A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein.

The COVID-19 pandemic has underscored the critical need for the advancement of diagnostic and therapeutic platforms. These platforms rely on the rapid development of molecular binders that should facilitate surveillance and swift intervention against viral infections. In this study, we have evaluated by three independent research groups the binding characteristics of various published RNA and DNA aptamers targeting the spike protein of the SARS-CoV-2 virus. For this comparative analysis, we have employed different techniques such as biolayer interferometry (BLI), enzyme-linked oligonucleotide assay (ELONA), and flow cytometry. Our data show discrepancies in the reported specificity and affinity among several of the published aptamers and underline the importance of standardized methods, the impact of biophysical techniques, and the controls used for aptamer characterization. We expect our results to contribute to the selection and application of suitable aptamers for the detection of SARS-CoV-2.

Cost-effective evaluation of Aptamer candidates in SELEX-based Aptamer isolation.

Aptamers are short, single-stranded nucleic acids with high affinity and specificity for various targets, making them valuable in diagnostics and therapeutics. Their isolation traditionally involves a time-consuming and costly process called SELEX. While SELEX methods have evolved to improve binding and amplification, the crucial step of aptamer identification from sequencing data remains expensive and often overlooked. Common identification methods require modification of aptamer candidates with labels like biotin or fluorescent dyes, which becomes costly and cumbersome for high-throughput sequencing data. This paper presents an efficient and cost-effective approach to streamline aptamer identification. It employs asymmetric polymerase chain reaction (PCR) to generate modified single-stranded DNA copies of aptamer candidates, simplifying the modification process. By using excess modified forward primers and limited reverse primers, this method reduces costs since only unmodified candidates need to be synthesized initially. The approach was demonstrated with an IgE protein aptamer and successfully applied to identify aptamers from a pool of 12 candidates against a monoclonal antibody. The validity of the results was further confirmed through the direct synthesis of fluorophore-conjugated aptamer candidates, yielding consistent outcomes while reducing the cost by threefold. This approach addresses a critical bottleneck in aptamer discovery by significantly reducing the time and cost associated with aptamer identification, facilitating aptamer-based research and making aptamers more accessible for various applications in diagnostics and therapeutics.

The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.

Aptamers are single-stranded DNA or RNA that bind to specific targets such as proteins, thus having similar characteristics to antibodies. It can be synthesized at a lower cost, with no batch-to-batch variations, and is easier to modify chemically than antibodies, thus potentially being used as therapeutic and biosensing agents. The current method for RNA aptamer identification in vitro uses the SELEX method, which is considered inefficient due to its complex process. Computational models of aptamers have been used to predict and study the molecular interaction of modified aptamers to improve affinity. In this study, we generated three-dimensional models of five RNA aptamers from their sequence using mFold, RNAComposer web server, and molecular dynamics simulation. The model structures were then evaluated and compared with the experimentally determined structures. This study showed that the combination of mFold, RNAComposer, and molecular dynamics simulation could generate 14-16, 28, or 29 nucleotides length of 3D RNA aptamer with similar geometry and topology to the experimentally determined structures. The non-canonical basepair structure of the aptamer loop was formed through the MD simulation, which also improved the three-dimensional RNA aptamers model. Clustering analysis was recommended to choose the more representative model.

Comparison of Aptamer Signaling Mechanisms Reveals Disparities in Sensor Response and Strategies to Eliminate False Signals.

Aptamers are nucleic acid-based affinity reagents that have been incorporated into a variety of molecular sensor formats. However, many aptamer sensors exhibit insufficient sensitivity and specificity for real-world applications, and although considerable effort has been dedicated to improving sensitivity, sensor specificity has remained largely neglected and understudied. In this work, we have developed a series of sensors using aptamers for the small-molecule drugs flunixin, fentanyl, and furanyl fentanyl and compare their performance─in particular, focusing on their specificity. Contrary to expectations, we observe that sensors using the same aptamer operating under the same physicochemical conditions produce divergent responses to interferents depending on their signal transduction mechanism. For instance, aptamer beacon sensors are susceptible to false-positives from interferents that weakly associate with DNA, while strand-displacement sensors suffer from false-negatives due to interferent-associated signal suppression when both the target and interferent are present. Biophysical analyses suggest that these effects arise from aptamer-interferent interactions that are either nonspecific or induce aptamer conformational changes that are distinct from those induced by true target-binding events. We also demonstrate strategies for improving the sensitivity and specificity of aptamer sensors with the development of a "hybrid beacon," wherein the incorporation of a complementary DNA competitor into an aptamer beacon selectively hinders interferent─but not target─binding and signaling, while simultaneously overcoming signal suppression by interferents. Our results highlight the need for systematic and thorough testing of aptamer sensor response and new aptamer selection methods that optimize specificity more effectively than traditional counter-SELEX.

Risk assessment of selected pharmaceuticals on wildlife with nanomaterials based aptasensors.

Pharmaceuticals have improved human and veterinary health tremendously over the years. But the implications of the presence of pharmaceuticals in the environment on terrestrial, avian, and aquatic organisms are still not fully comprehended. The bioaccumulation and biomagnifications of these chemicals through the food chain have long-term effects on the wildlife. The detection and quantification of such pharmaceutical residues in the environment is a tedious process and quicker methods are needed. Aptasensors are one such quick and reliable method for the identification of pharmaceutical residues in the wildlife. Aptasensors are a class of biosensors that work on the principles of biological recognition of elements. The aptamers are unique biological recognition elements with high specificity and affinity to various targets. Their efficiency makes them a very promising candidate for such sensitive research. In this review, the pharmaceutical threats to wildlife and their detection techniques using aptasensors have been discussed.

A simple, rapid and low-cost qPCR assay for evaluating the severity of exosomal PD-L1-mediated T cell exhaustion in blood samples.

A novel dual-aptamer activated proximity-induced qPCR assay was developed for the quantitative analysis of exosomal PD-L1 on T cell-exosome complexes in blood samples.

Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach.

Oligonucleotide-based aptamers, which have a three-dimensional structure with a single-stranded fragment, feature various characteristics with respect to size, toxicity, and permeability. Accordingly, aptamers are advantageous in terms of diagnosis and treatment and are materials that can be produced through relatively simple experiments. Systematic evolution of ligands by exponential enrichment (SELEX) is one of the most widely used experimental methods for generating aptamers; however, it is highly expensive and time-consuming. To reduce the related costs, recent studies have used in silico approaches, such as aptamer-protein interaction (API) classifiers that use sequence patterns to determine the binding affinity between RNA aptamers and proteins. Some of these methods generate candidate RNA aptamer sequences that bind to a target protein, but they are limited to producing candidates of a specific size. In this study, we present a machine learning approach for selecting candidate sequences of various sizes that have a high binding affinity for a specific sequence of a target protein. We applied the Monte Carlo tree search (MCTS) algorithm for generating the candidate sequences using a score function based on an API classifier. The tree structure that we designed with MCTS enables nucleotide sequence sampling, and the obtained sequences are potential aptamer candidates. We performed a quality assessment using the scores of docking simulations. Our validation datasets revealed that our model showed similar or better docking scores in ZDOCK docking simulations than the known aptamers. We expect that our method, which is size-independent and easy to use, can provide insights into searching for an appropriate aptamer sequence for a target protein during the simulation step of SELEX.

Development of nucleic acid aptamer-based lateral flow assays: A robust platform for cost-effective point-of-care diagnosis.

Lateral flow assay (LFA) has made a paradigm shift in the in vitro diagnosis field due to its rapid turnaround time, ease of operation and exceptional affordability. Currently used LFAs predominantly use antibodies. However, the high inter-batch variations, error margin and storage requirements of the conventional antibody-based LFAs significantly impede its applications. The recent progress in aptamer technology provides an opportunity to combine the potential of aptamer and LFA towards building a promising platform for highly efficient point-of-care device development. Over the past decades, different forms of aptamer-based LFAs have been introduced for broad applications ranging from disease diagnosis, agricultural industry to environmental sciences, especially for the detection of antibody-inaccessible small molecules such as toxins and heavy metals. But commercial aptamer-based LFAs are still not used widely compared with antibodies. In this work, by analysing the key issues of aptamer-based LFA design, including immobilization strategies, signalling methods, and target capturing approaches, we provide a comprehensive overview about aptamer-based LFA design strategies to facilitate researchers to develop optimised aptamer-based LFAs.

Antidelaminating, Thermally Stable, and Cost-Effective Flexible Kapton Platforms for Nitrate Sensors, Mercury Aptasensors, Protein Sensors, and p-Type Organic Thin-Film Transistors.

The inkjet printing of metal electrodes on polymer films is a desirable manufacturing process due to its simplicity but is limited by the lack of thermal stability and serious delaminating flaws in various aqueous and organic solutions. Kapton, adopted worldwide due to its superior thermal durability, allows the high-temperature sintering of nanoparticle-based metal inks. By carefully selecting inks (Ag and Au) and Kapton substrates (Kapton HN films with a thickness of 135 µm and a thermal resistance of up to 400 °C) with optimal printing parameters and simplified post-treatments (sintering), outstanding film integrity, thermal stability, and antidelaminating features were obtained in both aqueous and organic solutions without any pretreatment strategy (surface modification). These films were applied in four novel devices: a solid-state ion-selective (IS) nitrate (NO3-) sensor, a single-stranded DNA (ssDNA)-based mercury (Hg2+) aptasensor, a low-cost protein printed circuit board (PCB) sensor, and a long-lasting organic thin-film transistor (OTFT). The IS NO3- sensor displayed a linear sensitivity range between 10-4.5 and 10-1 M (r2 = 0.9912), with a limit of detection of 2 ppm for NO3-. The Hg2+ sensor exhibited a linear correlation (r2 = 0.8806) between the change in the transfer resistance (RCT) and the increasing concentration of Hg2+. The protein PCB sensor provided a label-free method for protein detection. Finally, the OTFT demonstrated stable performance, with mobility values in the linear (µlin) and saturation (µsat) regimes of 0.0083 ± 0.0026 and 0.0237 ± 0.0079 cm2 V-1 S-1, respectively, and a threshold voltage (Vth) of -6.75 ± 3.89 V.

The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application.

Aptamers are oligonucleotides and peptides around 15-100 bases in length and are suitable as detection probes or as therapeutics molecules. There are growing interests in the aptamer screening approach through computational simulation methods. DNA and RNA modelling lacks of validation on their predicted 3D structures due to less number of validation tools, unlike protein structures. We suggest an approach to design the stem-loop/hairpin for the three dimensional structure of DNA aptamers through serial applications of computational prediction methods by comparing the simulated structures with the experimental data deposited in PDB Data bank, followed by MD simulations. The result shows minimal structural differences were observed between the designed and the original NMR aptamers, and the stem-loop conformational structures were also retained during the MD thus suggesting the proposed aptamers designing methods are able to synthesize a high quality molecular structure of hairpin aptamers, comparable to the NMR structures.

Assembly and in vitro assessment of a powerful combination: aptamer-modified exosomes combined with gold nanorods for effective photothermal therapy.

Due to good biocompatibility and plasma membrane similarity, the nanosized exosomes are ideal drug carriers. Near-infrared (NIR) photothermal therapy is an emerging method for cancer treatment in which photothermal agents absorb the energy of external NIR light to generate high temperatures in a targeted region to effectively kill cancer cells. Gold nanorods (AuNRs) have been found to provide a prominent photothermal performance, while aptamers can precisely target surface markers on cells with high affinity and specificity. In this study, exosomes were mildly functionalized by integrating them with aptamers and AuNRs to assemble a powerful combination Apt-Exos-AuNRs (AEARs) with good specificity and an effective photothermal killing action on cancer cells. The structure, hydrodynamic diameters, zeta potential, UV-vis absorption spectra and stability of the AEARs were further characterized. In addition, using a cell model, the cancer cell targeting ability of the AEARs and its cellular uptake were observed. Moreover, its photothermal killing effect on various human cancer cells in vitro was validated by a CCK-8 assay as well as apoptosis analysis, the results of which suggest this exosomes-based nanomaterial can serve as a novel and broad-spectrum platform for precision cancer therapy.

Detection of B-type natriuretic peptide by establishing a low-cost and replicable fluorescence resonance energy transfer platform.

Aiming at the establishment of a sensitive and specific diagnostic method for early heart failure (HF), we developed a cost-effective fluorescence resonance energy transfer (FRET) platform for the detection of B-type natriuretic peptide (BNP), a characteristic biomarker of HF. Graphene oxide (GO) was selected as the FRET receptor in view of its advantages including commercial availability, low-cost and chemical stability, and dye-modified aptamer was used as the energy donor of FRET as well as in charge of the specific recognition of BNP. Based on the ON (strong emission) and OFF (quenching) states of FRET in the presence and absence of BNP, respectively, specific detection of BNP was achieved in the range 0.074-0.56 pg/mL with a limit of detection as low as 45 fg/mL (3σ). This FRET platform was applied to detect BNP in 45 blood samples to demonstrate its practicability in clinical diagnosis. Compared to the commonly used Siemens method (chemiluminescence immunoassay, CLIA) in hospital, our approach is more accurate and specific for HF diagnosis with areas under the receiver operating characteristic curves of 0.869 (95% CI 0.733-1.00, P < 0.05) vs 0.850 (95% CI 0.703-0.997, P < 0.05) and specificity of 68.8% vs 65.6%. This platform is promising in early diagnosis of HF through ultrasensitive and specific detection of BNP. Graphical abstract To solve the clinical diagnostic problem for early heart failure (HF) which lacks sensitivity and specificity, we established a cost-effective and rapid fluorescence analysis method based on fluorescence resonance energy transfer (FRET) platform for the detection of B-type natriuretic peptide (BNP), a characteristic biomarker of HF.

A cost-effective fluorescence biosensor for cocaine based on a "mix-and-detect" strategy.

The efficient detection of illicit drugs such as cocaine continues to be important for the fight against drug trafficking. Herein, we report a one-step method for rapid and specific cocaine detection. The method is based on our finding that small-molecule Thioflavin T (ThT) can act as a fluorescence indicator, which can be bonded with the anti-cocaine aptamer (MNS-4.1) to generate an enhanced fluorescence signal. More interestingly, upon cocaine binding, the intercalated ThT can be replaced, causing a drastic fluorescence reduction. We further optimized the sequence of MNS-4.1 and a new anti-cocaine aptamer (coc.ap2-GC) was obtained. This aptamer showed a higher affinity to both ligands, which increased the ThT binding fluorescence intensity and showed the highest quenching efficiency. Based on the fluorescence change induced by competitive binding, cocaine detection could be accomplished by a "mix-and-detect" strategy within seconds. Such a label-free method exhibits high sensitivity to cocaine with a low detection limit of 250 nM. Moreover, the practical sample analysis (2.5% human urine and saliva) also exhibits good precision and high sensitivity.

A low-cost paper-based aptasensor for simultaneous trace-level monitoring of mercury (II) and silver (I) ions.

Mercury (Hg2+) and silver (Ag+) ions possess the harmful effects on public health and environment that makes it essential to develop the sensing techniques with great sensitivity for the ions. Metal ions commonly coexist in the different biological and environmental systems. Hence, it is an urgent demand to design a simple method for the simultaneous detection of metal ions, peculiarly in the case of coexisting Hg2+ and Ag+. This study introduces a low-cost paper-based aptasensor to monitor Hg2+ and Ag+, simultaneously. The strategy of the sensing array is according to the conformational changes of Hg2+- and Ag+-specific aptamers and their release from the GO surface after the injection of the target sample on the sensing platform. Through monitoring the fluorescence recovery changes against the concentrations of the ions, Hg2+ and Ag+ can be determined as low as 1.33 and 1.01 pM. The paper-based aptasensor can simultaneously detect the ions within about 10 min. The aptasensor is applied prosperously to monitor Hg2+ and Ag+ in human serum, water, and milk. The designed aptasensor with the main advantages of simplicity and feasibility holds the supreme potential to develop a cost-effective sensing method for environmental monitoring, food control, and human diagnostics.

Monitoring Plant Health with Near-Infrared Fluorescent H2O2 Nanosensors.

Near-infrared (nIR) fluorescent single-walled carbon nanotubes (SWCNTs) were designed and interfaced with leaves of Arabidopsis thaliana plants to report hydrogen peroxide (H2O2), a key signaling molecule associated with the onset of plant stress. The sensor nIR fluorescence response (>900 nm) is quenched by H2O2 with selectivity against other stress-associated signaling molecules and within the plant physiological range (10-100 H2O2 µM). In vivo remote nIR imaging of H2O2 sensors enabled optical monitoring of plant health in response to stresses including UV-B light (-11%), high light (-6%), and a pathogen-related peptide (flg22) (-10%), but not mechanical leaf wounding (<3%). The sensor's high biocompatibility was reflected on similar leaf cell death (<5%) and photosynthetic rates to controls without SWCNT. These optical nanosensors report early signs of stress and will improve our understanding of plant stress communication, provide novel tools for precision agriculture, and optimize the use of agrochemicals in the environment.

D-shaped plastic optical fibre aptasensor for fast thrombin detection in nanomolar range.

The development of optical biosensors for the rapid and costless determination of clinical biomarkers is of paramount importance in medicine. Here we report a fast and low-cost biosensor based on a plasmonic D-shaped plastic optical fibre (POF) sensor derivatized with an aptamer specific for the recognition of thrombin, the target marker of blood homeostasis and coagulation cascade. In particular, we designed a functional interface based on a Self Assembled Monolayer (SAM) composed of short Poly Ethylene Glycol (PEG) chains and biotin-modified PEG thiol in ratio 8:2 mol:mol, these latter serving as baits for the binding of the aptamer through streptavidin-chemistry. The SAM was studied by X-ray Photoelectron Spectroscopy (XPS) analysis, static contact angle (CA), Surface Plasmon Resonance (SPR) in POFs, and fluorescence microscopy on gold surface. The optimized SAM composition enabled the immobilization of about 112 ng/cm2 of aptamer. The thrombin detection exploiting POF-Aptasensor occurred in short times (5-10 minutes), the reached Limit of Detection (LOD) was about 1 nM, and the detection range was 1.6-60 nM, indicating the POF-Aptasensor well addresses the needs for a low-cost, simple to use and to realize, rapid, small size and portable diagnostic platform.

Three-dimensional nitrogen-doped mesoporous carbon nanomaterials derived from plant biomass: Cost-effective construction of label-free electrochemical aptasensor for sensitively detecting alpha-fetoprotein.

We synthesized three kinds of nitrogen-doped nanoporous carbon nanomaterials (represented by N-mC) through a cost-effective method, that is, pyrolysis of plant biomasses (grass, flower, and peanut shells). We further explored their potential as sensitive bioplatforms for electrochemical label-free aptasensors to facilitate the early detection of alpha-fetoprotein (AFP). Chemical structure characterizations revealed that rich functional groups coexisted in as-synthesized N-mC nanomaterials, such as C-C, C-O, C=O, C-N, and COOH. Among the three kinds of N-mC nanomaterials, the one derived from grass (N-mCg) exhibited the lowest carbon defect degree, the highest ID/IG ratio in the Raman spectra, and the largest specific surface area (186.2 m2 g-1). Consequently, N-mCg displayed excellent electrochemical activity and strong affinity toward aptamer strands, further endowing the corresponding aptasensor with sensitive detection ability for AFP. Electrochemical impedance spectroscopy (EIS) and differential pulse voltammetry (DPV) were used to investigate the whole detection procedure for AFP. The EIS and DPV results showed that the fabricated N-mCg-based aptasensor possessed an extremely low limit of detection of 60.8 and 61.8 fg·mL-1 (s/n = 3), respectively, for detecting AFP within a wide linear range from 0.1 pg mL-1 to 100 ng mL-1. Moreover, the aptasensor displayed acceptable selectivity and applicability, high reproducibility, and excellent stability in serum samples of cancer patients. Therefore, the proposed cost-effective and label-free strategy based on the nitrogen-doped nanoporous carbon derived from plant biomass is a promising approach for the early detection of various tumor markers.

Facile, Rapid, and Low-Cost Electrophoresis Titration of Thrombin by Aptamer-Linked Magnetic Nanoparticles and a Redox Boundary Chip.

An aptamer-linked assay of a target biomarker (e.g., thrombin) is facing the challenges of long-term run, complex performance, and expensive instrument, unfitting clinical diagnosis in resource-limited areas. Herein, a facile chip electrophoresis titration (ET) model was proposed for rapid, portable, and low-cost assay of thrombin via aptamer-linked magnetic nanoparticles (MNPs), redox boundary (RB), and horseradish peroxidase (HRP). In the electrophoresis titration-redox boundary (ET-RB) model, thrombin was chosen as a model biomarker, which could be captured within 15 min by MNP-aptamer 1 and HRP-aptamer 2, forming a sandwich complex of (MNP-aptamer 1)-thrombin-(HRP-aptamer 2). After MNP separation and chromogenic reaction of 3,3',5,5'-tetramethylbenzidine (TMB) within 10 min, an ET-RB run could be completed within 5 min based on the reaction between a 3,3',5,5'-tetramethylbenzidine radical cation (TMB•+) and l-ascorbic acid in the ET channel. The systemic experiments based on the ET-RB method revealed that the sandwich complex could be formed and the thrombin content could be assayed via an ET-RB chip, demonstrating the developed model and method. In particular, the ET-RB method had the evident merits of simplicity, rapidity (less than 30 min), and low cost as well as portability and visuality, in contrast to the currently used thrombin assay. In addition, the developed method had high selectivity, sensitivity (limit of detection of 0.04 nM), and stability (intraday: 3.26%, interday: 6.07%) as well as good recovery (urine: 97-102%, serum: 94-103%). The developed model and method have potential to the development of a point-of-care testing assay in resource-constrained conditions.

Development of a structure-switching aptamer-based nanosensor for salicylic acid detection.

Salicylic acid (SA) is a phytohormone regulating immune responses against pathogens. SA and its derivatives can be found in diverse food products, medicines, cosmetics and preservatives. While salicylates have potential disease-preventative activity, they can also cause health problems to people who are hypersensitive. The current SA detection methods are costly, labor-intensive and require bulky instruments. In this study, a structure-switching aptamer-based nanopore thin film sensor was developed for cost-effective, rapid, sensitive and simple detection of SA in both buffer and plant extracts. SA is a challenging target for aptamer selection using conventional systemic evolution of ligands by exponential enrichment (SELEX) due to its small size and scarcity of reactive groups for immobilization. By immobilizing the SELEX library instead of SA and screening the library using a structure-switching SELEX approach, a high affinity SA aptamer was identified. The nanopore thin film sensor platform can detect as low as 0.1 µM SA. This is much better than the sensitivity of antibody-based detection method. This nanosensor also exhibited good selectivity among SA and its common metabolites and can detect SA in Arabidopsis and rice using only about 1 µl plant extracts within less than 30 min. The integration of SA aptamer and nanopore thin film sensor provides a promising solution for low-cost, rapid, sensitive on-site detection of SA.

Porous Silicon-Based Aptasensors: The Next Generation of Label-Free Devices for Health Monitoring.

Aptamers are artificial nucleic acid ligands identified and obtained from combinatorial libraries of synthetic nucleic acids through the in vitro process SELEX (systematic evolution of ligands by exponential enrichment). Aptamers are able to bind an ample range of non-nucleic acid targets with great specificity and affinity. Devices based on aptamers as bio-recognition elements open up a new generation of biosensors called aptasensors. This review focuses on some recent achievements in the design of advanced label-free optical aptasensors using porous silicon (PSi) as a transducer surface for the detection of pathogenic microorganisms and diagnostic molecules with high sensitivity, reliability and low limit of detection (LoD).