Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing

Power and Sensitivity Management of Carbon Nanotube Transistor Glucose Biosensors

Continuous glucose monitoring (CGM), which is significant for the daily management of diabetes, requires a low-power-consumption sensor system that can track low nanomolar levels of glucose in physiological fluids, such as sweat and tears. However, traditional electrochemical methods are limited to analytes in micromolar to millimolar ranges and entail high power consumption. Carbon nanotube (CNT) film field-effect transistors (FETs) are promising for constructing extremely sensitive biosensors, but their wide applications in CGM are limited by the strong screening effect of physiological fluids and the zero charge of glucose molecules. In this study, we demonstrate a glucose aptamer-modified CNT FET biosensor to realize a highly sensitive CGM system with sub-nW power consumption by applying a suitable gate voltage. A positive gate voltage can enlarge the effective Debye screening length at the double layer to reduce the local ion population nearby and then improve the sensitivity of the FET-based biosensors by 5 times. We construct CNT FET sensors for CGM with a limit of detection of 0.5 fM, a record dynamic range up to 109, and a power consumption down to ∼100 pW. The proposed field-modulated sensing performance scheme is applicable to other aptamer-based FET biosensors for detecting neutral or less charged molecules and opens opportunities to develop facilely modulated, highly sensitive, low-power, and noninvasive CGM systems.

Challenges for Field-Effect-Transistor-Based Graphene Biosensors

Owing to its outstanding physical properties, graphene has attracted attention as a promising biosensor material. Field-effect-transistor (FET)-based biosensors are particularly promising because of their high sensitivity that is achieved through the high carrier mobility of graphene. However, graphene-FET biosensors have not yet reached widespread practical applications owing to several problems. In this review, the authors focus on graphene-FET biosensors and discuss their advantages, the challenges to their development, and the solutions to the challenges. The problem of Debye screening, in which the surface charges of the detection target are shielded and undetectable, can be solved by using small-molecule receptors and their deformations and by using enzyme reaction products. To address the complexity of sample components and the detection mechanisms of graphene-FET biosensors, the authors outline measures against nonspecific adsorption and the remaining problems related to the detection mechanism itself. The authors also introduce a solution with which the molecular species that can reach the sensor surfaces are limited. Finally, the authors present multifaceted approaches to the sensor surfaces that provide much information to corroborate the results of electrical measurements. The measures and solutions introduced bring us closer to the practical realization of stable biosensors utilizing the superior characteristics of graphene.

Wearing the Lab: Advances and Challenges in Skin-Interfaced Systems for Continuous Biochemical Sensing

Continuous, on-demand, and, most importantly, contextual data regarding individual biomarker concentrations exemplify the holy grail for personalized health and performance monitoring. This is well-illustrated for continuous glucose monitoring, which has drastically improved outcomes and quality of life for diabetic patients over the past 2 decades. Recent advances in wearable biosensing technologies (biorecognition elements, transduction mechanisms, materials, and integration schemes) have begun to make monitoring of other clinically relevant analytes a reality via minimally invasive skin-interfaced devices. However, several challenges concerning sensitivity, specificity, calibration, sensor longevity, and overall device lifetime must be addressed before these systems can be made commercially viable. In this chapter, a logical framework for developing a wearable skin-interfaced device for a desired application is proposed with careful consideration of the feasibility of monitoring certain analytes in sweat and interstitial fluid and the current development of the tools available to do so. Specifically, we focus on recent advancements in the engineering of biorecognition elements, the development of more robust signal transduction mechanisms, and novel integration schemes that allow for continuous quantitative analysis. Furthermore, we highlight the most compelling and promising prospects in the field of wearable biosensing and the challenges that remain in translating these technologies into useful products for disease management and for optimizing human performance.

Two-Dimensional Oxide Crystals for Device Applications: Challenges and Opportunities

Atomically thin two-dimensional (2D) oxide crystals have garnered considerable attention because of their remarkable physical properties and potential for versatile applications. In recent years, significant advancements have been made in the design, preparation, and application of ultrathin 2D oxides, providing many opportunities for new-generation advanced technologies. This review focuses on the controllable preparation of 2D oxide crystals and their applications in electronic and optoelectronic devices. Based on their bonding nature, the various types of 2D oxide crystals are first summarized, including both layered and nonlayered crystals, as well as their current top-down and bottom-up synthetic approaches. Subsequently, in terms of the unique physical and electrical properties of 2D oxides, recent advances in device applications are emphasized, including photodetectors, field-effect transistors, dielectric layers, magnetic and ferroelectric devices, memories, and gas sensors. Finally, conclusions and future prospects of 2D oxide crystals are presented. It is hoped that this review will provide comprehensive and insightful guidance for the development of 2D oxide crystals and their device applications.

Modular Aptamer Switches for the Continuous Optical Detection of Small-Molecule Analytes in Complex Media

Aptamers are a promising class of affinity reagents because signal transduction mechanisms can be built into the reagent, so that they can directly produce a physically measurable output signal upon target binding. However, endowing the signal transduction functionality into an aptamer remains a trial-and-error process that can compromise its affinity or specificity and typically requires knowledge of the ligand binding domain or its structure. In this work, a design architecture that can convert an existing aptamer into a "reversible aptamer switch" whose kinetic and thermodynamic properties can be tuned without a priori knowledge of the ligand binding domain or its structure is described. Finally, by combining these aptamer switches with evanescent-field-based optical detection hardware that minimizes sample autofluorescence, this study demonstrates the first optical biosensor system that can continuously measure multiple biomarkers (dopamine and cortisol) in complex samples (artificial cerebrospinal fluid and undiluted plasma) with second and subsecond-scale time responses at physiologically relevant concentration ranges.

Solid-State Nanopores for Biomolecular Analysis and Detection

Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.

Organic Electrochemical Transistor Aptasensor for Interleukin-6 Detection

We demonstrate an organic electrochemical transistor (OECT) biosensor for the detection of interleukin 6 (IL6), an important biomarker associated with various pathological processes, including chronic inflammation, inflammaging, cancer, and severe COVID-19 infection. The biosensor is functionalized with oligonucleotide aptamers engineered to bind specifically IL6. We developed an easy functionalization strategy based on gold nanoparticles deposited onto a poly(3,4-ethylenedioxythiophene) doped with polystyrenesulfonate (PEDOT:PSS) gate electrode for the subsequent electrodeposition of thiolated aptamers. During this functionalization step, the reduction of sulfide bonds allows for simultaneous deposition of a blocking agent. A detection range from picomolar to nanomolar concentrations for IL6 was achieved, and the selectivity of the device was assessed against Tumor Necrosis Factor (TNF), another cytokine involved in the inflammatory processes.

Electrochemical Aptamer-Based Biosensors for Measurements in Undiluted Human Saliva

Although blood remains a gold standard diagnostic fluid for most health exams, it involves an unpleasant and relatively invasive sampling procedure (finger pricking or venous draw). Saliva contains many relevant and useful biomarkers for diagnostic purposes, and its collection, in contrast, is noninvasive and can be obtained with minimal effort. Current saliva analyses are, however, achieved using chromatography or lateral flow assays, which, despite their high accuracy and sensitivity, can demand expensive laboratory-based instruments operated by trained personnel or offer only semiquantitative results. In response, we investigated electrochemical aptamer-based (E-AB) biosensors, a reagentless sensing platform, to allow for continuous and real-time measurements directly in undiluted, unstimulated human whole saliva. As a proof-of-concept study, we developed E-AB biosensors capable of detecting low-molecular-weight analytes (glucose and adenosine monophosphate (AMP)). To our knowledge, we report the first E-AB sensor for glucose, an approach that is inherently independent of its chemical reactivity in contrast to home glucometers. For these three sensors, we evaluated their figures of merits, stability, and reusability over short- and long-term exposure directly in saliva. In doing so, we found that E-AB sensors allow rapid and convenient molecular measurements in whole saliva with unprecedented sensitivities in the pico- to nanomolar regime and could be regenerated and reused up to 7 days when washed and stored in phosphate-buffered saline at room temperature. We envision that salivary molecular measurements using E-AB sensors are a promising alternative to invasive techniques and can be used for improved point-of-care clinical diagnosis and at-home measurements.

Capture-SELEX of DNA Aptamers for Sulforhodamine B and Fluorescein

While many dye binding aptamers have been reported, most of them were for light-up aptamers that can significantly enhance the quantum yield of fluorophores. Sulforhodamine B (SRhB) was used as a target previously to select both DNA and RNA aptamers, and the DNA aptamer was a G-quadruplex that can bind to a number of rhodamine analogs. In addition, the previous selections were performed by immobilizing the target molecules. In this work, the library immobilization method was used to respectively select aptamers for SRhB and fluorescein. The SRhB aptamer has a non-G-quadruplex structure with a Kd of 1.0 μM measured from isothermal titration calorimetry. Upon titration of the aptamer, the fluorescence of SRhB increased 2.5-fold, and this aptamer does not require Mg2+ for binding. Rhodamine B has even tighter binding suggesting binding through the xanthene moiety of the dyes. No binding was detected for fluorescein. For the fluorescein selection, a dominant aptamer sequence with a Kd of 147 μM was obtained. This study provides two new aptamers for two important fluorophores that can be used to study aptamer-based separation, dye detection and catalysis. Comparison of these aptamers also provides insights into the effect of functional groups on aptamer binding.

Advances in ligand-specific biosensing for structurally similar molecules

The specificity of biological systems makes it possible to develop biosensors targeting specific metabolites, toxins, and pollutants in complex medical or environmental samples without interference from structurally similar compounds. For the last two decades, great efforts have been devoted to creating proteins or nucleic acids with novel properties through synthetic biology strategies. Beyond augmenting biocatalytic activity, expanding target substrate scopes, and enhancing enzymes' enantioselectivity and stability, an increasing research area is the enhancement of molecular specificity for genetically encoded biosensors. Here, we summarize recent advances in the development of highly specific biosensor systems and their essential applications. First, we describe the rational design principles required to create libraries containing potential mutants with less promiscuity or better specificity. Next, we review the emerging high-throughput screening techniques to engineer biosensing specificity for the desired target. Finally, we examine the computer-aided evaluation and prediction methods to facilitate the construction of ligand-specific biosensors.

Advances in Bioelectrode Design for Developing Electrochemical Biosensors

The critical performance factors such as selectivity, sensitivity, operational and storage stability, and response time of electrochemical biosensors are governed mainly by the function of their key component, the bioelectrode. Suitable design and fabrication strategies of the bioelectrode interface are essential for realizing the requisite performance of the biosensors for their practical utility. A multifaceted attempt to achieve this goal is visible from the vast literature exploring effective strategies for preparing, immobilizing, and stabilizing biorecognition elements on the electrode surface and efficient transduction of biochemical signals into electrical ones (i.e., current, voltage, and impedance) through the bioelectrode interface with the aid of advanced materials and techniques. The commercial success of biosensors in modern society is also increasingly influenced by their size (and hence portability), multiplexing capability, and coupling in the interface of the wireless communication technology, which facilitates quick data transfer and linked decision-making processes in real-time in different areas such as healthcare, agriculture, food, and environmental applications. Therefore, fabrication of the bioelectrode involves careful selection and control of several parameters, including biorecognition elements, electrode materials, shape and size of the electrode, detection principles, and various fabrication strategies, including microscale and printing technologies. This review discusses recent trends in bioelectrode designs and fabrications for developing electrochemical biosensors. The discussions have been delineated into the types of biorecognition elements and their immobilization strategies, signal transduction approaches, commonly used advanced materials for electrode fabrication and techniques for fabricating the bioelectrodes, and device integration with modern electronic communication technology for developing electrochemical biosensors of commercial interest.

Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets

Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In particular, divalent cations (Mg2+ and Ca2+) present in brain fluid, have been shown to affect the conformational dynamics of aptamers upon target recognition. Thus, for biosensors that transduce aptamer structure switching as the signal response, it is critical to interrogate the influence of divalent cations on each unique aptamer sequence. Herein, we demonstrate the potential of molecular dynamics (MD) simulations to predict the behaviour of dopamine and serotonin aptamers on sensor surfaces. The simulations enable molecular-level visualization of aptamer conformational changes that, in some cases, are significantly influenced by divalent cations. The correlations of theoretical simulations with experimental findings validate the potential for MD simulations to predict aptamer-specific behaviors on biosensors.

Apta FastZ: An Algorithm for the Rapid Identification of Aptamers with Defined Binding Affinities

Real-time biomolecular monitoring requires biosensors based on affinity reagents, such as aptamers, with moderate to low affinities for the best binding dynamics and signal gain. We recently reported Pro-SELEX, an approach that utilizes parallelized SELEX and high-content bioinformatics for the selection of aptamers with predefined binding affinities. The Pro-SELEX pipeline relies on an algorithm, termed AptaZ, that can predict the binding affinities of selected aptamers. The original AptaZ algorithm is computationally complex and slows the overall throughput of Pro-SELEX. Here, we present Apta FastZ, a rapid equivalent of AptaZ. The Apta FastZ algorithm considers the spare nature of the sequences from SELEX and is coded to avoid unnecessary comparison between sequences. As a result, Apta FastZ achieved a 10 to 40-fold faster computing speed compared to the original AptaZ algorithm while maintaining identical outcomes, allowing the bioinformatics to be completed within 1-10 h for large-scale data sets. We further validated the affinity of myeloperoxidase aptamers predicted by Apta FastZ by experiments and observed a high level of linear correlation between predicted scores and measured affinities. Taken together, the implementation of Apta FastZ could greatly accelerate the current Pro-SELEX workflow, allowing customized aptamers to be discovered within 3 days using preselected DNA libraries.

Interface-Engineered Field-Effect Transistor Electronic Devices for Biosensing

Promising advances in molecular medicine have promoted the urgent requirement for reliable and sensitive diagnostic tools. Electronic biosensing devices based on field-effect transistors (FETs) exhibit a wide range of benefits, including rapid and label-free detection, high sensitivity, easy operation, and capability of integration, possessing significant potential for application in disease screening and health monitoring. In this perspective, the tremendous efforts and achievements in the development of high-performance FET biosensors in the past decade are summarized, with emphasis on the interface engineering of FET-based electrical platforms for biomolecule identification. First, an overview of engineering strategies for interface modulation and recognition element design is discussed in detail. For a further step, the applications of FET-based electrical devices for in vitro detection and real-time monitoring in biological systems are comprehensively reviewed. Finally, the key opportunities and challenges of FET-based electronic devices in biosensing are discussed. It is anticipated that a comprehensive understanding of interface engineering strategies in FET biosensors will inspire additional techniques for developing highly sensitive, specific, and stable FET biosensors as well as emerging designs for next-generation biosensing electronics.

Real-time selective detection of dopamine and serotonin at nanomolar concentration from complex in vitro systems

Electrochemical sensors provide means for real-time monitoring of neurotransmitter release events, which is a relatively easy process in simple electrolytes. However, this does not apply to in vitro environments. In cell culture media, competitively adsorbing molecules are present at concentrations up to 350 000-fold excess compared to the neurotransmitter-of-interest. Because detection of dopamine and serotonin requires direct adsorption of the analyte to electrode surface, a significant loss of sensitivity occurs when recording is performed in the in vitro environment. Despite these challenges, our single-walled carbon nanotube (SWCNT) sensor was capable of selectively measuring dopamine and serotonin from cell culture medium at nanomolar concentration in real-time. A primary midbrain culture was used to prove excellent biocompatibility of our SWCNT electrodes, which is a necessity for brain-on-a-chip models. Most importantly, our sensor was able to electrochemically record spontaneous transient activity from dopaminergic cell culture without altering the culture conditions, which has not been possible earlier. Drug discovery and development requires high-throughput screening of in vitro models, being hindered by the challenges in non-invasive characterization of complex neuronal models such as organoids. Our neurotransmitter sensors could be used for real-time monitoring of complex neuronal models, providing an alternative tool for their characterization non-invasively.

A liquid crystal-based sensor exploiting the aptamer-mediated recognition at the aqueous/liquid crystal interface for sensitive detection of serotonin

We report here a liquid crystal (LC)-based sensor for detecting serotonin (5-HT); the proposed sensor uses target-specific aptamer recognition at a cationic surfactant decorated-aqueous/LC interface. Our detection strategy focuses on the orientational transition of LCs upon biological interactions at the interface. In this sensing system, the cationic surfactant hexadecyltrimethylammonium bromide (CTAB) forms a self-assembled monolayer at the aqueous/LC interface and triggers the homeotropic orientation of LCs. After introducing the 5-HT specific aptamer, an electrostatic attraction occurs between the cationic CTAB and anionic aptamer. This interaction destructs the surfactant monolayer at the interface, inducing reorganization of LC alignment from homeotropic to tilted conditions. In the increasing 5-HT levels, specific binding between 5-HT and the aptamer diminishes the interaction between the aptamer and CTAB, thereby maintaining the homeotropic alignment of LCs. The orientational transition of the LCs was observed under a polarized optical microscope. The developed biosensor has a linear detection range from 1 to 1000 nM and a detection limit of 1.68 nM. Moreover, the sensor was applied to a human urine sample and a detection limit of 2.25 nM was obtained. Overall, the designed LC-based sensor is a sensitive, simple, cost effective, and selective platform for detecting 5-HT in aqueous solutions.

Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano- and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein-protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.

Affinity-Switchable Interaction of Biotin and Streptavidin for the Signal-ON Detection of Small Molecules

Lateral flow assay (LFA) based on gold nanoparticles (AuNPs) is a widely used analytical device for the rapid analysis of environmental hazards and biomarkers. Typically, a sandwich-type format is used for macromolecule detection, in which the appearance of a red test line indicates a positive result (Signal-ON). In contrast, small molecule detection usually relies on a competitive assay, where the absence of a test line indicates positive testing (Signal-OFF). However, such a "Signal-OFF" reading is usually detected within a narrower dynamic range and tends to generate false-negative signals at a low concentration. Moreover, inconsistent readings between macromolecule and small molecule testing might lead to misinterpretation when used by nonskilled individuals. Herein, we report a "Signal-ON" small molecule competitive assay based on the sterically modulated affinity-switchable interaction of biotin and streptavidin. In the absence of a small molecule target, a large steric hindrance can be imposed on the biotin to prevent interaction with streptavidin. However, in the presence of the small molecule target, this steric effect is removed, allowing the biotin to bind to streptavidin and generate the desired test line. In this article, we demonstrate the selective detection of two small molecule drugs, sulfonamides and trimethoprim, using this simple and modular affinity-switchable lateral flow assay (ASLFA). We believe that this affinity-switchable approach can also be adapted in drug discovery and clinical diagnosis, where the competitive assay format is always used for the rapid analysis of small molecules.

Continuous Real-Time Detection of Serotonin Using an Aptamer-Based Electrochemical Biosensor

Serotonin (5-HT) is a critical neurotransmitter involved in many neuronal functions, and 5-HT depletion has been linked to several mental diseases. The fast release and clearance of serotonin in the extracellular space, low analyte concentrations, and a multitude of interfering species make the detection of serotonin challenging. This work presents an electrochemical aptamer-based biosensing platform that can monitor 5-HT continuously with high sensitivity and selectivity. Our electrochemical sensor showed a response time of approximately 1 min to a step change in the serotonin concentration in continuous monitoring using a single-frequency EIS (electrochemical impedance spectroscopy) technique. The developed sensing platform was able to detect 5-HT in the range of 25-150 nM in the continuous sample fluid flow with a detection limit (LOD) of 5.6 nM. The electrochemical sensor showed promising selectivity against other species with similar chemical structures and redox potentials, including dopamine (DA), norepinephrine (NE), L-tryptophan (L-TP), 5-hydroxyindoleacetic acid (5-HIAA), and 5-hydroxytryptophan (5-HTP). The proposed sensing platform is able to achieve high selectivity in the nanomolar range continuously in real-time, demonstrating the potential for monitoring serotonin from neurons in organ-on-a-chip or brain-on-a-chip-based platforms.

Multiplexed SELEX for Sulfonamide Antibiotics Yielding a Group-Specific DNA Aptamer for Biosensors

The widespread use of sulfonamide (SA) antibiotics in animal husbandry has led to residues of SAs in the environment, causing adverse effects to the ecosystem and a risk of bacterial resistance, which is a potential threat to public health. Therefore, it is highly desirable to develop simple, high-throughput methods that can detect multiple SAs simultaneously. In this study, we isolated aptamers with different specificities based on a multi-SA systematic evolution of ligands by the exponential enrichment (SELEX) strategy using a mixture of sulfadimethoxine (SDM), sulfaquinoxaline (SQX), and sulfamethoxazole (SMZ). Three aptamers were obtained, and one of them showed a similar binding to all tested SAs, with dissociation constant (Kd) ranging from 0.22 to 0.63 μM. For the other two aptamers, one is specific for SQX, and the other is specific for SDM and sulfaclozine. A label-free detection method based on the broad-specificity aptamer was developed for the simultaneous detection of six SAs, with detection of limits ranging from 0.14 to 0.71 μM in a lake water sample. The aptasensor has no binding for other broad-spectrum antibiotics such as β-lactam antibiotics, quinolones, tetracyclines, and chloramphenicol. This work provides a promising biosensor for rapid, multiresidue, and high-throughput detection of SAs, as well as a shortcut for the preparation of different specific recognition elements required for the detection of broad-spectrum antibiotics.

Highly Uniform DNA Monolayers Generated by Freezing-Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood

Assembling DNA on solid surfaces is fundamental to surface-based DNA technology. However, precise control over DNA conformation and organization at solid-liquid interfaces remains a challenge, resulting in limited stability and sensitivity in biosensing applications. We herein communicate a simple and robust method for creating highly uniform DNA monolayers on gold surfaces by a freeze-thawing process. Using Raman spectroscopy, fluorescent imaging, and square wave voltammetry, we demonstrate that thiolated DNA is concentrated and immobilized on gold surfaces with an upright conformation. Moreover, our results reveal that the freezing-induced DNA surfaces are more uniform, leading to improved DNA stability and target recognition. Lastly, we demonstrate the successful detection of a model drug in undiluted whole blood while mitigating the effects of biofouling. Our work not only provides a simple approach to tailor the DNA-gold surface for biosensors but also sheds light on the unique behavior of DNA oligonucleotides upon freezing on the liquid-solid interface.

Detecting and differentiating neurotransmitters using ultraviolet plasmonic engineered native fluorescence

Detecting neurotransmitters with high sensitivity and selectivity is important to understand their roles in biological functions. Current detection methods for neurotransmitters suffer from poor sensitivity or selectivity. In this article, we propose ultraviolet (UV) plasmonic engineered native fluorescence as a new sensing mechanism to detect neurotransmitters with high sensitivity and selectivity. We measured the native fluorescence of three monoamine neurotransmitters, dopamine (DA), norepinephrine (NE), and 3,4-dihydroxyphenylacetic acid (DOPAC). The average net enhancement and total photon yield enhancement on an aluminum hole array with 300 nm hole spacing substrate were found to be 50× and 60×, for the three molecules. We also observed a 1.5-1.7× reduction in the dominant photon bleaching rate on an aluminum hole array compared to an aluminum-thin film substrate. The photobleaching rates of the native fluorescence of DA, NE and DOPAC were found to be highly sensitive to their molecular structures and can be further engineered by UV plasmonic substrates. The differences in the photobleaching rates for DA and NE were 2× and 1.6× larger on an aluminum thin film and an aluminum hole array than on a silicon substrate. As a proof-of-concept experiment, we mixed DA with NE at different concentration ratios and measured the average photobleaching rates of the mixture. We found that the average photobleaching rate is proportional to the concentration of NE in the mixture. Our findings demonstrate the potential of UV plasmonic engineered native fluorescence to achieve sensitive and selective detection of neurotransmitters.

Covalent functionalisation controlled by molecular design for the aptameric recognition of serotonin in graphene-based field-effect transistors

In the last decade, solution-gated graphene field effect transistors (GFETs) showed their versatility in the development of a miniaturized multiplexed platform for electrophysiological recordings and sensing. Due to their working mechanism, the surface functionalisation and immobilisation of receptors are pivotal to ensure the proper functioning of devices. Herein, we present a controlled covalent functionalisation strategy based on molecular design and electrochemical triggering, which provide a monolayer-like functionalisation of micro-GFET arrays retaining the electronic properties of graphenes. The functionalisation layer as a receptor was then employed as the linker for serotonin aptamer conjugation. The micro-GFET arrays display sensitivity toward the target analyte in the micromolar range in a physiological buffer (PBS 10 mM). The sensor allows the in-flow real-time monitoring of serotonin transient concentrations with fast and reversible responses.

Supramolecular Nucleic Acid-Based Organosilica Nanoparticles Responsive to Physical and Biological Inputs

Organosilica nanoparticles that contain responsive organic building blocks as constitutive components of the silica network offer promising opportunities for the development of innovative drug formulations, biomolecule delivery, and diagnostic tools. However, the synthetic challenges required to introduce dynamic and multifunctional building blocks have hindered the realization of biomimicking nanoparticles. In this study, capitalizing on our previous research on responsive nucleic acid-based organosilica nanoparticles, we combine the supramolecular programmability of nucleic acid (NA) interactions with sol-gel chemistry. This approach allows us to create dynamic supramolecular bridging units of nucleic acids in a silica-based scaffold. Two peptide nucleic acid-based monoalkoxysilane derivatives, which self-assemble into a supramolecular bis-alkoxysilane through direct base pairing, were chosen as the noncovalent units inserted into the silica network. In addition, a bridging functional NA aptamer leads to the specific recognition of ATP molecules. In a one-step bottom-up approach, the resulting supramolecular building blocks can be used to prepare responsive organosilica nanoparticles. The supramolecular Watson-Crick-Franklin interactions of the organosilica nanoparticles result in a programmable response to external physical (i.e., temperature) and biological (i.e., DNA and ATP) inputs and thus pave the way for the rational design of multifunctional silica materials with application from drug delivery to theranostics.

Peptide-Functionalized Carbon Nanotube Chemiresistors: The Effect of Nanotube Density on Gas Sensing

Biorecognition element (BRE)-based carbon nanotube (CNT) chemiresistors have tremendous potential to serve as highly sensitive, selective, and power-efficient volatile organic compound (VOC) sensors. While many research groups have studied BRE-functionalized CNTs in material science and device development, little attention has been paid to optimizing CNT density to improve chemiresistor performance. To probe the effect of CNT density on VOC detection, we present the chemiresistor-based sensing results from two peptide-based CNT devices counting more than 60 different individual measurements. We find that a lower CNT density shows a significantly higher noise level and device-to-device variation while exhibiting mildly better sensitivity. Further investigation with SEM images suggests that moderately high CNT density with a stable connection of the nanotube network is desirable to achieve the best signal-to-noise ratio. Our results show an essential design guideline for tuning the nanotube density to provide sensitive and stable chemiresistors.

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.

Molecularly Imprinted Polymer Interface on Screen-Printed ZnO Nanorod Field Effect Transistors for Serotonin Detection in Clinical Samples

Ultrasensitive detection of serotonin is crucial for the early diagnosis of several diseases like Parkinson's and Alzheimer's. Most of the existing detection strategies are still not suitable for sensitive point-of-care applications. This study presents direct molecular imprinting of serotonin on the surface of three-dimensional zinc oxide (ZnO) nanorod devices connected in a field effect transistor (FET) configuration to achieve ultrasensitive, real-time, and rapid detection with a convenient and affordable approach, which has significant potential for translation to clinical settings. This strategy has enabled pushing the detection limit to 0.1 fM in a physiological analyte in real time with screen-printed electrodes, thereby resulting in the convenient batch fabrication of sensors for clinical validation. The response of the sensor with the clinical sample has been correlated with that of the gold standard and has been observed to be statistically similar.

Highly Effective and Efficient Self-Assembled Multilayer-Based Electrode Passivation for Operationally Stable and Reproducible Electrolyte-Gated Transistor Biosensors

To ensure the operational stability of transistor-based biosensors in aqueous electrolytes during multiple measurements, effective electrode passivation is crucially important for reliable and reproducible device performances. This paper presents a highly effective and efficient electrode passivation method using a facile solution-processed self-assembled multilayer (SAML) with excellent insulation property to achieve operational stability and reproducibility of electrolyte-gated transistor (EGT) biosensors. The SAML is created by the consecutive self-assembly of three different molecular layers of 1,10-decanedithiol, vinyl-polyhedral oligomeric silsesquioxane, and 1-octadecanethiol. This passivation enables EGT to operate stably in phosphate-buffered saline (PBS) during repeated measurements over multiple cycles without short-circuiting. The SAML-passivated EGT biosensor is fabricated with a solution-processed In2O3 thin film as an amorphous oxide semiconductor working both as a semiconducting channel in the transistor and as a functionalizable biological interface for a bioreceptor. The SAML-passivated EGT including In2O3 thin film is demonstrated for the detection of Tau protein as a biomarker of Alzheimer's disease while employing a Tau-specific DNA aptamer as a bioreceptor and a PBS solution with a low ionic strength to diminish the charge-screening (Debye length) effect. The SAML-passivated EGT biosensor functionalized with the Tau-specific DNA aptamer exhibits ultrasensitive, quantitative, and reliable detection of Tau protein from 1 × 10-15 to 1 × 10-10 M, covering a much larger range than clinical needs, via changes in different transistor parameters. Therefore, the SAML-based passivation method can be effectively and efficiently utilized for operationally stable and reproducible transistor-based biosensors. Furthermore, this presented strategy can be extensively adapted for advanced biomedical devices and bioelectronics in aqueous or physiological environments.

Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers

Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.

Selection of regioselective DNA aptamer for detection of homocysteine in nondeproteinized human plasma

Small molecule-binding aptamers often suffer from high cross reactivity to structure analogues in biological samples, limiting their value for clinical diagnosis. Herein, we present a method to overcome this issue, by performing binding-inhibited organic reaction-based regioselective selection of aptamers against homocysteine (Hcy), which is a marker for diagnosing many disorders including stroke and Alzheimer's. This approach has led to isolation of a DNA aptamer that binds to the alkane thiol chain of Hcy with exceptional specificity against cysteine. It also binds with oxidized Hcy at weaker affinity. Using this new aptamer, we produced a reusable fluorescent optical fiber aptasensor for direct and validated detection of both free and total Hcy in nondeproteinized patient plasma in the diagnostic concentration range. The binding site-specific aptamer selection and optical-fiber-sensing strategy can expand the practical utility of aptamers in clinical diagnosis.

G-Quadruplex-Filtered Selective Ion-to-Ion Current Amplification for Non-Invasive Ion Monitoring in Real Time

Living cells efflux intracellular ions for maintaining cellular life, so intravital measurements of specific ion signals are of significant importance for studying cellular functions and pharmacokinetics. In this work, de novo synthesis of artificial K+ -selective membrane and its integration with polyelectrolyte hydrogel-based open-junction ionic diode (OJID) is demonstrated, achieving a real-time K+ -selective ion-to-ion current amplification in complex bioenvironments. By mimicking biological K+ channels and nerve impulse transmitters, in-line K+ -binding G-quartets are introduced across freestanding lipid bilayers by G-specific hexylation of monolithic G-quadruplex, and the pre-filtered K+ flow is directly converted to amplified ionic currents by the OJID with a fast response time at 100 ms intervals. By the synergistic combination of charge repulsion, sieving, and ion recognition, the synthetic membrane allows K+ transport exclusively without water leakage; it is 250× and 17× more permeable toward K+ than monovalent anion, Cl- , and polyatomic cation, N-methyl-d-glucamine+ , respectively. The molecular recognition-mediated ion channeling provides a 500% larger signal for K+ as compared to Li+ (0.6× smaller than K+ ) despite the same valence. Using the miniaturized device, non-invasive, direct, and real-time K+ efflux monitoring from living cell spheroids is achieved with minimal crosstalk, specifically in identifying osmotic shock-induced necrosis and drug-antidote dynamics.

Electrochemically-gated graphene broadband microwave waveguides for ultrasensitive biosensing

Identification of non-amplified DNA sequences and single-base mutations is essential for molecular biology and genetic diagnostics. This paper reports a novel sensor consisting of electrochemically-gated graphene coplanar waveguides coupled with a microfluidic channel. Upon exposure to analytes, propagation of electromagnetic waves in the waveguides is modified as a result of interactions with the fringing field and modulation of graphene dynamic conductivity resulting from electrostatic gating. Probe DNA sequences are immobilised on the graphene surface, and the sensor is exposed to DNA sequences which either perfectly match the probe, contain a single-base mismatch or are unrelated. By monitoring the scattering parameters at frequencies between 50 MHz and 50 GHz, unambiguous and reproducible discrimination of the different strands is achieved at concentrations as low as one attomole per litre (1 aM). By controlling and synchronising frequency sweeps, electrochemical gating, and liquid flow in the microfluidic channel, the sensor generates multidimensional datasets. Advanced data analysis techniques are utilised to take full advantage of the richness of the dataset. A classification accuracy >97% between all three sequences is achieved using different Machine Learning models, even in the presence of simulated noise and low signal-to-noise ratios. The sensor exceeds state-of-the-art sensitivity of field-effect transistors and microwave sensors for the identification of single-base mismatches.

Implantable Hydrogel-Protective DNA Aptamer-Based Sensor Supports Accurate, Continuous Electrochemical Analysis of Drugs at Multiple Sites in Living Rats

The ability to track the levels of specific molecules, such as drugs, metabolites, and biomarkers, in the living body, in real time and for long durations, would improve our understanding of health and our ability to diagnose, treat, and monitor disease. To this end, we are developing electrochemical aptamer-based (EAB) biosensors, a general platform supporting high-frequency, real-time molecular measurements in the living body. Here we report that the use of an agarose hydrogel protective layer for EAB sensors significantly improves their signaling stability when deployed in the complex, highly time-varying environments found in vivo. The improved stability is sufficient that these hydrogel-protected sensors achieved good baseline stability and precision when deployed in situ in the veins, muscles, bladder, or tumors of living rats without the use of the drift correction approaches traditionally required in such placements. Finally, our implantable gel-protective EAB sensors achieved good biocompatibility when deployed in vivo in the living rats without causing any severe inflammation.

Advances in field-effect biosensors towards point-of-use

The future of medical diagnostics calls for portable biosensors at the point of care, aiming to improve healthcare by reducing costs, improving access, and increasing quality-what is called the 'triple aim'. Developing point-of-care sensors that provide high sensitivity, detect multiple analytes, and provide real time measurements can expand access to medical diagnostics for all. Field-effect transistor (FET)-based biosensors have several advantages, including ultrahigh sensitivity, label-free and amplification-free detection, reduced cost and complexity, portability, and large-scale multiplexing. They can also be integrated into wearable or implantable devices and provide continuous, real-time monitoring of analytesin vivo, enabling early detection of biomarkers for disease diagnosis and management. This review analyzes advances in the sensitivity, parallelization, and reusability of FET biosensors, benchmarks the limit of detection of the state of the art, and discusses the challenges and opportunities of FET biosensors for future healthcare applications.

An antibody-based molecular switch for continuous small-molecule biosensing

We present a generalizable approach for designing biosensors that can continuously detect small-molecule biomarkers in real time and without sample preparation. This is achieved by converting existing antibodies into target-responsive "antibody-switches" that enable continuous optical biosensing. To engineer these switches, antibodies are linked to a molecular competitor through a DNA scaffold, such that competitive target binding induces scaffold switching and fluorescent signaling of changing target concentrations. As a demonstration, we designed antibody-switches that achieve rapid, sample preparation-free sensing of digoxigenin and cortisol in undiluted plasma. We showed that, by substituting the molecular competitor, we can further modulate the sensitivity of our cortisol switch to achieve detection at concentrations spanning 3.3 nanomolar to 3.3 millimolar. Last, we integrated this switch with a fiber optic sensor to achieve continuous sensing of cortisol in a buffer and blood with <5-min time resolution. We believe that this modular sensor design can enable continuous biosensor development for many biomarkers.

Dual-Aptamer Drift Canceling Techniques to Improve Long-Term Stability of Real-Time Structure-Switching Aptasensors

This paper presents a dual-aptamer scheme to mitigate signal drifts caused by structure-switching aptamers during long-term monitoring. Electrochemical aptamer-based (E-AB) biosensors have recently shown great potential for continuous in vivo monitoring. However, the accuracy of detection is often limited by signaling drifts. Traditional approaches rely on kinetic differential measurements (KDM) coupled with square-wave voltammetry to eliminate these drifts. Yet, we have discovered that KDM does not apply universally to all aptamers, as their responses at different SWV frequencies heavily rely on their structure-switching characteristics and the electron transfer (ET) kinetics of the redox reporters. In light of this, we propose a "dual-aptamer" scheme that utilizes two aptamers, each responding differently to the same target molecule to cancel out drift. These paired aptamers are identified through (1) screening from an existing pool of aptamers and (2) engineering the signaling behavior of the redox reporters. We demonstrate the differential signaling of the aptamer pair in the presence of ampicillin and ATP molecules and show that the pair exhibits similar drifts in undiluted goat serum. By implementing drift cancelation, sensor drift is reduced by a factor of 370. Additionally, the differential signaling enables an increased recording throughput by leveraging differential readout electronics. The authors believe that the proposed technique holds significant benefits for long-term in vivo monitoring.

Truncated Electrochemical Aptasensor with Enhanced Antifouling Capability for Highly Sensitive Serotonin Detection

Accurate determination of serotonin (ST) provides insight into neurological processes and enables applications in clinical diagnostics of brain diseases. Herein, we present an electrochemical aptasensor based on truncated DNA aptamers and a polyethylene glycol (PEG) molecule-functionalized sensing interface for highly sensitive and selective ST detection. The truncated aptamers have a small size and adopt a stable stem-loop configuration, which improves the accessibility of the aptamer for the analyte and enhances the sensitivity of the aptasensor. Upon target binding, these aptamers perform a conformational change, leading to a variation in the Faraday current of the redox tag, which was recorded by square wave voltammetry (SWV). Using PEG as blocking molecules minimizes nonspecific adsorption of other interfering molecules and thus endows an enhanced antifouling ability. The proposed electrochemical aptamer sensor showed a wide range of detection lasting from 0.1 nM to 1000 nM with a low limit of detection of 0.14 nM. Owing to the unique properties of aptamer receptors, the aptasensor also exhibits high selectivity and stability. Furthermore, with the reduced unspecific adsorption, assaying of ST in human serum and artificial cerebrospinal fluid (aCSF) showed excellent performance. The reported strategy of utilizing antifouling PEG describes a novel approach to building antifouling aptasensors and holds great potential for neurochemical investigations and clinical diagnosis.

Extended-Gate Field-Effect Transistor Consisted of a CD9 Aptamer and MXene for Exosome Detection in Human Serum

Cancer progresses silently to the terminal stage of the impossible operable condition. There are many limitations in the treatment options of cancer, but diagnosis in an early stage can improve survival rates and low recurrence. Exosomes are the biomolecules released from cancer cells and are promising candidates for clinical diagnosis. Among them, the cluster of differentiation 9 (CD9) protein is an important exosomal biomarker that can be used for exosome determination. Therefore, here, a CD9 aptamer was first synthesized and applied to an extended-gate field-effect transistor (EGFET)-type biosensor containing a disposable sensing membrane to suggest the possibility of detecting exosomes in a clinical environment. Systematically evaluating ligands using the exponential enrichment (SELEX) technique was performed to select nucleic acid sequences that can specifically target the CD9 protein. Exosomes were detected according to the electrical signal changes on a membrane, which is an extended gate using an Au microelectrode. The fabricated biosensor showed a limit of detection (LOD) of 10.64 pM for CD9 proteins, and the detection range was determined from 10 pM to 1 μM in the buffer. In the case of the clinical test, the LOD and detection ranges of exosomes in human serum samples were 6.41 × 102 exosomes/mL and 1 × 103 to 1 × 107 exosomes/mL, respectively, showing highly reliable results with low error rates. These findings suggest that the proposed aptasensor can be a powerful tool for a simple and early diagnosis of exosomes.

Capture-SELEX for Chloramphenicol Binding Aptamers for Labeled and Label-Free Fluorescence Sensing

Chloramphenicol (CAP) is a potent antibiotic. Due to its side effects, CAP is currently banned in most countries, but it is still found in many food products and in the environment. Developing aptamer-based biosensors for the detection of CAP has interested many researchers. While both RNA and DNA aptamers were previously reported for CAP, they were all obtained by immobilization of the CAP base, which omitted the two chlorine atoms. In this work, DNA aptamers were selected using the library-immobilized method and free unmodified CAP. Three families of aptamers were obtained, and the best one named CAP1 showed a dissociation constant (Kd) of 9.8 μM using isothermal titration calorimetry (ITC). A fluorescent strand-displacement sensor showed a limit of detection (LOD) of 14 μM CAP. Thioflavin T (ThT) staining allowed label-free detection of CAP with a LOD of 1 μM in buffer, 1.8 μM in Lake Ontario water, and 3.6 μM in a wastewater sample. Comparisons were made with previously reported aptamers, and ITC failed to show binding of a previously reported 80-mer aptamer. Due to the small size and well-defined secondary structures of CAP1, this aptamer will find analytical applications for environmental and food monitoring.

Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer

The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.

Cross-Binding of Four Adenosine/ATP Aptamers to Caffeine, Theophylline, and Other Methylxanthines

The classical DNA aptamer for adenosine and ATP was selected twice using ATP as the target in 1995 and 2005, respectively. In 2022, this motif appeared four more times from selections using adenosine, ATP, theophylline, and caffeine as targets, suggesting that this aptamer can also bind methylxanthines. In this work, using thioflavin T fluorescence spectroscopy, this classical DNA aptamer showed Kd values for adenosine, theophylline, and caffeine of 9.5, 101, and 131 μM, respectively, and similar Kd values were obtained using isothermal titration calorimetry. Binding to the methylxanthines was also observed for the newly selected Ade1301 aptamer but not for the Ade1304 aptamer. The RNA aptamer for ATP also had no binding to the methylxanthines. Molecular dynamics simulations were performed using the classical DNA and RNA aptamers based on their NMR structures, and the simulation results were consistent with the experimental observations, explaining the selectivity profiles. This study suggests that a broader range of target analogues need to be tested for aptamers. For the detection of adenosine and ATP, the Ade1304 aptamer is a better choice due to its better selectivity.

Amplification-Free Detection of SARS-CoV-2 Down to Single Virus Level by Portable Carbon Nanotube Biosensors

The rapid and sensitive detection of trace-level viruses in a simple and reliable way is of great importance for epidemic prevention and control. Here, a multi-functionalized floating gate carbon nanotube field effect transistor (FG-CNT FET) based biosensor is reported for the single virus level detection of SARS-CoV-2 virus antigen and RNA rapidly with a portable sensing platform. The aptamers functionalized sensors can detect SARS-CoV-2 antigens from unprocessed nasopharyngeal swab samples within 1 min. Meanwhile, enhanced by a multi-probe strategy, the FG-CNT FET-based biosensor can detect the long chain RNA directly without amplification down to single virus level within 1 min. The device, constructed with packaged sensor chips and a portable sensing terminal, can distinguish 10 COVID-19 patients from 10 healthy individuals in clinical tests both by the RNAs and antigens by a combination detection strategy with an combined overall percent agreement (OPA) close to 100%. The results provide a general and simple method to enhance the sensitivity of FET-based biochemical sensors for the detection of nucleic acid molecules and demonstrate that the CNT FG FET biosensor is a versatile and reliable integrated platform for ultrasensitive multibiomarker detection without amplification and has great potential for point-of-care (POC) clinical tests.

Multiplex Protein Profiling by Low-Signal-Loss Single-Cell Western Blotting with Fluorescent-Quenching Aptamers

Single-cell western blotting (scWB) is a prevalent technique for high-resolution protein analysis on low-abundance cell samples. However, the extensive signal loss during repeated antibody stripping precludes multiplex protein detection. Herein, we introduce Fluorescent-quenching Aptamer-based Single-cell Western Blotting (FAS-WB) for multiplex protein detection at single-cell resolution. The minimal size of aptamer probes allows rapid in-gel penetration, diffusion, and elution. Meanwhile, the fluorophore-tagged aptamers, coordinated with complementary quenching strands, avoid the massive signal loss conventionally caused by antibody stripping during repeated staining. Such a strategy also facilitates multiplex protein analysis with a limited number of fluorescent tags. We demonstrated FAS-WB for co-imaging four biomarker proteins (EpCAM, PTK7, HER2, CA125) at single-cell resolution with lower signal loss and enhanced signal-to-noise ratio compared to conventional antibody-based scWB. Being more time-saving (less than 25 min per cycle) and economical (1/1000 cost of conventional antibody probes), FAS-WB offers a highly efficient platform for profiling multiplex proteins at single-cell resolution.

Rapid genetic screening with high quality factor metasurfaces

Genetic analysis methods are foundational to advancing personalized medicine, accelerating disease diagnostics, and monitoring the health of organisms and ecosystems. Current nucleic acid technologies such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) rely on sample amplification and can suffer from inhibition. Here, we introduce a label-free genetic screening platform based on high quality (high-Q) factor silicon nanoantennas functionalized with nucleic acid fragments. Each high-Q nanoantenna exhibits average resonant quality factors of 2,200 in physiological buffer. We quantitatively detect two gene fragments, SARS-CoV-2 envelope (E) and open reading frame 1b (ORF1b), with high-specificity via DNA hybridization. We also demonstrate femtomolar sensitivity in buffer and nanomolar sensitivity in spiked nasopharyngeal eluates within 5 minutes. Nanoantennas are patterned at densities of 160,000 devices per cm2, enabling future work on highly-multiplexed detection. Combined with advances in complex sample processing, our work provides a foundation for rapid, compact, and amplification-free molecular assays.

Nanomaterials enabled and enhanced DNA-based biosensors

DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to physically detectable signals, various nanomaterials have been extensively exploited to take advantage of their optical and surface properties. A popular sensing scheme is through the adsorption of a fluorescently-labeled DNA probe, where detection is achieved by target-induced probe desorption and fluorescence recovery. Another method is to use DNA to protect the colloidal stability of nanomaterials, where subsequent target binding can decrease the protection ability and induce aggregation; this method has mainly been used for gold nanoparticles. This Perspective summarizes some of our work in examining the sensing mechanisms, and we articulate the importance of the understanding of DNA/surface and target/surface interactions for the development of practical DNA-based biosensors.

Tools and techniques for the discovery of therapeutic aptamers: recent advances

INTRODUCTION

The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers.

AREAS COVERED

The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility.

EXPERT OPINION

The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.

Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor

Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.

Triple-Peak Photoluminescence of DNA-Hybrid Alq3 Crystals Emitting a Depressed Single Peak upon Bio-Recognition

The green organic semiconductor, tris-(8-hydroxyquinoline)aluminum (Alq₃), was hybridized with DNA growing in the shape of hexagonal prismatic crystals. In this study, we applied hydrodynamic flow to the fabrication of Alq₃ crystals doped with DNA molecules. The hydrodynamic flow in the Taylor-Couette reactor induced nanoscale pores in the Alq₃ crystals, especially at the side part of the particles. The particles exhibited distinctly different photoluminescence emissions divided into three parts compared to common Alq₃-DNA hybrid crystals. We named this particle a "three-photonic-unit". After treatment with complementary target DNA, the three-photonic-unit Alq₃ particles doped with DNAs were found to emit depressed luminescence from side parts of the particles. This novel phenomenon would expand the technological value of these hybrid crystals with divided photoluminescence emissions toward a wider range of bio-photonic applications.

A functional group-guided approach to aptamers for small molecules

Aptameric receptors are important biosensor components, yet our ability to identify them depends on the target structures. We analyzed the contributions of individual functional groups on small molecules to binding within 27 target-aptamer pairs, identifying potential hindrances to receptor isolation-for example, negative cooperativity between sterically hindered functional groups. To increase the probability of aptamer isolation for important targets, such as leucine and voriconazole, for which multiple previous selection attempts failed, we designed tailored strategies focused on overcoming individual structural barriers to successful selections. This approach enables us to move beyond standardized protocols into functional group-guided searches, relying on sequences common to receptors for targets and their analogs to serve as anchors in regions of vast oligonucleotide spaces wherein useful reagents are likely to be found.

Plug-and-play fiber-optic sensors based on engineered cells for neurochemical monitoring at high specificity in freely moving animals

In vivo detection of neurochemicals, including neurotransmitters and neuromodulators, is critical for both understanding brain mechanisms and diagnosing brain diseases. However, few sensors are competent in monitoring neurochemical dynamics in vivo at high specificity. Here, we propose the fiber-optic probes based on engineered cells (FOPECs) for plug-and-play, real-time detection of neurochemicals in freely moving animals. Taking advantages of life-evolved neurochemical receptors as key components, the chemical specificity of FOPECs is unprecedented. We demonstrate the applications of FOPECs in real-time monitoring of neurochemical dynamics under various physiology and pathology conditions. With no requirement of viral infection in advance and no dependence on animal species, FOPECs can be widely adopted in vertebrates, such as mice, rats, rabbits, and chickens. Moreover, FOPECs can be used to monitor drug metabolisms in vivo. We demonstrated the neurochemical monitoring in blood circulation systems in vivo. We expect that FOPECs will benefit not only neuroscience study but also drug discovery.