Challenges and opportunities for small molecule aptamer development

Emerging Biohybrids of Aptamer-Based Nano-Biosensing Technologies for Effective Early Cancer Detection

Cancer is a leading global cause of mortality, which underscores the imperative of early detection for improved patient outcomes. Biorecognition molecules, especially aptamers, have emerged as highly effective tools for early and accurate cancer cell identification. Aptamers, with superior versatility in synthesis and modification, offer enhanced binding specificity and stability compared with conventional antibodies. Hence, this article reviews diagnostic strategies employing aptamer-based biohybrid nano-biosensing technologies, focusing on their utility in detecting cancer biomarkers and abnormal cells. Recent developments include the synthesis of nano-aptamers using diverse nanomaterials, such as metallic nanoparticles, metal oxide nanoparticles, carbon-derived substances, and biohybrid nanostructures. The integration of these nanomaterials with aptamers significantly enhances sensitivity and specificity, promising innovative and efficient approaches for cancer diagnosis. This convergence of nanotechnology with aptamer research holds the potential to revolutionize cancer treatment through rapid, accurate, and non-invasive diagnostic methods.

Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review

In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.

Selection of structure-induced aptamer targeting small molecule based on capillary sieving electrophoresis

In this study, a structure-induced aptamer targeting small molecules was selected using capillary sieving electrophoresis (CSE). CSE was conducted using a capillary filled with a background solution containing hydroxypropyl cellulose as a sieving matrix to separate the aptamer candidates by changing their structures via complexation. Before aptamer selection, the original random-sequence DNA library was used to create structure-not-preorganized DNA sub-library containing straight-chain-like structures using CSE. Next, a structure-induced aptamer targeting L-tyrosinamide was selected from the prepared sub-library. Six aptamer candidates were selected, one of which showed a binding ability comparable to that of the reported L-tyrosinamide aptamer and selectivity toward the analogs. These results indicated that the proposed method can be applied to select structure-induced aptamers that target small molecules.

Selection, characterization, and biosensing applications of DNA aptamers targeting cyanotoxin BMAA

Scientists have established a connection between environmental exposure to toxins like β-N-methylamino-l-alanine (BMAA) and a heightened risk of neurodegenerative disorders. BMAA is a byproduct from certain strains of cyanobacteria that are present in ecosystems worldwide and is renowned for its bioaccumulation and biomagnification in seafood. The sensitivity, selectivity, and reproducibility of the current analytical techniques are insufficient to support efforts regarding food safety and environment monitoring adequately. This work outlines the in vitro selection of BMAA-specific DNA aptamers via the systematic evolution of ligands through exponential enrichment (SELEX). Screening and characterization of the full-length aptamers was achieved using the SYBR Green (SG) fluorescence displacement assay. Aptamers BMAA_159 and BMAA_165 showed the highest binding affinities, with dissociation constants (Kd) of 2.2 ± 0.1 μM and 0.32 ± 0.02 μM, respectively. After truncation, the binding affinity was confirmed using a BMAA-conjugated fluorescence assay. The Kd values for BMAA_159_min and BMAA_165_min were 6 ± 1 μM and 0.63 ± 0.02 μM, respectively. Alterations in the amino proton region studied using solution nuclear magnetic resonance (NMR) provided further evidence of aptamer-target binding. Additionally, circular dichroism (CD) spectroscopy revealed that BMAA_165_min forms hybrid G-quadruplex (G4) structures. Finally, BMAA_165_min was used in the development of an electrochemical aptamer-based (EAB) sensor that accomplished sensitive and selective detection of BMAA with a limit of detection (LOD) of 1.13 ± 0.02 pM.

Ultrahigh Throughput Evolution of Tryptophan Synthase in Droplets via an Aptamer Sensor

Tryptophan synthase catalyzes the synthesis of a wide array of noncanonical amino acids and is an attractive target for directed evolution. Droplet microfluidics offers an ultrahigh throughput approach to directed evolution (up to 107 experiments per day), enabling the search for biocatalysts in wider regions of sequence space with reagent consumption minimized to the picoliter volume (per library member). While the majority of screening campaigns in this format on record relied on an optically active reaction product, a new assay is needed for tryptophan synthase. Tryptophan is not fluorogenic in the visible light spectrum and thus falls outside the scope of conventional droplet microfluidic readouts, which are incompatible with UV light detection at high throughput. Here, we engineer a tryptophan DNA aptamer into a sensor to quantitatively report on tryptophan production in droplets. The utility of the sensor was validated by identifying five-fold improved tryptophan synthases from ∼100,000 protein variants. More generally, this work establishes the use of DNA-aptamer sensors with a fluorogenic read-out in widening the scope of droplet microfluidic evolution.

Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications

Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.

A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules

This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.

IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution

SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.

Assessment of the structural change of DNA by binding with a small molecule based on capillary sieving electrophoresis

In this study, capillary sieving electrophoresis (CSE) using polymer solutions was used to evaluate the structural changes in nucleic acids upon complexation with small molecules. As the model target and nucleic acids, L-tyrosinamide (Tyr-Am) and its aptamer, which is a type of DNA specifically binding to Tyr-Am, were selected. CSE was conducted using a capillary filled with background solution (BGS) containing hydroxypropyl cellulose (HPC) as a sieving matrix. When Tyr-Am or tyrosine was added to the BGS in CSE, the ratio of mobility differences of the Tyr-Am-aptamer complex increased compared to that of the free aptamer without the addition of Tyr-Am. In contrast, when other amino acids or their analogs were added, results showed no apparent change or decreases in electrophoretic mobility. These results indicate that the proposed method can be applied to assess structural changes in nucleic acids that target small molecules.

Polymeric integration of structure-switching aptamers on transistors for histamine sensing

Aptamers that undergo large conformational rearrangements at the surface of electrolyte-gated field-effect transistor (EG-FETs)-based biosensors can overcome the Debye length limitation in physiological high ionic strength environments. For the sensitive detection of small molecules, carbon nanotubes (CNTs) that approach the dimensions of analytes of interest are promising channel materials for EG-FETs. However, functionalization of CNTs with bioreceptors using frequently reported surface modification strategies (e.g., π-π stacking), requires highly pristine CNTs deposited through methods that are incompatible with low-cost fabrication methods and flexible substrates. In this work, we explore alternative non-covalent surface chemistry to functionalize CNTs with aptamers. We harnessed the adhesive properties of poly-D-lysine (PDL), to coat the surface of CNTs and then grafted histamine-specific DNA aptamers electrostatically in close proximity to the CNT semiconducting channel. The layer-by-layer assembly was monitored by complementary techniques such as X-ray photoelectron spectroscopy, optical waveguide lightmode spectroscopy, and fluorescence microscopy. Surface characterization confirmed histamine aptamer integration into PDL-coated CNTs and revealed ∼5-fold higher aptamer surface coverage when using CNT networks with high surface areas. Specific aptamers assembled on EG-CNTFETs enabled histamine detection in undiluted high ionic strength solutions in the concentration range of 10 nM to 100 μM. Sequence specificity was demonstrated via parallel measurements with control EG-CNTFETs functionalized with scrambled DNA. Histamine aptamer-modified EG-CNTFETs showed high selectivity vs. histidine, the closest structural analog and precursor to histamine. Taken together, these results implied that target-specific aptamer conformational changes on CNTs facilitate signal transduction, which was corroborated by circular dichroism spectroscopy. Our work suggests that layer-by-layer polymer chemistry enables integration of structure-switching aptamers into flexible EG-CNTFETs for small-molecule biosensing.

Sensing Levofloxacin with an RNA Aptamer as a Bioreceptor

To combat the growing threat of antibiotic resistance, environmental testing for antibiotic contamination is gaining an increasing role. This study aims to develop an easy-to-use assay for the detection of the fluoroquinolone antibiotic levofloxacin. Levofloxacin is used in human and veterinary medicine and has been detected in wastewater and river water. An RNA aptamer against levofloxacin was selected using RNA Capture-SELEX. The 73 nt long aptamer folds into three stems with a central three-way junction. It binds levofloxacin with a Kd of 6 µM and discriminates the closely related compound ciprofloxacin. Furthermore, the selection process was analyzed using a next-generation sequencing approach to better understand the sequence evolution throughout the selection. The aptamer was used as a bioreceptor for the development of a lateral flow assay. The biosensor exploited the innate characteristic of RNA Capture-SELEX to select aptamers that displace a complementary DNA oligonucleotide upon ligand binding. The lateral flow assay achieved a limit of visual detection of 100 µM. While the sensitivity of this assay constrains its immediate use in environmental testing, the present study can serve as a template for the selection of RNA aptamer-based biosensors.

Isolation and Identification of the High-Affinity DNA Aptamer Target to the Brain-Derived Neurotrophic Factor (BDNF)

Aptamers are functional oligonucleotide ligands used for the molecular recognition of various targets. The natural characteristics of aptamers make them an excellent alternative to antibodies in diagnostics, therapeutics, and biosensing. DNA aptamers are mainly single-stranded oligonucleotides (ssDNA) that possess a definite binding to targets. However, the application of aptamers to the fields of brain health and neurodegenerative diseases has been limited to date. Herein, a DNA aptamer against the brain-derived neurotrophic factor (BDNF) protein was obtained by in vitro selection. BDNF is a potential biomarker of brain health and neurodegenerative diseases and has functions in the synaptic plasticity and survival of neurons. We identified eight aptamers that have binding affinity for BDNF from a 50-nucleotide library. Among these aptamers, NV_B12 showed the highest sensitivity and selectivity for detecting BDNF. In an aptamer-linked immobilized sorbent assay (ALISA), the NV_B12 aptamer strongly bound to BDNF protein, in a dose-dependent manner. The dissociation constant (Kd) for NV_B12 was 0.5 nM (95% CI: 0.4-0.6 nM). These findings suggest that BDNF-specific aptamers could be used as an alternative to antibodies in diagnostic and detection assays for BDNF.

Development of a novel tobramycin dependent riboswitch

We herein report the selection and characterization of a new riboswitch dependent on the aminoglycoside tobramycin. Its dynamic range rivals even the tetracycline dependent riboswitch to be the current best performing, synthetic riboswitch that controls translation initiation. The riboswitch was selected with RNA Capture-SELEX, a method that not only selects for binding but also for structural changes in aptamers on binding. This study demonstrates how this method can fundamentally reduce the labour required for the de novo identification of synthetic riboswitches. The initially selected riboswitch candidate harbours two distinct tobramycin binding sites with KDs of 1.1 nM and 2.4 μM, respectively, and can distinguish between tobramycin and the closely related compounds kanamycin A and B. Using detailed genetic and biochemical analyses and 1H NMR spectroscopy, the proposed secondary structure of the riboswitch was verified and the tobramycin binding sites were characterized. The two binding sites were found to be essentially non-overlapping, allowing for a separate investigation of their contribution to the activity of the riboswitch. We thereby found that only the high-affinity binding site was responsible for regulatory activity, which allowed us to engineer a riboswitch from only this site with a minimal sequence size of 33 nt and outstanding performance.

Point-of-Care Prostate Specific Antigen Testing: Examining Translational Progress toward Clinical Implementation

Prostate cancer (PCa) is the second most common male cancer and is attributable to over 375,000 deaths annually. Prostate specific antigen (PSA) is a key biomarker for PCa and therefore measuring patient PSA levels is an important aspect of the diagnostic pathway. Automated immunoassays are currently utilized for PSA analysis, but they require a laboratory setting with specialized equipment and trained personnel. This results in high diagnostic costs, extended therapeutic turnaround times, and restrictions on testing capabilities in resource-limited settings. Consequently, there is a strong drive to develop point-of-care (PoC) PSA tests that can offer accurate, low-cost, and rapid results at the time and place of the patient. However, many emerging PoC tests experience a trade-off between accuracy, affordability, and accessibility which distinctly limits their translational potential. This review comprehensively assesses the translational advantages and limitations of emerging laboratory-level and commercial PoC tests for PSA determination. Electrochemical and optical PSA sensors from 2013 to 2023 are systematically examined. Furthermore, we suggest how the translational potential of emerging tests can be optimized to achieve clinical implementation and thus improve PCa diagnosis globally.

Emerging Applications of Nanobiosensors in Pathogen Detection in Water and Food

Food and waterborne illnesses are still a major concern in health and food safety areas. Every year, almost 0.42 million and 2.2 million deaths related to food and waterborne illness are reported worldwide, respectively. In foodborne pathogens, bacteria such as Salmonella, Shiga-toxin producer Escherichia coli, Campylobacter, and Listeria monocytogenes are considered to be high-concern pathogens. High-concern waterborne pathogens are Vibrio cholerae, leptospirosis, Schistosoma mansoni, and Schistosima japonicum, among others. Despite the major efforts of food and water quality control to monitor the presence of these pathogens of concern in these kinds of sources, foodborne and waterborne illness occurrence is still high globally. For these reasons, the development of novel and faster pathogen-detection methods applicable to real-time surveillance strategies are required. Methods based on biosensor devices have emerged as novel tools for faster detection of food and water pathogens, in contrast to traditional methods that are usually time-consuming and are unsuitable for large-scale monitoring. Biosensor devices can be summarized as devices that use biochemical reactions with a biorecognition section (isolated enzymes, antibodies, tissues, genetic materials, or aptamers) to detect pathogens. In most cases, biosensors are based on the correlation of electrical, thermal, or optical signals in the presence of pathogen biomarkers. The application of nano and molecular technologies allows the identification of pathogens in a faster and high-sensibility manner, at extremely low-pathogen concentrations. In fact, the integration of gold, silver, iron, and magnetic nanoparticles (NP) in biosensors has demonstrated an improvement in their detection functionality. The present review summarizes the principal application of nanomaterials and biosensor-based devices for the detection of pathogens in food and water samples. Additionally, it highlights the improvement of biosensor devices through nanomaterials. Nanomaterials offer unique advantages for pathogen detection. The nanoscale and high specific surface area allows for more effective interaction with pathogenic agents, enhancing the sensitivity and selectivity of the biosensors. Finally, biosensors' capability to functionalize with specific molecules such as antibodies or nucleic acids facilitates the specific detection of the target pathogens.

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

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

Pesticide biosensors: trends and progresses

Pesticides, chemical substances extensively employed in agriculture to optimize crop yields, pose potential risks to human and environmental health. Consequently, regulatory frameworks are in place to restrict pesticide residue concentrations in water intended for human consumption. These regulations are implemented to safeguard consumer safety and mitigate any adverse effects on the environment and public health. Although gas chromatography- and liquid chromatography-mass spectrometry (GC-MS and LC-MS) are highly efficient techniques for pesticide quantification, their use is not suitable for real-time monitoring due to the need for sophisticated laboratory pretreatment of samples prior to analysis. Since they would enable analyte detection with selectivity and sensitivity without sample pretreatment, biosensors appear as a promising alternative. These consist of a bioreceptor allowing for specific recognition of the target and of a detection platform, which translates the biological interaction into a measurable signal. As early detection systems remain urgently needed to promptly alert and act in case of pollution, we review here the biosensors described in the literature for pesticide detection to advance their development for use in the field.

Clinical applications of smart wearable sensors

Smart wearable sensors are electronic devices worn on the body that collect, process, and transmit various physiological data. Compared to traditional devices, their advantages in terms of portability and comfort have made them increasingly important in the medical field. This review takes a unique clinical physician's standpoint, diverging from conventional sensor-type-based classifications, and provides a comprehensive overview of the diverse clinical applications of wearable sensors in recent years. In this review, we categorize these applications according to different diseases, encompassing skin diseases and injuries, cardiovascular diseases, abnormal human motion, as well as endocrine and metabolic disorders. Additionally, we discuss the challenges and perspectives hindering the development of sensors for clinical use, emphasizing the critical need for interdisciplinary collaboration between medical and engineering professionals. Overall, this review would serve as an important reference for the future direction of sensor devices in clinical use.

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

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

Porphyrin-based ligand interaction with G-quadruplex: Metal cation effects

The G-quadruplex planar-ligand complex is used to detect heavy metal cations such as Ag+ , Cu2+ , Pb2+ , Hg2+ , organic molecules, nucleic acids, and proteins. The interaction of the three planar porphyrins (L1), 5,10,15,20-tetrakis (1-ethyl-1-λ4 -pyridine-4-yl) porphyrin (L2), and 5,10,15,20-tetrakis (1-methyl-1-λ4 -pyridine-4-yl) porphyrin (L3), coming from the porphyrin family, with G-quadruplex obtained from human DNA telomeres in the presence of lithium, sodium, potassium, rubidium, cesium, magnesium, and calcium ions was studied by molecular dynamics simulation. When G-quadruplex containing divalent ions of magnesium and calcium interacts with L1, L2, and L3 ligands, the hydrogen bonds of the lower G-quadruplex sheet are more affected by ligands and the distance between guanines in the lower tetrad increases. In the case of G-quadruplex interactions containing monovalent ions with ligands, the hydrogen bond between the sheets does not follow a specific trend. For example, in the presence of lithium ions, the upper and middle sheets are more affected by ligands, while they are less affected by ligands in the presence of sodium. The binding pocket and the binding energy of the three ligands to the G-quadruplex were also obtained in the various systems. The results show that ligands make the G-quadruplex more stable through the penetration between the sheets and the interaction with the loops. Among the ligands mentioned, the interaction level of the ligand L2 is greater than the others. Our calculations are consistent with the previous experimental observations so that it can help to understand the molecular mechanism of porphyrin interaction and its derivatives with the G-quadruplex.

In vitro selection of aptamers and their applications

The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.

Electrochemical aptasensor based on exonuclease III-mediated signal amplification for sensitive detection of vomitoxin in cornmeal

Vomitoxin (DON) residues in grains are of great concern to public health. Herein, a label-free aptasensor was constructed to detect DON distributed in grains. Cerium-based metal-organic framework composite gold nanoparticles (CeMOF@Au) were used as substrate materials to facilitate electron transfer and provided more binding sites for DNA. The separation of DON-aptamer (Apt) complex and cDNA was achieved by magnetic separation technique based on magnetic beads (MBs), ensuring the specificity of the aptasensor. Exonuclease III (Exo III)-assisted cDNA cycling process strategy would be triggered when cDNA was separated and introduced to the sensing interface for further signal amplification. Under optimal conditions, the constructed aptasensor presented a wide detection range from 1 × 10^-8 mg·mL^-1 to 5 × 10^-4 mg·mL^-1 for DON, and the detection limit was 1.79 × 10^-9 mg·mL^-1, including a satisfactory recovery in cornmeal sample spiked with DON. The results showed that the proposed aptasensor had high reliability and promising application potential in detecting DON.

An aptamer-based depot system for sustained release of small molecule therapeutics

Delivery of hydrophilic small molecule therapeutics by traditional drug delivery systems is challenging. Herein, we have used the specific interaction between DNA aptamers and drugs to create simple and effective drug depot systems. The specific binding of a phosphorothioate-modified aptamer to drugs formed non-covalent aptamer/drug complexes, which created a sustained release system. We demonstrated the effectiveness of this system with small hydrophilic molecules, the site 1 sodium channel blockers tetrodotoxin and saxitoxin. The aptamer-based delivery system greatly prolonged the duration of local anesthesia and reduced systemic toxicity. The beneficial effects of the aptamers were restricted to the compounds they were specific to. These studies establish aptamers as a class of highly specific, modifiable drug delivery systems, and demonstrate potential usefulness in the management of postoperative pain.

Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors

Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.

Anti-CD44 antibodies grafted immunoaffinity Fe3O4@MnO2 nanozymes with highly oxidase-like catalytic activity for specific detection of triple-negative breast cancer MDA-MB-231 cells

Cell-enzyme-linked immunosorbent assay (CELISA) is extensively applied for cancer diagnosis and screening because of its simple operation, high sensitivity, and intuitive color change. However, the unstable horseradish peroxidase (HRP), hydrogen peroxide (H₂O₂) and non-specificity have led to a high false negative rate, which limits its application. In this study, we have developed an innovative immunoaffinity nanozyme aided CELISA based on anti-CD44 monoclonal antibodies (mAbs) bioconjugated manganese dioxide-modified magnetite nanoparticles (Fe₃O₄@MnO₂ NPs) for the specific detection of triple-negative breast cancer MDA-MB-231 cells. The ^CD44FM nanozymes were fabricated to replace unstable HRP and H₂O₂ to counteract possible negative effects in conventional CELISA. Results suggested that ^CD44FM nanozymes displayed remarkable oxidase-like activities over an extensive pH and temperature range. The bioconjugation of CD44 mAbs enabled ^CD44FM nanozymes to enter MDA-MB-231 cells selectively via over-expressed CD44 antigens on the membrane surface of these cells, and then catalyzed oxidation of the chromogenic substrate TMB, further achieving specific detection of these cells. Additionally, this study exhibited high sensitivity and low detection limit for MDA-MB-231 cells with a quantitation range of just 186 cells. To sum up, this report developed a simple, specific and sensitive assay platform based on ^CD44FM nanozymes, which could provide a promising strategy for targeted diagnosis and screening of breast cancer.

Isolation of a novel DNA aptamer against LipL32 as a potential diagnostic agent for the detection of pathogenic Leptospira

Leptospirosis is a potentially life-threatening zoonosis caused by pathogenic Leptospira and for rapid diagnostics, direct detection is desirable. LipL32 protein is the most suitable biomarker for direct detection. DNA aptamers are sought to be generated against LipL32 by Systemic Evolution of Ligands via Exponential Enrichment (SELEX). LepDapt-5a is the most potent aptamer candidate among all the candidates, as determined by direct Enzyme-linked Aptasorbent Assay (ELASA). LepDapt-5a was predicted to form a G-quadruplex structure as predicted by QGRS Mapper and validated experimentally by direct ELASA. The diagnostic potential of the aptamer was further tested on a direct and sandwich ELASA platform. A LOD of 106 mL-1 and 105 mL-1 were estimated by direct and sandwich ELASA platforms, respectively, which are within the range associated with leptospiremia levels. The dot blot assay developed was able to attain a LOD of 104 CFU mL-1 against pathogenic Leptospira, which is also within the leptospiremia level. This is the first-ever DNA aptamer and hybrid-heterodimeric aptamer constructed against LipL32. The diagnostic potentiality of the LepDapt-5a DNA aptamer was proven on three major diagnostic platforms, which are direct ELASA, sandwich ELASA, and aptamer-based dot assay.

Advances and perspectives in the analytical technology for small peptide hormones analysis: A glimpse to gonadorelin

In the last twenty years, we have witnessed an important evolution of bioanalytical approaches moving from conventional lab bench instrumentation to simpler, easy-to-use techniques to deliver analytical responses on-site, with reduced analysis times and costs. In this frame, affinity reagents production has also jointly advanced from natural receptors to biomimetic, abiotic receptors, animal-free produced. Among biomimetic ones, aptamers, and molecular imprinted polymers (MIPs) play a leading role. Herein, our motivation is to provide insights into the evolution of conventional and innovative analytical approaches based on chromatography, immunochemistry, and affinity sensing referred to as peptide hormones. Indeed, the analysis of peptide hormones represents a current challenge for biomedical, pharmaceutical, and anti-doping analysis. Specifically, as a paradigmatic example, we report the case of gonadorelin, a neuropeptide that in recent years has drawn a lot of attention as a therapeutic drug misused in doping practices during sports competitions.

Continuous Square Wave Voltammetry for High Information Content Interrogation of Conformation Switching Sensors

Square wave voltammetry (SWV) is a voltammetric technique for measuring Faradaic current while minimizing contributions from non-Faradaic processes. In square wave voltammetry, the potential waveform applied to a working electrode and the current sampling protocols followed are designed to minimize contributions from non-Faradaic processes (i.e., double layer charging) to improve voltammetric sensitivity. To achieve this, the current is measured at the end of each forward and reverse potential pulse after allowing time for non-Faradaic currents to decay exponentially. A consequence of sampling current at the end of a potential pulse is that the current data from the preceding time of the potential pulse are discarded. These discarded data can provide information about the non-Faradaic contributions as well as information about the redox system including charge transfer rates. In this paper, we introduce continuous square wave voltammetry (cSWV), which utilizes the continuous collection of current to maximize the information content obtainable from a single voltammetry sweep eliminating the need for multiple scans. cSWV enables acquiring a multitude of voltammograms corresponding to various frequencies and, thus, different scan rates from a single sweep. An application that benefits significantly from cSWV is conformation switching, functional nucleic acid sensors. We demonstrate the utility of cSWV on two representative small molecules targeting electrochemical, aptamer-based sensors. Moreover, we show that cSWV provides comparable results to those obtained from traditional square wave voltammetry, but with cSWV, we are able to acquire dynamic information about the sensor surfaces enabling rapid calibration and optimization of sensing performance. We also demonstrate cSWV on soluble redox markers. cSWV can potentially become a mainstay technique in the field of conformation switching sensors.

Direct Identification of Label-Free Gram-Negative Bacteria with Bioreceptor-Free Concentric Interdigitated Electrodes

This investigation demonstrates an electrochemical method for directly identifying unlabeled Gram-negative bacteria without other additives or labeling agents. After incubation, the bacterial cell surface is linked to the interdigitated electrode through electroadsorption. Next, these cells are exposed to a potential difference between the two electrodes. The design geometry of an electrode has a significant effect on the electrochemical detection of Gram-negative bacteria. Therefore, electrode design geometry is a crucial factor that needs to be considered when designing electrodes for electrochemical sensing. They provide the area for the reaction and are responsible for transferring electrons from one electrode to another. This work aims to study the available design in the commercial market to determine the most suitable electrode geometry with a high detection sensitivity that can be used to identify and quantify bacterial cells in normal saline solutions. To work on detecting bacterial cells without the biorecognition element, we have to consider the microelectrode's design, which makes it very susceptible to bacteria size. The concentration-dilution technique measures the effect of the concentration on label-free Gram-negative bacteria in a normal saline solution without needing bio-recognized elements for a fast screening evaluation. This method's limit of detection (LOD) cannot measure concentrations less than 102 CFU/mL and cannot distinguish between live and dead cells. Nevertheless, this approach exhibited excellent detection performance under optimal experimental conditions and took only a few hours.

Facile Expansion of the Variety of Orthogonal Ligand/Aptamer Pairs for Artificial Riboswitches

An RNA aptamer that induces suitable conformational changes upon binding to a user-defined ligand allows us to artificially construct a riboswitch, a ligand-dependent and cis-acting gene regulatory RNA. Although such an aptamer can be obtained through in vitro selection, it is still challenging to rationally expand the variety of orthogonal ligand/aptamer (ligand/riboswitch) pairs. To achieve this in a facile, selection-free way, we herein focused on a specific type of ligand, 6-nt nanosized DNA (nDNA) and its aptamer that was previously selected to construct a eukaryotic artificial riboswitch. Specifically, we merely mutated one or more possible Watson-Crick base pairs in the nDNA/aptamer (nDNA/riboswitch) interactions into another base pair or pairs. Using two sets that each had 16 comprehensive mutations, we obtained three groups of several orthogonal nDNA/riboswitch pairs. These pairs could be used to create complex gene circuits, including multiple simultaneous and/or multistep cascading regulations in synthetic biology.

Wearable and flexible electrochemical sensors for sweat analysis: a review

Flexible wearable sweat sensors allow continuous, real-time, noninvasive detection of sweat analytes, provide insight into human physiology at the molecular level, and have received significant attention for their promising applications in personalized health monitoring. Electrochemical sensors are the best choice for wearable sweat sensors due to their high performance, low cost, miniaturization, and wide applicability. Recent developments in soft microfluidics, multiplexed biosensing, energy harvesting devices, and materials have advanced the compatibility of wearable electrochemical sweat-sensing platforms. In this review, we summarize the potential of sweat for medical detection and methods for sweat stimulation and collection. This paper provides an overview of the components of wearable sweat sensors and recent developments in materials and power supply technologies and highlights some typical sensing platforms for different types of analytes. Finally, the paper ends with a discussion of the challenges and a view of the prospective development of this exciting field.

Immobilization-Free Determination of Dissociation Constants Independent of Ligand Size Using MicroScale Thermophoresis

The quantitative characterization of aptamer-ligand interactions is an important step in the aptamer development process. However, certain pitfalls impede K_D determination, especially when working with small molecule ligands. These include altered binding behavior caused by ligand immobilization. Further, the compulsory requirement for major differences in size between the bound and unbound state makes small molecule ligands ineligible for separation-based methods. MicroScale Thermophoresis circumvents such limitations as binding is accurately quantified with both binding partners free in solution and independent of ligand size. In this chapter, we present a protocol for the characterization of a DNA aptamer binding to its small molecule ligand daunorubicin.

Target-switch SELEX: Screening with alternating targets to generate aptamers to conserved terminal dipeptides

Systematic evolution of ligands by exponential enrichment (SELEX) encompasses a wide variety of high-throughput screening techniques for producing nucleic acid binders to molecular targets through directed evolution. We describe here the design and selection steps for discovery of DNA aptamers with specificity for the two consecutive N-terminal amino acids (AAs) of a small peptide (8-10 amino acids). This bead-based method may be adapted for applications requiring binders which recognize a specific portion of the desired target. For complete details on the use and execution of this protocol, please refer to Hong et al. (2022).

Discovery of a Highly Specific Anti-methotrexate (MTX) DNA Aptamer for Antibody-Independent MTX Detection

High-dose methotrexate (MTX) therapy is used to treat a wide variety of cancers such as leukemia and lymphoma, while the resulting high blood concentration of MTX faces a risk of life-threatening side effects, so it is essential to monitor the concentration carefully. Currently, the MTX concentration is measured using antibody-based kits in a clinical setting; however, the heterogeneity and batch-to-batch variation of antibodies potentially compromise the detection limit. Here, we developed MTX detection systems with chemically synthesizable homogeneous oligonucleotides. Microbead-assisted capillary electrophoresis (MACE)-SELEX against MTX successfully identified MS^mt7 with a similar level of specificity to anti-MTX antibodies within three rounds. The 3'-end of MS^mt7 was coupled to a peroxidase-like hemin-DNAzyme to construct a bifunctional oligonucleotide for MTX sensing, where MTX in 50% human serum was detected with a limit of detection (LoD) of 118 nM. Furthermore, amplifying the DNAzyme region with rolling circle amplification significantly improved the sensitivity with an LoD of 290 pM. Presented oligonucleotide-based MTX detection systems will pave the way for antibody-independent MTX detection with reliability and less cost in the laboratory and the clinic.

Aptamer nucleotide analog drug conjugates in the targeting therapy of cancers

Aptamers are short single-strand oligonucleotides that can form secondary and tertiary structures, fitting targets with high affinity and specificity. They are so-called "chemical antibodies" and can target specific biomarkers in both diagnostic and therapeutic applications. Systematic evolution of ligands by exponential enrichment (SELEX) is usually used for the enrichment and selection of aptamers, and the targets could be metal ions, small molecules, nucleotides, proteins, cells, or even tissues or organs. Due to the high specificity and distinctive binding affinity of aptamers, aptamer-drug conjugates (ApDCs) have demonstrated their potential role in drug delivery for cancer-targeting therapies. Compared with antibodies which are produced by a cell-based bioreactor, aptamers are chemically synthesized molecules that can be easily conjugated to drugs and modified; however, the conventional ApDCs conjugate the aptamer with an active drug using a linker which may add more concerns to the stability of the ApDC, the drug-releasing efficiency, and the drug-loading capacity. The function of aptamer in conventional ApDC is just as a targeting moiety which could not fully perform the advantages of aptamers. To address these drawbacks, scientists have started using active nucleotide analogs as the cargoes of ApDCs, such as clofarabine, ara-guanosine, gemcitabine, and floxuridine, to replace all or part of the natural nucleotides in aptamer sequences. In turn, these new types of ApDCs, aptamer nucleotide analog drug conjugates, show the strength for targeting efficacy but avoid the complex drug linker designation and improve the synthetic efficiency. More importantly, these classic nucleotide analog drugs have been used for many years, and aptamer nucleotide analog drug conjugates would not increase any unknown druggability risk but improve the target tumor accumulation. In this review, we mainly summarized aptamer-conjugated nucleotide analog drugs in cancer-targeting therapies.

Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets

Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.

Aptamer Selection Based on Microscale Electrophoretic Filtration Using a Hydrogel-Plugged Capillary Device

This study reports a novel aptamer selection method based on microscale electrophoretic filtration. Aptamers are versatile materials that recognize specific targets and are attractive for their applications in biosensors, diagnosis, and therapy. However, their practical applications remain scarce due to issues with conventional selection methods, such as complicated operations, low-efficiency separation, and expensive apparatus. To overcome these drawbacks, a selection method based on microscale electrophoretic filtration using a capillary partially filled with hydrogel was developed. The electrophoretic filtration of model target proteins (immunoglobulin E (IgE)) using hydrogel, the electrokinetic injection of DNAs to interact with the trapped proteins, the elimination of DNAs with weak interactions, and the selective acquisition of aptamer candidates with strong interactions were successfully demonstrated, revealing the validity of the proposed concept. Two aptamer candidates for IgE were obtained after three selection cycles, and their affinity for the target was confirmed to be less than 1 nM based on their dissociation constant (K_D) values. Therefore, the proposed method allows for the selection of aptamers with simple operations, highly effective separation based on electrophoresis and filtration, and a relatively cheap apparatus with disposable devices.

Unveiling the underpinnings of various non-conventional ELISA variants: a review article

INTRODUCTION

Enzyme-linked immunosorbent assay (ELISA) is a key bio-analytical technique used for the detection of a large array of antigenic substances of scientific, clinical, food safety, and environmental importance. The assay primarily involves capturing and detecting target analytes using specific antigen-antibody interactions. The wide usage of ELISA shoulders on its high specificity and reproducibility. Notwithstanding, the conventional microwell plate-based format of ELISA has some major drawbacks, such as long assay time (4 - 18 h), large sample volumes requirement (100 - 200 μL), lack of multiplicity, and burdensome procedures that limit its utility in rapid and affordable diagnostics.

AREAS COVERED

Here, we reviewed microfluidic-ELISA, paper-ELISA, aptamer-ELISA, and those based on novel incubation such as heat-ELISA, pressure-ELISA, microwave-ELISA, and sound-ELISA. Further, the current trends and future prospects of these ELISA protocols in clinical diagnostics are discussed.

EXPERT OPINION

The reviewed non-conventional ELISA formats are relatively rapid, require low reagent volumes, are multiplexable, and could be performed in a low-cost setup. In our opinion, these non-conventional variants of ELISA are on a par with the conventional format for clinical diagnostics and fundamental biological research and hold added clinical translational potential for quick, inexpensive, and convenient measurements.

Future perspectives on aptamer for application in food authentication

Food fraudulence and food contamination are major concerns, particularly among consumers with specific dietary, cultural, lifestyle, and religious requirements. Current food authentication methods have several drawbacks and limitations, necessitating the development of a simpler, more sensitive, and rapid detection approach for food screening analysis, such as an aptamer-based biosensor system. Although the use of aptamer is growing in various fields, aptamer applications for food authentication are still lacking. In this review, we discuss the limitations of existing food authentication technologies and describe the applications of aptamer in food analyses. We also project several potential targets or marker molecules to be targeted in the SELEX process. Finally, this review highlights the drawbacks of current aptamer technologies and outlines the potential route of aptamer selection and applications for successful food authentication. This review provides an overview of the use of aptamer in food research and its potential application as a molecular reporter for rapid detection in food authentication process. Developing databases to store all biochemical profiles of food and applying machine learning algorithms against the biochemical profiles are urged to accelerate the identification of more reliable biomarker molecules as aptamer targets for food authentication.

On-chip selection of adenosine aptamer using graphene oxide-coated magnetic nanoparticles

Systematic evolution of ligands by exponential enrichment (SELEX) is a method that is generally used for developing aptamers, which have arisen the promising alternatives for antibodies. However, conventional SELEX methods have limitations, such as a limited selection of target molecules, time-consuming and complex fabrication processes, and labor-intensive processes, which result in low selection yields. Here, we used (i) graphene oxide (GO)-coated magnetic nanoparticles in the selection process for separation and label-free detection and (ii) a multilayered microfluidic device manufactured using a three-dimensionally printed mold that is equipped with automated control valves to achieve precise fluid flows. The developed on-chip aptamer selection device and GO-coated magnetic nanoparticles were used to screen aptamer candidates for adenosine in eight cycles of the selection process within approximately 2 h for each cycle. Based on results from isothermal titration calorimetry, an aptamer with a dissociation constant of 18.6 ± 1.5 μM was selected. Therefore, the on-chip platform based on GO-coated magnetic nanoparticles provides a novel label-free screening technology for biosensors and micro/nanobiotechnology for achieving high-quality aptamers.

Efficient Screening of Pesticide Diazinon-Binding Aptamers Using the Sol-Gel-Coated Nanoporous Membrane-Assisted SELEX Process and Next-Generation Sequencing

Aptamer-based methods for detecting pesticides are more efficient than antibody-based methods by high thermal stability, low molecular weight, easy modification, and low cost. In this study, the systematic evolution of ligands by exponential enrichment (SELEX) process, combined with next-generation sequencing (NGS), was performed to select aptamers specific to the pesticide, diazinon, which was fixed on a sol-gel-coated nanoporous-anodized aluminum oxide membrane to overcome the immobilization effect of general method and simplify the elution step. The frequency of specific nucleotide sequences obtained after SELEX rounds was directly analyzed using NGS to eliminate the time-consuming cloning process used in the general SELEX methods. Nine sequences with the highest frequency after SELEX round 10 followed by NGS were selected and tested to derive their binding affinity with the target, diazinon, through circular dichroism (CD) spectrophotometry. The CD signal difference of the aptamer candidates ranged from 0.13 to 2.242 mdeg between diazinon-only treated and diazinon-aptamer-treated samples at a wavelength near 270 nm. Aptamer D-4, which had the highest binding affinity from CD spectrophotometry analysis, showed no cross-reactivity with non-target pesticides, such as baycarb, bifenthrin, and pyridaben, but interacted with the other pesticides, fipronil and 2-phenylphenol. Therefore, an aptamer was effectively screened by selection of high-frequency candidates after SELEX-NGS followed by CD analysis with the highest difference signal. A follow-up study is needed to confirm whether the proposed SELEX process combined with NGS for the discovery of aptamers for new targets can further shorten the SELEX cycle by reducing the number of SELEX rounds to 10 or less.