Direct detection of human adenovirus or SARS-CoV-2 with ability to inform infectivity using DNA aptamer-nanopore sensors

Molecular engineering of functional DNA molecules toward point-of-care diagnostic devices

The pursuit of rapid, sensitive, and specific diagnostic methodologies is imperative across diverse applications, including the detection of pathogens and disease biomarkers, food safety testing and environmental monitoring. Point-of-care testing (POCT) is characterized by its portability, ease of use, rapidity, and affordability, emerging as an attractive alternative for traditional diagnostics. Over recent years, the incorporation of functional DNA (fDNA) into POC diagnostic devices has emerged as a groundbreaking advancement, significantly enhancing sensitivity, specificity, and user-friendliness. In this review, we explore the innovative applications of fDNA in POC devices, highlighting its potential to revolutionize diagnostics by providing rapid, portable, and precise solutions. We discuss the unique advantages of fDNA, including its stability in complex biological matrices and its ability to recognize a wide range of targets. Furthermore, we explore the potential synergy between fDNA and cutting-edge technologies, such as nanotechnology and artificial intelligence (AI), to forge a path toward more personalized and accessible healthcare solutions. Despite significant progress, challenges remain in translating these innovations from the bench to the clinic. This review aims to provide a comprehensive overview of the current status of fDNA-based POCT devices and future directions for their development, emphasizing their critical role in meeting the global demand for accessible, efficient, and precise diagnostic solutions.

Elucidating the molecular docking and binding dynamics of aptamers with spike proteins across SARS-CoV-2 variants of concern

DNA aptamers with high binding affinity against SARS-CoV-2 spike proteins have been selected and analyzed. To better understand the binding affinities between DNA aptamers and spike proteins (S-proteins) of relevant variants of concerns (VOCs), in silico and in vitro characterization are excellent approaches to implement. Here, we identified and generated DNA aptamer sequences targeting the S-protein of SARS-CoV-2 VOCs through systematic evolution of ligands by exponential enrichment (SELEX). In silico, prediction of aptamer binding was conducted, followed by a step-by-step workflow for secondary and tertiary aptamer structures determination, modeling, and molecular docking to target S-protein. The in silico strategy was limited to only providing predictions of possible outcomes based on scores, and ranking was complemented by characterization and analysis of identified DNA aptamers using a direct enzyme-linked oligonucleotides assay (ELONA), which showed dissociation constants (K d) within the 32 nM-193 nM range across the three significant VOCs. These three highly specific VOCs aptamers (Alpha Apt, Delta Apt, and Omicron Apt) can be further studied as potential candidates for both diagnostic and therapeutic applications.

Aptamer and DNAzyme Based Colorimetric Biosensors for Pathogen Detection

The detection of pathogens is critical for preventing and controlling health hazards across clinical, environmental, and food safety sectors. Functional nucleic acids (FNAs), such as aptamers and DNAzymes, have emerged as versatile molecular tools for pathogen detection due to their high specificity and affinity. This review focuses on the in vitro selection of FNAs for pathogens, with emphasis on the selection of aptamers for specific biomarkers and intact pathogens, including bacteria and viruses. Additionally, the selection of DNAzymes for bacterial detection is discussed. The integration of these FNAs into colorimetric biosensors has enabled the development of simple, cost-effective diagnostic platforms. Both non-catalytic and catalytic colorimetric biosensors are explored, including those based on gold nanoparticles, polydiacetylenes, protein enzymes, G-quadruplexes, and nanozymes. These biosensors offer visible detection through color changes, making them ideal for point-of-care diagnostics. The review concludes by highlighting current challenges and future perspectives for advancing FNA-based colorimetric biosensing technologies for pathogen detection.

Fighting Mutations with Mutations: Evolutionarily Adapting a DNA Aptamer for High-Affinity Recognition of Mutated Spike Proteins of SARS-CoV-2

An on-going challenge with COVID-19, which has huge implications for future pandemics, is the rapid emergence of viral variants that makes diagnostic tools less accurate, calling for rapid identification of recognition elements for detecting new variants caused by mutations. We hypothesize that we can fight mutations of the viruses with mutations of existing recognition elements. We demonstrate this concept via rapidly evolving an existing DNA aptamer originally selected for the spike protein (S-protein) of wildtype SARS-CoV-2 to enhance the interaction with the same protein of the Omicron variants. The new aptamer, MBA5SA1, has acquired 22 mutations within its 40-nucleotide core sequence and improved its binding affinity for the S-proteins of diverse Omicron subvariants by >100-fold compared to its parental aptamer (improved from nanomolar to picomolar affinity). Deep sequencing analysis reveals dynamic competitions among several MBA5SA1 variants in response to increasing selection pressure imposed during in vitro selection, with MBA5SA1 being the final winner of the competition. Additionally, MBA5SA1 was implemented into an enzyme-linked aptamer binding assay (ELABA), which was applied for detecting Omicron variants in the saliva of infected patients. The assay produced a sensitivity of 86.5 % and a specificity of 100 %, which were established with 83 clinical samples.

Sensing creatinine in urine via the iontronic response of enzymatic single solid-state nanochannels

In this study, we investigate the integration of the enzyme creatinine deiminase into solid-state nanopore walls through electrostatic assembly for the development of creatinine sensors. In these asymmetric single nanochannels, ionic transport is determined by the surface charge inside the channel, resulting in diode-like behavior that rectifies ionic current. The efficiency of such rectification depends on the surface charge density. In the presence of creatinine, the enzymatic reaction generates ammonium, leading to an increase in local pH near the channel, which can be detected through changes in transmembrane ionic transport response. Changes in rectification efficiency can be well correlated with the analyte concentration, allowing for a detection limit of 5 nM creatinine. Furthermore, this solid-state nanopore-based device is capable of sensing in diluted urine samples, showing a good linear correlation between the response and the logarithm of the creatinine concentration over a wide range of concentrations (50 nM-100 μM). These results demonstrate the potential of systems based on the integration of enzymes that induce pH changes and solid-state nanopores for the development of biomarker sensors capable of operating in complex real samples.

Genetically Encoded Fluorogenic DNA Aptamers for Imaging Metabolite in Living Cells

Genetically encoded fluorescent protein and fluorogenic RNA sensors are indispensable tools for imaging biomolecules in cells. To expand the toolboxes and improve the generalizability and stability of this type of sensor, we report herein a genetically encoded fluorogenic DNA aptamer (GEFDA) sensor by linking a fluorogenic DNA aptamer for dimethylindole red with an ATP aptamer. The design enhances red fluorescence by 4-fold at 650 nm in the presence of ATP. Additionally, upon dimerization, it improves the signal-to-noise ratio by 2-3 folds. We further integrated the design into a plasmid to create a GEFDA sensor for sensing ATP in live bacterial and mammalian cells. This work expanded genetically encoded sensors by employing fluorogenic DNA aptamers, which offer enhanced stability over fluorogenic proteins and RNAs, providing a novel tool for real-time monitoring of an even broader range of small molecular metabolites in biological systems.

Sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay for spatial imaging of glycoRNAs in single cells

Glycosylated RNAs (glycoRNAs) have recently emerged as a new class of molecules of substantial interest owing to their potential roles in cellular processes and diseases. However, studying glycoRNAs is challenging owing to the lack of effective research tools including, but not limited to, imaging techniques to study the spatial distribution of glycoRNAs. Recently, we reported the development of a glycoRNA imaging technique, called sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA), to visualize sialic acid-containing glycoRNAs with high sensitivity and specificity. Here we describe the experimental design principles and detailed step-by-step procedures for ARPLA-assisted glycoRNA imaging across multiple cell types. The procedure includes details for target selection, oligo design and preparation, optimized steps for RNA in situ hybridization, glycan recognition, proximity ligation, rolling circle amplification and a guideline for image acquisition and analysis. With properly designed probe sets and cells prepared, ARPLA-based glycoRNA imaging can typically be completed within 1 d by users with expertise in biochemistry and fluorescence microscopy. The ARPLA approach enables researchers to explore the spatial distribution, trafficking and functional contributions of glycoRNAs in various cellular processes.

The role of metagenomic next-generation sequencing in diagnosing and managing post-kidney transplantation infections

Kidney transplantation (KT) is a life-saving treatment for patients with end-stage renal disease, but post-transplant infections remain one of the most significant challenges. These infections, caused by a variety of pathogens, can lead to prolonged hospitalization, graft dysfunction, and even mortality, particularly in immunocompromised patients. Traditional diagnostic methods often fail to identify the causative organisms in a timely manner, leading to delays in treatment and poorer patient outcomes. This review explores the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of post-KT infections. mNGS allows for the rapid, comprehensive detection of a wide range of pathogens, including bacteria, viruses, fungi, and parasites, without the need for culture-based techniques. We discuss the advantages of mNGS in early and accurate pathogen identification, its role in improving patient management, and the potential challenges in its clinical implementation. Additionally, we consider the future prospects of mNGS in overcoming current diagnostic limitations and its potential for guiding targeted therapies, particularly in detecting antimicrobial resistance and emerging pathogens. This review emphasizes the promise of mNGS as an essential tool in improving the diagnosis and treatment of infections in KT recipients.

Harnessing concerted functions in confined environments: cascading enzymatic reactions in nanofluidic biosensors for sensitive detection of arginine

We developed an arginine-responsive biosensor by integrating cascade enzymatic reactions into nanochannels functionalized with weak polyelectrolytes, which serve as "reactive signal amplifiers." This approach enhances device performance and broadens the detectable analyte range by generating high local analyte concentrations. The nanofluidic biosensor operates rapidly (<5 minutes) with a low detection limit of 3 μM.

Metal-Organic Framework Sub-Nanochannels within the Confined Micropipettes: Precise Construction Makes It a Universal Aptamer-Based Sensing Platform

It is crucial to precisely construct metal-organic framework (MOF) sub-nanochannels at the tip of micro/nanopipettes for fundamental research and sensing applications. The quality of the MOF modification plays a significant role in influencing subsequent research, particularly in sensing applications. In this work, we present a precise method of constructing MOF sub-nanochannels at the tip of glass micropipettes, which serve as a universal aptamer-based sensing platform for the selective detection of proteins. In situ scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS) mapping, and fluorescence microscopy results demonstrate that the synthesized MOF (UiO-66) nanocrystals fully block the orifice of glass micropipettes (UiO-66-GMs) without forming any nanometer-scale cracks and remain confined within the geometric boundaries of the orifice. The terminal phosphate-modified aptamer readily binds to the surface of UiO-66-GMs through metal (Zr)-phosphate coordination, ultimately forming the aptamer sensor (Apt-UiO-66-GMs). The selective quantification of proteins is achieved via a decrease in current resulting from protein binding to the aptamer. Our results indicate that the precisely constructed Apt-UiO-66-GMs sensor enables highly selective and sensitive detection of SARS-CoV-2 nucleocapsid protein and holds potential for real sample detection. Furthermore, given the sharp tip of the micropipets and the external sensing interface we have constructed, our aptamer-based sensing platform also opens avenues for single-cell analysis and in vivo sensing.

Recent Advances in DNA Nanotechnology-Based Sensing Platforms for Rapid Virus Detection

Several major viral pandemics in history have significantly impacted the public health of human beings. The COVID-19 pandemic has further underscored the critical need for early detection and screening of infected individuals. However, current detection techniques are confronted with deficiencies in sensitivity and accuracy, restricting the capability of detecting trace amounts of viruses in human bodies and in the environments. The advent of DNA nanotechnology has opened up a feasible solution for rapid and sensitive virus determination. By harnessing the designability and addressability of DNA nanostructures, a range of rapid virus sensing platforms have been proposed. This review overviewed the recent progress, application, and prospect of DNA nanotechnology-based rapid virus detection platforms. Furthermore, the challenges and developmental prospects in this field were discussed.

In silico selection of aptamers against SARS-CoV-2

Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes. Typically generated by conventional SELEX, the inherent drawbacks of the process including the time-consuming, cumbersome and resource-intensive nature catalysed the move to adopt in silico approaches to isolate aptamers. Impressive performances of these in silico-derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the in silico approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the in silico selection of aptamers against SARS-CoV-2 by providing insights into the basic steps involved, which comprise the selection of the initial single-stranded nucleic acids, determination of the secondary and tertiary structures and in silico approaches that include both rigid docking and molecular dynamics simulations. The different approaches involving aptamers against SARS-CoV-2 were illuminated and the need to verify these aptamers by experimental validation was also emphasized. Cognizant of the need to continuously improve aptamers, the strategies embraced thus far for post-in silico selection modifications were enumerated. Shedding light on the steps involved in the in silico selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future.

Viral aptamer screening and aptamer-based biosensors for virus detection: A review

Virus-induced infectious diseases have a detrimental effect on public health and exert significant influence on the global economy. Therefore, the rapid and accurate detection of viruses is crucial for effectively preventing and diagnosing infections. Aptamer-based detection technologies have attracted researchers' attention as promising solutions. Aptamers, small single-stranded DNA or RNA screened via systematic evolution of ligands by exponential enrichment (SELEX), possess a high affinity towards their target molecules. Numerous aptamers targeting viral marker proteins or virions have been developed and widely employed in aptamer-based biosensors (aptasensor) for virus detection. This review introduces SELEX schemes for screening aptamers and discusses distinctive SELEX strategies designed explicitly for viral targets. Furthermore, recent advances in aptamer-based biosensing methods for detecting common viruses using different virus-specific aptamers are summarized. Finally, limitations and prospects associated with developing of aptamer-based biosensors are discussed.

Beta-Barrel Nanopores as Diagnostic Sensors: An Engineering Perspective

Biological nanopores are ultrasensitive and highly attractive platforms for disease diagnostics, including the sequencing of viral and microbial genes and the detection of biomarkers and pathogens. To utilize biological nanopores as diagnostic sensors, they have been engineered through various methods resulting in the accurate and highly sensitive detection of biomarkers and disease-related biomolecules. Among diverse biological nanopores, the β-barrel-containing nanopores have advantages in nanopore engineering because of their robust structure, making them well-suited for modifications. In this review, we highlight the engineering approaches for β-barrel-containing nanopores used in single-molecule sensing for applications in early diagnosis and prognosis. In the highlighted studies, β-barrel nanopores can be modified by genetic mutation to change the structure; alter charge distributions; or add enzymes, aptamers, and protein probes to enhance sensitivity and accuracy. Furthermore, this review discusses challenges and future perspectives for advancing nanopore-based diagnostic sensors.

Manipulating Ion Transport Regimes in Nanomembranes via a "Pore-in-Pore" Approach Enabled by the Synergy of Metal-Organic Frameworks and Solid-State Nanochannels

Solid-state nanochannels (SSNs) have emerged as promising platforms for controlling ionic transport at the nanoscale. SSNs are highly versatile, and this feature can be enhanced through their combination with porous materials such as Metal-Organic Frameworks (MOF). By selection of specific building blocks and experimental conditions, different MOF architectures can be obtained, and this can influence the ionic transport properties through the nanochannel. Herein, we study the effects of confined synthesis of Zr-based UiO-66 MOF on the ion transport properties of single bullet-shaped poly(ethylene terephthalate) (PET) nanochannels. We have found that emerging textural properties from the MOF phase play a determinant role in controlling ionic transport through the nanochannel. We demonstrate that a transition from ion current saturation regimes to diode-like regimes can be obtained by employing different synthetic approaches, namely, counterdiffusion synthesis, where MOF precursors are kept separate and forced to diffuse through the nanochannel, and one-pot synthesis, where both precursors are placed at both ends of the channel. Also, by considering the dependence of the charge state of the UiO-66 MOF on the protonation degree, pH changes offered a mechanism to tune the iontronic output (and selectivity) among different regimes, including anion-driven rectification, cation-driven rectification, ion current saturation, and ohmic behavior. Furthermore, Poisson-Nernst-Planck (PNP) simulations were employed to rationalize the different iontronic outputs observed experimentally for membranes modified by different methods. Our results demonstrate a straightforward tool to synthesize MOF-based SSN membranes with tunable ion transport regimes.

Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform

F luorogenic ap tamers (FAPs) have become an increasingly important tool in cellular sensing and pathogen diagnostics. However, fine-tuning FAPs for enhanced performance remains challenging even with the structural details provided by X-ray crystallography. Here we present a novel approach to optimize a DNA-based FAP (D-FAP), Lettuce, on repurposed Illumina next-generation sequencing (NGS) chips. When substituting its cognate chromophore, DFHBI-1T, with TO1-biotin, Lettuce not only shows a red-shifted emission peak by 53 nm (from 505 to 558 nm), but also a 4-fold bulk fluorescence enhancement. After screening 8,821 Lettuce variants complexed with TO1-biotin, the C14T mutation is found to exhibit an improved apparent dissociated constant ( vs. 0.82 µM), an increased quantum yield (QY: 0.62 vs. 0.59) and an elongated fluorescence lifetime (τ: 6.00 vs. 5.77 ns), giving 45% more ensemble fluorescence than the canonical Lettuce/TO1-biotin complex. Molecular dynamic simulations further indicate that the π-π stacking interaction is key to determining the coordination structure of TO1-biotin in Lettuce. Our screening-and-simulation pipeline can effectively optimize FAPs without any prior structural knowledge of the canonical FAP/chromophore complexes, providing not only improved molecular probes for fluorescence sensing but also insights into aptamer-chromophore interactions.

High-precision high-speed nanopore ping-pong control system based on field programmable gate array

"Molecular ping-pong," emerging as a control strategy in solid-state nanopore technology, presents a highly promising approach for repetitive measurements of single biomolecules, such as DNA. This paper introduces a high-precision, high-speed nanopore molecular ping-pong control system consisting of a home-built trans-impedance amplifier (TIA), a control system based on a Field Programmable Gate Array (FPGA), and a LabVIEW program operating on the host personal computer. Through feedback compensation and post-stage boosting, the TIA achieves a high bandwidth of about 200 kHz with a gain of 100 MΩ, along with low input-referred current noise of 1.6 × 10-4 pA2/Hz at 1 kHz and 1.1 × 10-3 pA2/Hz at 100 kHz. The FPGA-based control system demonstrates a minimum overall response time (tdelay) of 6.5 μs from the analog input current signal trigger to the subsequent reversal of the analog output drive voltage signal, with a control precision of 1 μs. Additionally, a LabVIEW program has been developed to facilitate rapid data exchange and communication with the FPGA program, enabling real-time signal monitoring, parameter adjustment, and data storage. Successful recapture of individual DNA molecules at various tdelay, resulting in an improvement in capture rate by up to 2 orders of magnitude, has been demonstrated. With unprecedented control precision and capture efficiency, this system provides robust technical support and opens novel research avenues for nanopore single-molecule sensing and manipulation.

Sample Processing and Concentration Methods for Viruses from Foods and the Environment Prior to Detection

Viruses are the leading cause of foodborne illness globally. Concentration of viruses from samples is important for detection because viral contamination of foods often occurs at low levels. In general, virus concentration methods can be classified as either nonspecific, exploiting the relatively homogeneous physicochemical properties of the virus to separate/concentrate it from the sample matrix, or specific, relying on recognition elements such as antibodies to specifically capture and separate viruses from foods. Numerous nonspecific and specific techniques for virus concentration have been reported, each with its own advantages and limitations. Factors to consider can include reagent and equipment costs, time-to-result, ease of use, and potential to eliminate matrix-associated inhibitors. The purpose of this review is to survey the different foodborne virus concentration techniques and their efficacy in various food and environmental matrices as well as discuss some emerging techniques for purification and concentration of viral pathogens from food samples.

Role of Natural Binding Proteins in Therapy and Diagnostics

This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.

Advances in nanofluidic field-effect transistors: external voltage-controlled solid-state nanochannels for stimulus-responsive ion transport and beyond

Ion channels, intricate protein structures facilitating precise ion passage across cell membranes, are pivotal for vital cellular functions. Inspired by the remarkable capabilities of biological ion channels, the scientific community has ventured into replicating these principles in fully abiotic solid-state nanochannels (SSNs). Since the gating mechanisms of SSNs rely on variations in the physicochemical properties of the channel surface, the modification of their internal architecture and chemistry constitutes a powerful strategy to control the transport properties and, consequently, render specific functionalities. In this framework, both the design of the nanofluidic platform and the subsequent selection and attachment of different building blocks gain special attention. Similar to biological ion channels, functional SSNs offer the potential to finely modulate ion transport in response to various stimuli, leading to innovations in a variety of fields. This comprehensive review delves into the intricate world of ion transport across stimuli-responsive SSNs, focusing on the development of external voltage-controlled nanofluidic devices. This kind of field-effect nanofluidic technology has attracted special interest due to the possibility of real-time reconfiguration of the ion transport with a non-invasive strategy. These properties have found interesting applications in drug delivery, biosensing, and nanoelectronics. This document will address the fundamental principles of ion transport through SSNs and the construction, modification, and applications of external voltage-controlled SSNs. It will also address future challenges and prospects, offering a comprehensive perspective on this evolving field.

Spatial imaging of glycoRNA in single cells with ARPLA

Little is known about the biological roles of glycosylated RNAs (glycoRNAs), a recently discovered class of glycosylated molecules, because of a lack of visualization methods. We report sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA) to visualize glycoRNAs in single cells with high sensitivity and selectivity. The signal output of ARPLA occurs only when dual recognition of a glycan and an RNA triggers in situ ligation, followed by rolling circle amplification of a complementary DNA, which generates a fluorescent signal by binding fluorophore-labeled oligonucleotides. Using ARPLA, we detect spatial distributions of glycoRNAs on the cell surface and their colocalization with lipid rafts as well as the intracellular trafficking of glycoRNAs through SNARE protein-mediated secretory exocytosis. Studies in breast cell lines suggest that surface glycoRNA is inversely associated with tumor malignancy and metastasis. Investigation of the relationship between glycoRNAs and monocyte-endothelial cell interactions suggests that glycoRNAs may mediate cell-cell interactions during the immune response.

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.

Single-Crystal Silicon Nanotubes, Hollow Nanocones, and Branched Nanotube Networks

We report a general approach for the synthesis of single-crystal silicon nanotubes, involving epitaxial deposition of silicon shells on germanium nanowire templates followed by removal of the germanium template by selective wet etching. By exploiting advances in the synthesis of germanium nanowires, we were able to rationally tune the nanotube internal diameters (5-80 nm), wall thicknesses (3-12 nm), and taper angles (0-9°) and additionally demonstrated branched silicon nanotube networks. Field effect transistors fabricated from p-type nanotubes exhibited a strong gate effect, and fluid transport experiments demonstrated that small molecules could be electrophoretically driven through the nanotubes. These results demonstrate the suitability of silicon nanotubes for the design of nanoelectrofluidic devices.

Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis

Chemical modification of aptamers is an important step to improve their performance and stability in biological media. This can be performed either during their identification (mod-SELEX) or after the in vitro selection process (post-SELEX). In order to reduce the complexity and workload of the post-SELEX modification of aptamers, we have evaluated the possibility of improving a previously reported, chemically modified aptamer by combining enzymatic synthesis and nucleotides bearing bioisosteres of the parent cubane side-chains or substituted cubane moieties. This method lowers the synthetic burden often associated with post-SELEX approaches and allowed to identify one additional sequence that maintains binding to the PvLDH target protein, albeit with reduced specificity. In addition, while bioisosteres often improve the potency of small molecule drugs, this does not extend to chemically modified aptamers. Overall, this versatile method can be applied for the post-SELEX modification of other aptamers and functional nucleic acids.

Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods

The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.

A highly selective and sensitive electrochemical sensor for tetracycline resistant genes detection based on the non-covalent interaction of graphene oxide and nucleobase

Antibiotic resistance genes (ARGs) are causing worldwide environmental problems, however, the traditional analytical methods and test equipment for them are time-consuming and expensive. The electrochemical sensor using the non-covalent bond between graphene oxide (GO) and single-stranded tet (ss-tet) was established for specific tetracycline resistance genes (tet, composed of ss-tet and complementary ss-tet (ss-tet') in water) detection, which preparation time was only 35 min and far less than most reported sensors based on covalent bond. As the result of the detection for tet, the developed sensor not only had the low detection limit of 50.0 pM (8.1 × 102 copies·mL-1), the short detection time within 42 min, but also had satisfactory stability, excellent reproducibility, and highly selectivity (RSD < 4.43 %). Besides, it also had acceptable accuracy comparing to the real-time quantitative polymerase chain reaction (RT-qPCR) and PCR array in tet detection. Noticeably, it also had been successfully applied to tetA detection in different water samples. In brief, the prepared non-covalent bond sensor is simple, rapid, and suitable for highly selective and sensitive detection of the ARGs in actual water.

Clinical Translation of Aptamers for COVID-19

The COVID-19 etiologic agent, SARS-CoV-2, continues to be one of the leading causes of death on a global scale. Although efficient methods for diagnosis and treatment of COVID-19 have been developed, new methods of battling SARS-CoV-2 variants and long COVID are still urgently needed. A number of aptamers have demonstrated tremendous potential to be developed into diagnostic and therapeutic agents for COVID-19. The translation of the aptamers for clinical uses, however, has been extremely slow. Overcoming the difficulties faced by aptamers would advance this technology toward clinical use for COVID-19 and other serious disorders.

A Colorimetric Biosensing Platform with Aptamers, Rolling Circle Amplification and Urease-Mediated Litmus Test

Here we report on an ultra-sensitive colorimetric sensing platform that takes advantage of both the strong amplification power of rolling circle amplification (RCA) and the high efficiency of a simple urease-mediated litmus test. The presence of a target triggers the RCA reaction, and urease-labelled DNA can hybridize to the biotinylated RCA products and be immobilized onto streptavidin-coated magnetic beads. The urease-laden beads are then used to hydrolyze urea, leading to an increase in pH that can be detected by a simple litmus test. We show this sensing platform can be easily integrated with aptamers for sensing diverse targets via the detection of human thrombin and platelet-derived growth factor (PDGF) utilizing structure-switching aptamers as well as SARS-CoV-2 in human saliva using a spike-binding trimeric DNA aptamer. Furthermore, we demonstrate that this colorimetric sensing platform can be integrated into a simple paper-based device for sensing applications.

Precise Detection of Viral RNA by Programming Multiplex Rolling Circle Amplification and Strand Displacement

Detection of viral infections (e.g., SARS-CoV-2) with high precision is critical to disease control and treatment. There is an urgent need to develop point-of-care detection methods to complement the gold standard laboratory-based PCR assay with comparable sensitivity and specificity. Herein, we developed a method termed mCAD to achieve ultraspecific point-of-care detection of SARS-CoV-2 RNA while maintaining high sensitivity by programming multiplex rolling circle amplification and toehold-mediated strand displacement reactions. RCA offers sufficient amplification of RNA targets for subsequent detection. Most importantly, a multilayer of detection specificity is implemented into mCAD via sequence-specific hybridization of nucleic acids across serial steps of this protocol to fully eliminate potential false-positive detections. Using mCAD, we demonstrated a highly specific, sensitive, and convenient visual detection of SARS-CoV-2 RNA from both synthetic and clinical samples, exhibiting performance comparable to qPCR. We envision that mCAD will find its broad applications in clinical prospects for nucleic acid detections readily beyond SARS-CoV-2 RNA.

Discovering covalent inhibitors of protein-protein interactions from trillions of sulfur(VI) fluoride exchange-modified oligonucleotides

Molecules that covalently engage target proteins are widely used as activity-based probes and covalent drugs. The performance of these covalent inhibitors is, however, often compromised by the paradox of efficacy and risk, which demands a balance between reactivity and selectivity. The challenge is more evident when targeting protein-protein interactions owing to their low ligandability and undefined reactivity. Here we report sulfur(VI) fluoride exchange (SuFEx) in vitro selection, a general platform for high-throughput discovery of covalent inhibitors from trillions of SuFEx-modified oligonucleotides. With SuFEx in vitro selection, we identified covalent inhibitors that cross-link distinct residues of the SARS-CoV-2 spike protein at its protein-protein interaction interface with the human angiotensin-converting enzyme 2. A separate suite of covalent inhibitors was isolated for the human complement C5 protein. In both cases, we observed a clear disconnection between binding affinity and cross-linking reactivity, indicating that direct search for the aimed reactivity-as enabled by SuFEx in vitro selection-is vital for discovering covalent inhibitors of high selectivity and potency.

Inactivation Kinetics and Replication Cycle Inhibition of Coxsackievirus B5 by Free Chlorine

The kinetics of coxsackievirus serotype B5 (CVB5) inactivation with free chlorine is characterized over a range of pH and temperature relevant to drinking water treatment with the primary goal of selecting experimental conditions used for assessing inactivation mechanisms. The inactivation kinetics identified in our study is similar to or slower than experimental data reported in the literature and thus provides a conservative representation of the kinetics of CVB5 inactivation for free chlorine that could be useful in developing future regulations for waterborne viral pathogens including adequate disinfection treatment for CVB5. Untreated and free chlorine-treated viruses, and host cells synchronized-infected with these viruses, are analyzed by a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method with the goal of quantitatively investigating the effect of free chlorine exposure on viral genome integrity, attachment to host cell, and viral genome replication. The inactivation kinetics observed results from a combination of hindering virus attachment to the host cell, inhibition of one or more subsequent steps of the replication cycle, and possibly genome damage.

Recent Advances in Biosensor Development for the Detection of Viral Particles in Foods: A Comprehensive Review

Viral foodborne diseases cause serious harm to human health and the economy. Rapid, accurate, and convenient approaches for detecting foodborne viruses are crucial for preventing diseases. Biosensors integrating electrochemical and optical properties of nanomaterials have emerged as effective tools for the detection of viruses in foods. However, they still face several challenges, including substantial sample preparation and relatively poor sensitivity due to complex food matrices, which limit their field applications. Hence, the purpose of this review is to provide an overview of recent advances in biosensing techniques, including electrochemical, SERS-based, and colorimetric biosensors, for detecting viral particles in food samples, with emerging techniques for extraction/concentration of virus particles from food samples. Moreover, the principle, design, and advantages/disadvantages of each biosensing method are comprehensively described. This review covers the recent development of rapid and sensitive biosensors that can be used as new standards for monitoring food safety and food quality in the food industry.

Nanofluidic diodes based on asymmetric bio-inspired surface coatings in straight glass nanochannels

In this study, we present nanofluidic diodes fabricated from straight glass nanochannels and functionalized using bio-inspired polydopamine (PDA) and poly-L-lysine (PLL) coatings. The resulting PDA coatings are shown to be asymmetric due to a combination of transport considerations which can be leveraged to provide a measure of control over the effective channel geometry. By subsequently introducing a layer of amine-bearing PLL chains covalently bound to the PDA, we enhance heterogeneities in the charge and ion distributions within the channel and enable significant current rectification between forward-bias and reverse-bias modes; our PDA-PLL-coated channels yielded a rectification ratio greater than 1000 in a 100 nm channel filled with 0.01× phosphate-buffered saline solution (PBS). We further demonstrated that at higher ionic strength conditions, reducing the solution pH increased the number of protonated amines within the PLL layer, amplifying the charge disparities along the channel and leading to greater rectification. As nanofluidic diodes with bipolar surface charge distributions tend to provide superior performance compared to those with a single wall charge polarity, we imposed a more bipolar charge distribution in our devices by partially coating our PDA-PLL-coated channels with negatively charged polyacrylic acid (PAA). These enhanced bipolar channels exhibited greater current rectification than the PDA-PLL-coated channels, reaching rectification ratios in excess of 100 even in more physiologically-relevant 1× PBS solutions. Our fabrication approach and the results herein provide a promising platform from which the scientific community can build upon in the relentless endeavor for improved sensitivity in biosensors and other analytical devices.

Highly-specific aptamer targeting SARS-CoV-2 S1 protein screened on an automatic integrated microfluidic system for COVID-19 diagnosis

Variants of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) have evolved such that it may be challenging for diagnosis and clinical treatment of the pandemic coronavirus disease-19 (COVID-19). Compared with developed SARS-CoV-2 diagnostic tools recently, aptamers may exhibit some advantages, including high specificity/affinity, longer shelf life (vs. antibodies), and could be easily prepared. Herein an integrated microfluidic system was developed to automatically carry out one novel screening process based on the systematic evolution of ligands by exponential enrichment (SELEX) for screening aptamers specific with SARS-CoV-2. The new screening process started with five rounds of positive selection (with the S1 protein of SARS-CoV-2). In addition, including non-target viruses (influenza A and B), human respiratory tract-related cancer cells (adenocarcinoma human alveolar basal epithelial cells and dysplastic oral keratinocytes), and upper respiratory tract-related infectious bacteria (including methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae), and human saliva were involved to increase the specificity of the screened aptamer during the negative selection. Totally, all 10 rounds could be completed within 20 h. The dissociation constant of the selected aptamer was determined to be 63.0 nM with S1 protein. Limits of detection for Wuhan and Omicron clinical strains were found to be satisfactory for clinical applications (i.e. 4.80 × 10¹ and 1.95 × 10² copies/mL, respectively). Moreover, the developed aptamer was verified to be capable of capturing inactivated SARS-CoV-2 viruses, eight SARS-CoV-2 pseudo-viruses, and clinical isolates of SARS-CoV-2 viruses. For high-variable emerging viruses, this developed integrated microfluidic system can be used to rapidly select highly-specific aptamers based on the novel SELEX methods to deal with infectious diseases in the future.

A Fast and Reversible Responsive Bionic Transmembrane Nanochannel for Dynamic Single-Cell Quantification of Glutathione

Biological channels can rapidly and continuously modulate ion transport behaviors in response to external stimuli, which play essential roles in manipulating physiological and pathological processes in cells. Here, to mimic the biological channels, a bionic nanochannel is developed by synergizing a cationic silicon-substituted rhodamine (SiRh) with a glass nanopipette for transmembrane single-cell quantification. Taking the fast and reversible nucleophilic addition reaction between glutathione (GSH) and SiRh, the bionic nanochannel shows a fast and reversible response to GSH, with its inner-surface charges changing between positive and negative charges, leading to a distinct and reversible switch in ionic current rectification (ICR). With the bionic nanochannel, spatiotemporal-resolved operation is performed to quantify endogenous GSH in a single cell, allowing for monitoring of intracellular GSH fluctuation in tumor cells upon photodynamic therapy and ferroptosis. Our results demonstrate that it is a feasible tool for in situ quantification of the endogenous GSH in single cells, which may be adapted to addressing other endogenous biomolecules in single cells by usage of other stimuli-responsive probes.

Diverse SARS-CoV-2 aptamers overcome variant antigenic shift

SARS-CoV-2 mutates rapidly as evidenced by the emergence of Omicron which causes changes in the recognition epitopes of most current neutralizing antibodies and immune evasion. Although aptamers are potential neutralizing agents for SARS-CoV-2 due to their unique molecular properties, it is difficult to compare their performances as assay conditions vary greatly, and their activity levels against variants remain unknown. Here, we evaluated the performances of 14 SARS-CoV-2 aptamers and provided a comprehensive analysis them, which we expect will improve the development of aptamer tools for SARS-CoV-2 diagnostics and therapeutics.

Repurposing CRISPR/Cas to Discover SARS-CoV-2 Detecting and Neutralizing Aptamers

RNA aptamers provide useful biological probes and therapeutic agents. New methodologies to screen RNA aptamers will be valuable by complementing the traditional Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Meanwhile, repurposing clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated systems (Cas) has expanded their utility far beyond their native nuclease function. Here, CRISmers, a CRISPR/Cas-based novel screening system for RNA aptamers based on binding to a chosen protein of interest in a cellular context, is presented. Using CRISmers, aptamers are identified specifically targeting the receptor binding domain (RBD) of the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two aptamer leads enable sensitive detection and potent neutralization of SARS-CoV-2 Delta and Omicron variants in vitro. Intranasal administration of one aptamer, further modified with 2'-fluoro pyrimidines (2'-F), 2'-O-methyl purines (2'-O), and conjugation with both cholesterol and polyethylene glycol of 40 kDa (PEG40K), achieves effective prophylactic and therapeutic antiviral activity against live Omicron BA.2 variants in vivo. The study concludes by demonstrating the robustness, consistency, and potential broad utility of CRISmers using two newly identified aptamers but switching CRISPR, selection marker, and host species.

Harnessing aptamers against COVID-19: a therapeutic strategy

The novel coronavirus crisis caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) was a global pandemic. Although various therapeutic approaches were developed over the past 2 years, novel strategies with more efficient applicability are required to target new variants. Aptamers are single-stranded (ss)RNA or DNA oligonucleotides capable of folding into unique 3D structures with robust binding affinity to a wide variety of targets following structural recognition. Aptamer-based theranostics have proven excellent capability for diagnosing and treating various viral infections. Herein, we review the current status and future perspective of the potential of aptamers as COVID-19 therapies.

Aptamer-based diagnosis of various SARS-CoV2 strains isolated from clinical specimens

The emergence of the SARS-CoV-2 virus, an unknown strain of coronavirus, has resulted in severe acute respiratory syndrome with high mortality rates worldwide. Due to the possibility of asymptomatic carriers, late diagnosis of infected individuals can lead to uncontrollable transmission of the disease, making early and accurate detection crucial in controlling the spread of the virus. In this study we identified high-binding-affinity aptamers targeting various strains of the SARS-CoV2 (COVID-19) virus, using the GO-Cell-SELEX (Graphene Oxide- Systematic Evolution of Ligands by Exponential Enrichment) strategy. A total of 96 aptamers were developed through 11 rounds of GO-Cell-SELEX from a random 40 nucleotide single-strand DNA (ssDNA) aptamer library. Using the surface plasmon resonance (SPR) method, the dissociation constant (Kd) values of all aptamers were calculated and two aptamers 52 and 91 with Kd 50 and 61 were selected for enzyme-linked apta-sorbent assay (ELASA). Aptamer 91 could detect various strains of the virus in above 97% of clinical samples obtained from nasopharyngeal swaps (NPS) specimens kept in viral transport media (VTM), confirmed by real-time PCR assay at COVID-19 Reference Diagnostic Laboratory of Iran, Pasture Institute. Aptamer 52 could detect the SARS-CoV2 virus in a competitive lateral flow assay (LFA) to be considered for a future designed kit. These two simple, specific, and sensitive tests can be used in combination for rapid and early diagnosis of various strains of the COVID-19 virus. Our results suggest that these two discovered aptamers present an opportunity for developing a new rapid aptamer-based coronavirus diagnostic kit.

Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations

Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.

A photonic resonator interferometric scattering microscope for label-free detection of nanometer-scale objects with digital precision in point-of-use environments

Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic source. The use of a photonic crystal substrate for interferemetric scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instrument's main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position. In this work, we characterize the system's performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosome, and ferritin protein.

Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis

Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.

CoVSense: Ultrasensitive Nucleocapsid Antigen Immunosensor for Rapid Clinical Detection of Wildtype and Variant SARS-CoV-2

The widespread accessibility of commercial/clinically-viable electrochemical diagnostic systems for rapid quantification of viral proteins demands translational/preclinical investigations. Here, Covid-Sense (CoVSense) antigen testing platform; an all-in-one electrochemical nano-immunosensor for sample-to-result, self-validated, and accurate quantification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N)-proteins in clinical examinations is developed. The platform's sensing strips benefit from a highly-sensitive, nanostructured surface, created through the incorporation of carboxyl-functionalized graphene nanosheets, and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) conductive polymers, enhancing the overall conductivity of the system. The nanoengineered surface chemistry allows for compatible direct assembly of bioreceptor molecules. CoVSense offers an inexpensive (<$2 kit) and fast/digital response (<10 min), measured using a customized hand-held reader (<$25), enabling data-driven outbreak management. The sensor shows 95% clinical sensitivity and 100% specificity (Ct<25), and overall sensitivity of 91% for combined symptomatic/asymptomatic cohort with wildtype SARS-CoV-2 or B.1.1.7 variant (N = 105, nasal/throat samples). The sensor correlates the N-protein levels to viral load, detecting high Ct values of ≈35, with no sample preparation steps, while outperforming the commercial rapid antigen tests. The current translational technology fills the gap in the workflow of rapid, point-of-care, and accurate diagnosis of COVID-19.

Integrating Water Purification with Electrochemical Aptamer Sensing for Detecting SARS-CoV-2 in Wastewater

Wastewater analysis of pathogens, particularly SARS-CoV-2, is instrumental in tracking and monitoring infectious diseases in a population. This method can be used to generate early warnings regarding the onset of an infectious disease and predict the associated infection trends. Currently, wastewater analysis of SARS-CoV-2 is almost exclusively performed using polymerase chain reaction for the amplification-based detection of viral RNA at centralized laboratories. Despite the development of several biosensing technologies offering point-of-care solutions for analyzing SARS-CoV-2 in clinical samples, these remain elusive for wastewater analysis due to the low levels of the virus and the interference caused by the wastewater matrix. Herein, we integrate an aptamer-based electrochemical chip with a filtration, purification, and extraction (FPE) system for developing an alternate in-field solution for wastewater analysis. The sensing chip employs a dimeric aptamer, which is universally applicable to the wild-type, alpha, delta, and omicron variants of SARS-CoV-2. We demonstrate that the aptamer is stable in the wastewater matrix (diluted to 50%) and its binding affinity is not significantly impacted. The sensing chip demonstrates a limit of detection of 1000 copies/L (1 copy/mL), enabled by the amplification provided by the FPE system. This allows the integrated system to detect trace amounts of the virus in native wastewater and categorize the amount of contamination into trace (<10 copies/mL), medium (10-1000 copies/mL), or high (>1000 copies/mL) levels, providing a viable wastewater analysis solution for in-field use.

Aptamers targeting SARS-COV-2: a promising tool to fight against COVID-19

SARS-CoV-2, the causative agent of COVID-19, remains among the main causes of global mortality. Although antigen/antibody-based immunoassays and neutralizing antibodies targeting SARS-CoV-2 have been successfully developed over the past 2 years, they are often inefficient and unreliable for emerging SARS-CoV-2 variants. Novel approaches against SARS-CoV-2 and its variants are therefore urgently needed. Aptamers have been developed for the detection and inhibition of several different viruses such as HIV, influenza viruses, Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV. Aptamers targeting SARS-CoV-2 represent a promising tool in the fight against COVID-19, which is of paramount importance for the current and any future pandemics. This review presents recent advances and future trends in the development of aptamer-based approaches for SARS-CoV-2 diagnosis and treatment.

Simultaneous identification of viruses and viral variants with programmable DNA nanobait

Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.

Functional nucleic acids as potent therapeutics against SARS-CoV-2 infection

The COVID-19 pandemic has posed a severe threat to human life and the global economy. Although conventional treatments, including vaccines, antibodies, and small-molecule inhibitors, have been broadly developed, they usually fall behind the constant mutation of SARS-CoV-2, due to the long screening process and high production cost. Functional nucleic acid (FNA)-based therapeutics are a newly emerging promising means against COVID-19, considering their timely adaption to different mutants and easy design for broad-spectrum virus inhibition. In this review, we survey typical FNA-related therapeutics against SARS-CoV-2 infection, including aptamers, aptamer-integrated DNA frameworks, functional RNA, and CRISPR-Cas technology. We first introduce the pathogenesis, transmission, and evolution of SARS-CoV-2, then analyze the existing therapeutic and prophylactic strategies, including their pros and cons. Subsequently, the FNAs are recommended as potent alternative therapeutics from their screening process and controllable engineering to effective neutralization. Finally, we put forward the remaining challenges of the existing field and sketch out the future development directions.

Electrical biosensing system utilizing ion-producing enzymes conjugated with aptamers for the sensing of severe acute respiratory syndrome coronavirus 2

Viral outbreaks, which include the ongoing coronavirus disease 2019 (COVID-19) pandemic provoked by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are a major global crisis that enormously threaten human health and social activities worldwide. Consequently, the rapid and repeated treatment and isolation of these viruses to control their spread are crucial to address the COVID-19 pandemic and future epidemics of novel emerging viruses. The application of cost-efficient, rapid, and easy-to-operate detection devices with miniaturized footprints as a substitute for the conventional optic-based polymerase chain reaction (PCR) and immunoassay tests is critical. In this context, semiconductor-based electrical biosensors are attractive sensing platforms for signal readout. Therefore, this study aimed to examine the electrical sensing of patient-derived SARS-CoV-2 samples by harnessing the activity of DNA aptamers directed against spike proteins on viral surfaces. We obtained rapid and sensitive virus detection beyond the Debye length limitation by exploiting aptamers coupled with alkaline phosphatases, which catalytically generate free hydrogen ions which can readily be measured on pH meters or ion-sensitive field-effect transistors. Furthermore, we demonstrated the detection of the viruses of approximately 100 copies/μL in 10 min, surpassing the capability of typical immunochromatographic assays. Therefore, our newly developed technology has great potential for point-of-care testing not only for SARS-CoV-2, but also for other types of pathogens and biomolecules.

Ultrafast and absolute quantification of SARS-CoV-2 on food using hydrogel RT-LAMP without pre-lysis

With rapid growing of environmental contact infection, more and more attentions are focused on the precise and absolute quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus on cold chain foods via point-of-care test (POCT). In this work, we propose a hydrogel-mediated reverse transcription loop-mediated isothermal amplification (RT-LAMP) for ultrafast and absolute quantification of SARS-CoV-2. Cross-linked hydrogel offers opportunities for digital single molecule amplification in nanoconfined spaces, facilitating the virus lysis, RNA reverse transcription and amplification process, which is about 3.4-fold faster than conventional bulk RT-LAMP. Ultrafast quantification of SARS-CoV-2 is accomplished in 15 min without virus pre-lysis and RNA extraction. The sensitivity can accurately quantify SARS-CoV-2 down to 0.5 copy/μL. Furthermore, the integrated system has an excellent specificity, reproducibility and storage stability, which can be also used to test SARS-CoV-2 on various cold chain fruits. The developed ultrafast and simple hydrogel RT-LAMP will be an enormous potential for surveillance of virus or other hazardous microbes in environmental, agricultural and food industry.