPB), for high-throughput profiling of miRNAs from organelles. The MOPB barcodes consist of heterochromatic fluorescent dye-loaded shell-core mesoporous silica nanoparticles modified with organelle targeting peptides and molecular beacon detection probes. Using mitochondria and endoplasmic reticulum as models, we encoded four Cy3/AMCA ER-MOPB and four Cy5/AMCA Mito-MOPB by varying the Cy3 and Cy5 intensity for distinguishing eight organelles' miRNAs. Significantly, the MOPB strategy successfully and accurately profiled eight subcellular organelle miRNAs' alterations in the drug-induced Ca²⁺ homeostasis breakdown. The approach should allow more widespread application of subcellular miRNAs and multiplexed subcellular protein biomarkers' monitoring for drug discovery, cellular metabolism, signaling transduction, and gene expression regulation readout.

Building programmable multicompartment artificial cells incorporating remotely activated protein channels using microfluidics and acoustic levitation

Intracellular compartments are functional units that support the metabolism within living cells, through spatiotemporal regulation of chemical reactions and biological processes. Consequently, as a step forward in the bottom-up creation of artificial cells, building analogous intracellular architectures is essential for the expansion of cell-mimicking functionality. Herein, we report the development of a droplet laboratory platform to engineer complex emulsion-based, multicompartment artificial cells, using microfluidics and acoustic levitation. Such levitated models provide free-standing, dynamic, definable droplet networks for the compartmentalisation of chemical species. Equally, they can be remotely operated with pneumatic, heating, and magnetic elements for post-processing, including the incorporation of membrane proteins; alpha-hemolysin; and mechanosensitive channel of large-conductance. The assembly of droplet networks is three-dimensionally patterned with fluidic input configurations determining droplet contents and connectivity, whilst acoustic manipulation can be harnessed to reconfigure the droplet network in situ. The mechanosensitive channel can be repeatedly activated and deactivated in the levitated artificial cell by the application of acoustic and magnetic fields to modulate membrane tension on demand. This offers possibilities beyond one-time chemically mediated activation to provide repeated, non-contact, control of membrane protein function. Collectively, this expands our growing capability to program and operate increasingly sophisticated artificial cells as life-like materials.

Encapsulated droplet interface bilayers as a platform for high-throughput membrane studies

Whilst it is highly desirable to produce artificial lipid bilayer arrays allowing for systematic high-content screening of membrane conditions, it remains a challenge due to the combined requirements of scaled membrane production, simple measurement access, and independent control over individual bilayer experimental conditions. Here, droplet bilayers encapsulated within a hydrogel shell are output individually into multi-well plates for simple, arrayed quantitative measurements. The afforded experimental throughput is used to conduct a 2D concentration screen characterising the synergistic pore-forming peptides Magainin2 and PGLa. Maximal enhanced activity is revealed at equimolar peptide concentrations via a membrane dye leakage assay, a finding consistent with models proposed from NMR data. The versatility of the platform is demonstrated by performing in situ electrophysiology, revealing low conductance pore activity (∼15 to 20 pA with 4.5 pA sub-states). In conclusion, this array platform addresses the aforementioned challenges and provides new and flexible opportunities for high-throughput membrane studies. Furthermore, the ability to engineer droplet networks within each construct paves the way for "lab-in-a-capsule" approaches accommodating multiple assays per construct and allowing for communicative reaction pathways.

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.

How capture affects polymer translocation in a solitary nanopore

DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in the presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way toward the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture, while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidence of the interpretation of the experimentally observed folds [M. Gershow and J. A. Golovchenko, Nat. Nanotechnol. 2, 775 (2007) and Mihovilovic et al., Phys. Rev. Lett. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding-that a charged tag attached at the 5' end of the DNA enhances both the multi-scan rate and the uni-directional translocation (5' → 3') probability that would benefit the genomic barcoding and sequencing experiments.

Synergistic Effect of Electrostatic Interaction and Ionic Dehydration on Asymmetric Ion Transport in Nanochannel/Ion Channel Composite Membrane

Ion transport in nanochannels of a size comparable to that of hydrated ions exhibits unique properties due to the synergistic effect of various forces. Here, we design a nanochannel/ion channel composite (NIC) membrane that shows a high ion current rectification (ICR) ratio in different electrolytes. Experimental and theoretical results demonstrate that the synergistic effect of electrostatic interaction and ionic dehydration plays an important role in regulating the ICR behavior of the NIC membrane. We find that electrostatic attraction between ions and the channel surface in the ultraconfined space increases the probability of ionic dehydarion, resulting in different dehydration energy costs for different ions. This further alters the driving force for ion transport and thus regulates ICR of the NIC membrane. This work provides fundamental knowledge of ion transport in ion channels, which aids in the understanding of the function of biological systems and the design of high-performance nanochannel devices.

Spatiotemporal stop-and-go dynamics of the mitochondrial TOM core complex correlates with channel activity

Single-molecule studies can reveal phenomena that remain hidden in ensemble measurements. Here we show the correlation between lateral protein diffusion and channel activity of the general protein import pore of mitochondria (TOM-CC) in membranes resting on ultrathin hydrogel films. Using electrode-free optical recordings of ion flux, we find that TOM-CC switches reversibly between three states of ion permeability associated with protein diffusion. While freely diffusing TOM-CC molecules are predominantly in a high permeability state, non-mobile molecules are mostly in an intermediate or low permeability state. We explain this behavior by the mechanical binding of the two protruding Tom22 subunits to the hydrogel and a concomitant combinatorial opening and closing of the two β-barrel pores of TOM-CC. TOM-CC could thus represent a β-barrel membrane protein complex to exhibit membrane state-dependent mechanosensitive properties, mediated by its two Tom22 subunits.

The application of single molecule nanopore sensing for quantitative analysis

Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.

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.

Dynamic Optical Visualization of Proton Transport Pathways at Water-Solid Interfaces

Probing proton transport is of vital importance for understanding cellular transport, surface catalysis and fuel cells. Conventional proton transport measurements rely on the use of electrochemical conductivity and do not allow for the direct visualization of proton transport pathways. The development of novel experimental techniques to spatiotemporally resolve proton transport is in high demand. Here, building upon the general conversion of aqueous proton flux into spatially resolved fluorescence signals, we optically visualize proton transport through nanopores and along hydrophilic interfaces. We observed that the fluorescence intensity increased at negative voltage due to lateral transport. Thanks to the temporal resolution of optical imaging, our technique further empowers the analysis of proton transport dynamics.

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

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

Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells

Biological nanopores for single-pore sensing have the advantage of size homogeneity, structural reproducibility, and channel amenability. In order to translate this to clinical applications, the functional biological nanopore must be inserted into a stable system for high-throughput analysis. Here we report factors that control the rate of pore insertion into polymer membrane and analyte translocation through the channel of viral DNA packaging motors of Phi29, T3 and T7. The hydrophobicity of aminol or carboxyl terminals and their relation to the analyte translocation were investigated. It was found that both the size and the hydrophobicity of the pore terminus are critical factors for direct membrane insertion. An N-terminus or C-terminus hydrophobic mutation is crucial for governing insertion orientation and subsequent macromolecule translocation due to the one-way traffic property. The N- or C-modification led to two different modes of application. The C-terminal insertion permits translocation of analytes such as peptides to enter the channel through the N terminus, while N-terminus insertion prevents translocation but offers the measurement of gating as a sensing parameter, thus generating a tool for detection of markers. A urokinase-type Plasminogen Activator Receptor (uPAR) binding peptide was fused into the C-terminal of Phi29 nanopore to serve as a probe for uPAR protein detection. The uPAR has proven to be a predictive biomarker in several types of cancer, including breast cancer. With an N-terminal insertion, the binding of the uPAR antigen to individual peptide probe induced discretive steps of current reduction due to the induction of channel gating. The distinctive current signatures enabled us to distinguish uPAR positive and negative tumor cell lines. This finding provides a theoretical basis for a robust biological nanopore sensing system for high-throughput macromolecular sensing and tumor biomarker detection.

An advanced optical-electrochemical nanopore measurement system for single-molecule analysis

Nanopore measurement has advanced in single-molecule analysis by providing a transient time and confined space window that only allows one interested molecule to exist. By optimization and integration of the electrical and optical analysis strategies in this transient window, the acquisition of comprehensive information could be achieved to resolve the intrinsic properties and heterogeneity of a single molecule. In this work, we present a roadmap to build a unified optical and electrochemical synchronous measurement platform for the research of a single molecule. We design a low-cost ultralow-current amplifier with low noise and high-bandwidth to measure the ionic current events as a single molecule translocates through a nanopore and combine a multi-functional optical system to implement the acquisition of the fluorescence, scattering spectrum, and photocurrent intensity of single molecule events in a nanopore confined space. Our system is a unified and unique platform for the protein nanopore, the solid-state nanopore, and the glass capillary nanopore, which has advantages in the comprehensive research of nanopore single-molecule techniques.

Enzymeless DNA Base Identification by Chemical Stepping in a Nanopore

The stepwise movement of a single biopolymer strand through a nanoscopic detector for the sequential identification of its building blocks offers a universal means for single-molecule sequencing. This principle has been implemented in portable sequencers that use enzymes to move DNA or RNA through hundreds of individual nanopore detectors positioned in an array. Nevertheless, its application to the sequencing of other biopolymers, including polypeptides and polysaccharides, has not progressed because suitable enzymes are lacking. Recently, we devised a purely chemical means to move molecules processively in steps comparable to the repeat distances in biopolymers. Here, with this chemical approach, we demonstrate sequential nucleobase identification during DNA translocation through a nanopore. Further, the relative location of a guanine modification with a chemotherapeutic platinum derivative is pinpointed with single-base resolution. After further development, chemical translocation might replace stepping by enzymes for highly parallel single-molecule biopolymer sequencing.

Microscopic Screening of Cyclodextrin Channel Blockers by DiffusiOptoPhysiology

Blockers of pore-forming toxins (PFTs) limit bacterial virulence by blocking relevant channel proteins. However, screening of desired blockers from a large pool of candidate molecules is not a trivial task. Acknowledging its advantages of low cost, high throughput, and multiplicity, DiffusiOptoPhysiology (DOP), an emerging nanopore technique that visually monitors the states of individual channel proteins without using any electrodes, has shown its potential use in the screening of channel blockers. By taking different α-hemolysin (α-HL) mutants as model PFTs and different cyclodextrins as model blockers, we report direct screening of pore blockers solely by using fluorescence microscopy. Different combinations of pores and blockers were simultaneously evaluated on the same DOP chip and a single-molecule resolution is directly achieved. The entire chip is composed of low-cost and biocompatible materials, which is fully disposable after each use. Though only demonstrated with cyclodextrin derivatives and α-HL mutants, this proof of concept has also suggested its generality to investigate other pore-forming proteins.

The NEOtrap - en route with a new single-molecule technique

This paper provides a perspective on potential applications of a new single-molecule technique, viz., the nanopore electro-osmotic trap (NEOtrap). This solid-state nanopore-based method uses locally induced electro-osmosis to form a hydrodynamic trap for single molecules. Ionic current recordings allow one to study an unlabeled protein or nanoparticle of arbitrary charge that can be held in the nanopore's most sensitive region for very long times. After motivating the need for improved single-molecule technologies, we sketch various possible technical extensions and combinations of the NEOtrap. We lay out diverse applications in biosensing, enzymology, protein folding, protein dynamics, fingerprinting of proteins, detecting post-translational modifications, and all that at the level of single proteins - illustrating the unique versatility and potential of the NEOtrap.

Biomimetic Nanocomposite Membranes with Ultrahigh Ion Selectivity for Osmotic Power Conversion

Ion transport in nanoconfinement exhibits significant features such as ionic rectification, ionic selectivity, and ionic gating properties, leading to the potential applications in desalination, water treatment, and energy conversion. Two-dimensional nanofluidics provide platforms to utilize this phenomenon for capturing osmotic energy. However, it is challenging to further improve the power output with inadequate charge density. Here we demonstrate a feasible strategy by employing Kevlar nanofiber as space charge donor and cross-linker to fabricate graphene oxide composite membranes. The coupling of space charge and surface charge, enabled by the stabilization of interlayer spacing, plays a key role in realizing high ion selectivity and the derived high-performance osmotic power conversion up to 5.06 W/m2. Furthermore, the output voltage of an ensemble of the membranes in series could reach 1.61 V, which can power electronic devices. The system contributes a further step toward the application of energy conversion.

Rapid and multiplex preparation of engineered Mycobacterium smegmatis porin A (MspA) nanopores for single molecule sensing and sequencing

Acknowledging its unique conical lumen structure, Mycobacterium smegmatis porin A (MspA) was the first type of nanopore that has successfully sequenced DNA. Recent developments of nanopore single molecule chemistry have also suggested MspA to be an optimum single molecule reactor. However, further investigations with this approach require heavy mutagenesis which is labor intensive and requires high end instruments for purifications. We here demonstrate an efficient and economic protocol which performs rapid and multiplex preparation of a variety of MspA mutants. The prepared MspA mutants were demonstrated in operations such as nanopore insertion, sequencing, optical single channel recording (oSCR), nanopore single molecule chemistry and nanopore rectification. The performance is no different from that of pores however prepared by other means. The time of all human operations and the cost for a single batch of preparation have been minimized to 40 min and 0.4$, respectively. This method is extremely useful in the screening of new MspA mutants, which has an urgent requirement in further investigations of new MspA nanoreactors. Its low cost and simplicity also enable efficient preparations of MspA nanopores for both industrial manufacturing and academic research.

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

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

Utilization of chromogenic enzyme substrates for signal amplification in multiplexed detection of biomolecules using surface mass spectrometry

MicroRNAs (miRNAs) are important post-transcriptional gene regulators and can serve as potential biomarkers for many diseases. Most of the current miRNA detection techniques require purification from biological samples, amplification, labeling, or tagging, which makes quantitative analysis of clinically relevant samples challenging. Here we present a new strategy for the detection of miRNAs with uniformity over a large area based on signal amplification using enzymatic reactions and measurements using time-of-flight secondary ion mass spectrometry (ToF-SIMS), a sensitive surface analysis tool. This technique has high sequence specificity through hybridization with a hairpin DNA probe and allows the identification of single-base mismatches that are difficult to distinguish by conventional mass spectrometry. We successfully detected target miRNAs in biological samples without purification, amplification, or labeling of target molecules. In addition, by adopting a well-known chromogenic enzymatic reaction from the field of biotechnology, we extended the use of enzyme-amplified signal enhancement ToF (EASE-ToF) to protein detection. Our strategy has advantages with respect to scope, quantification, and throughput over the currently available methods, and is amenable to multiplexing based on the outstanding molecular specificity of mass spectrometry (MS). Therefore, our technique not only has the potential for use in clinical diagnosis, but also provides evidence that MS can serve as a useful readout for biosensing to perform multiplexed analysis extending beyond the limitations of existing technology.

Single-molecule imaging of pore-forming toxin dynamics in droplet interface bilayers

Single-channel recording from pore-forming toxins (PFTs) provides a clear and direct molecular readout of toxin action. However to complete any mechanistic understanding of PFT behavior, this functional kinetic readout must be linked to the underlying changes in toxin structure, binding, conformation, or stoichiometry. Here we review how single-molecule imaging methods might be used to further our understanding of PFTs, and provide detailed practical guidance on the use of droplet interface bilayers as a method capable of examining both single-molecule fluorescence and single-channel electrical signals from PFTs.

Investigation of Fusion between Nanosized Lipid Vesicles and a Lipid Monolayer Toward Formation of Giant Lipid Vesicles with Various Kinds of Biomolecules

We determined the properties of fusion between large unilamellar vesicles (LUVs) and the lipid monolayer by measuring the fluorescence intensity of rhodamine-conjugated phospholipids in cell-sized lipid vesicles. The charge of LUVs (containing cationic lipids) and lipid droplets (containing anionic lipids) promoted lipid membrane fusion. We also investigated the formation of cell-sized lipid vesicles with asymmetric lipid distribution using this fusion method. Moreover, cell-sized asymmetric ganglioside vesicles can be generated from the planar lipid bilayer formed at the interface between the lipid droplets with/without LUVs containing ganglioside. The flip-flop dynamics of ganglioside were observed on the asymmetric ganglioside vesicles. This fusion method can be used to form asymmetric lipid vesicles with poor solubility in n-decane or lipid vesicles containing various types of membrane proteins for the development of complex artificial cell models.

Engineering of Broadband Nanoporous Semiconductor Photonic Crystals for Visible-Light-Driven Photocatalysis

A new class of semiconductor photonic crystals composed of titanium dioxide (TiO₂)-functionalized nanoporous anodic alumina (NAA) broadband-distributed Bragg reflectors (BDBRs) for visible-light-driven photocatalysis is presented. NAA-BDBRs produced by double exponential pulse anodization (DEPA) show well-resolved, spectrally tunable, broad photonic stop bands (PSBs), the width of which can be precisely tuned from 70 ± 6 to 153 ± 9 nm (in air) by progressive modification of the anodization period in the input DEPA profile. Photocatalytic efficiency of TiO₂-NAA-BDBRs with tunable PSB width upon visible-NIR illumination is studied using three model photodegradation reactions of organics with absorbance bands across the visible spectral regions. Analysis of these reactions allows us to elucidate the interplay of spectral distance between red edge of TiO₂-NAA-BDBRs' PSB, electronic bandgap, and absorbance band of model organics in harnessing visible photons for photocatalysis. Photodegradation reaction efficiency is optimal when the PSB's red edge is spectrally close to the electronic bandgap of the functional semiconductor coating. Photocatalytic performance decreases dramatically when the red edge of the PSB is shifted toward visible wavelengths. However, a photocatalytic recovery is observed when the PSB's red edge is judiciously positioned within the proximity of the absorption band of model organics, indicating that TiO₂-NAA-BDBRs can harness visible electromagnetic waves to speed up photocatalytic reactions by drastically slowing the group velocity of incident photons at specific spectral regions. Our advances provide new opportunities to better understand and engineer light-matter interactions for photocatalysis, using TiO₂-NAA-BDBRs as model nanoporous semiconductor platforms. These high-performing photocatalysts could find broad applicability in visible-NIR light harvesting for environmental remediation, green energy generation, and chemical synthesis.

Bioluminescent detection of isothermal DNA amplification in microfluidic generated droplets and artificial cells

Microfluidic droplet generation affords precise, low volume, high throughput opportunities for molecular diagnostics. Isothermal DNA amplification with bioluminescent detection is a fast, low-cost, highly specific molecular diagnostic technique that is triggerable by temperature. Combining loop-mediated isothermal nucleic acid amplification (LAMP) and bioluminescent assay in real time (BART), with droplet microfluidics, should enable high-throughput, low copy, sequence-specific DNA detection by simple light emission. Stable, uniform LAMP–BART droplets are generated with low cost equipment. The composition and scale of these droplets are controllable and the bioluminescent output during DNA amplification can be imaged and quantified. Furthermore these droplets are readily incorporated into encapsulated droplet interface bilayers (eDIBs), or artificial cells, and the bioluminescence tracked in real time for accurate quantification off chip. Microfluidic LAMP–BART droplets with high stability and uniformity of scale coupled with high throughput and low cost generation are suited to digital DNA quantification at low template concentrations and volumes, where multiple measurement partitions are required. The triggerable reaction in the core of eDIBs can be used to study the interrelationship of the droplets with the environment and also used for more complex chemical processing via a self-contained network of droplets, paving the way for smart soft-matter diagnostics.

Pore Structures for High-Throughput Nanopore Devices

Nanopore devices are expected to advance the next-generation of nanobiodevices because of their strong sensing and analyzing capabilities for single molecules and bioparticles. However, the device throughputs are not sufficiently high. Although analytes pass through a nanopore by electrophoresis, the electric field gradient is localized inside and around a nanopore structure. Thus, analytes located far from a nanopore cannot be driven by electrophoresis. Here, we report nanopore structures for high-throughput sensing, namely, inverted pyramid (IP)-shaped nanopore structures. Silicon-based IP-shaped nanopore structures create a homogeneous electric field gradient within a nanopore device, indicating that most of the analytes can pass through a nanopore by electrophoresis, even though the analytes are suspended far from the nanopore entrance. In addition, the nanostructures can be fabricated only by photolithography. The present study suggests a high potential for inverted pyramid shapes to serve as nanopore devices for high-throughput sensing.

Partially disordered nano-porous metallic oxide engineering: surface morphology controllability and multiple scattering properties

Random multiple light scattering in disordered photonics leads to interesting and unexpected physical phenomena. Here, we demonstrate two types of partially disordered nano-porous metallic oxide materials: disordered grating nano-pores and two-dimensional disordered nano-tubes, which are produced just with one-step anodic oxidation. The relations among the processing parameters, morphology properties and multiple scattering characteristics are investigated. The surface morphology controllability can be achieved by simply changing the processing direct voltages, leading to different scattering properties. The probabilistic model of partially disordered nano-porous metallic oxide is constructed according to the nano-structure characteristics of oxide, and the rigorous coupled wave analysis is utilized for optical field simulation to exhibit the theoretical multiple scattering properties. Futhermore, the experimental scattering fields are measured and are analysed by statistical method. The research focuses on the disorder caused by one-step oxidation, which is distinct from previous studies that introducing disorder into periodic materials, and would open up new prospects for sensing, bionics and structural color.

Critical Review: digital resolution biomolecular sensing for diagnostics and life science research

One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.

SERS Detection of Nucleobases in Single Silver Plasmonic Nanopores

Conventional ion current-based nanopore techniques that identify single molecules are hampered by limitations of providing only the ionic current information. Here, we introduce a silver nanotriangle-based nanopore (diameter < 50 nm) system for detecting molecule translocation using surface-enhanced Raman scattering. Rhodamine 6G is used as a model molecule to study the effect of an electric field (-1 V) on the mass transport. The four DNA bases also show significantly different SERS signals when they are transported into the plasmonic nanopore. The observations suggest that in the electric field, analyte molecules are driven into the nanopipette through the hot spot of the silver nanopore. The plasmonic nanopore shows great potential as a highly sensitive SERS platform for detecting molecule transport and paves the way for single molecule probing.

Evaluating the sensing performance of nanopore blockade sensors: A case study of prostate-specific antigen assay

The detection principle of nanopore sensors relies on measuring changes in electrical signal as analyte molecules translocate through a nanoscale pore. There are two challenges with this experimental construct when using nanopores for quantitative sensing with low detection limits in complex samples. The first is getting the analyte to the nanopore in a reasonable time frame and the second is other species in the sample also translocating through the nanopore and generating erroneous signals. We have developed a nanopore blockade sensor that alleviates the limitations of diffusion-limited mass transport and non-specific signals. Antibody-modified magnetic nanoparticles are utilized to deliver analytes of interest extracted from sample to an array of antibody-modified nanopores under a controlled electromagnet, resulting in long-term nanopore blocking events due to the formation of sandwiched immunocomplexes. Herein, this study reports on understanding some of important parameters in determining the performance of nanopore blockade sensing system, where prostate-specific antigen (PSA) is used as a model analyte. We describe the characterization of nanopore blockade sensing of PSA by (1) tuning on/off the electromagnet, (2) varying nanopore number in a nanopore chip, and (3) deploying the sensor in human plasma. Results show that magnetophoresis effectively facilitates active delivery and selective sensing of PSA to the nanopore. Nanopore chips with a larger number of nanopores are shown to receive more nanopore blockades for a given concentration of analyte. Furthermore, identifiable blockade events accounted for successful detection of PSA in plasma, indicate the high specificity of the sensing system.

Retarded Translocation of Nucleic Acids through α-Hemolysin Nanopore in the Presence of a Calcium Flux

Electrophysiological measurement of molecular translocation through a nanopore is the fundamental basis of nanopore sensing. Free translocation of nucleic acids however is normally so fast that the identities of the compounds are not clearly resolvable. Inspired by recent progress in fluorescence imaging based nanopore sensing, we found that during electrophysiology measurements, translocation of nucleic acids is also retarded whenever a calcium flux around the pore vicinity is established. The residence time of nucleic acids has been extended to tens of milliseconds, a result of the strong coupling between nucleic acids and free calcium ions. The methodology presented here is applicable to both DNAs and RNAs and is able to clearly discriminate between different RNA homopolymers. This offers new insights for calcium imaging based nanopore sensing and suggests a new strategy of electrophysiology-based nanopore sensing aimed at a retarded motion of nucleic acids.

Magnetic array-templated method for fabrication of polymer nanoporous films

This paper describes the development of a novel method of producing nanoporous polymeric membranes in a cost-effective and reproducible manner. The novelty of the technique hinges on the exploitation of a new type of sacrificial material & structures - self-assembled arrays of magnetic nanoparticles. The arrays are obtained through application of an external magnetic field to a thin layer of colloidal solution of superparamagnetic nanoparticles in a polymerizable monomer; this is followed by photopolymerisation. The resulting columnar structures form the pore templates which when selectively etched away leave an array of nanopores spanning across the polymeric film. The morphological characterisation of the nanopores by scanning electron microscopy and ionic conductivity revealed a very unusual sponge-like pore morphology. The applications which would benefit from the specific pore morphology and arrayed manufacturing are discussed.