Selection and identification of diethylstilbestrol-specific aptamers based on magnetic-bead SELEX

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.

A novel nanoparticle-based fluorescent sandwich immunoassay for specific detection of Salmonella Typhimurium

The diseases caused by foodborne pathogens have a serious impact on human health and social stability. Conventional detection methods can involve long assay times and complex pretreatment steps, making them unsuitable for rapid, large-scale analysis of food samples. We constructed a novel nano-fluorescence sandwich immunosorbent immunoassay (nano-FSIA) to rapidly detect Salmonella Typhimurium in food, based on strong covalent binding between streptavidin and biotin. We used antibodies coupled to large particle-size fluorescent microspheres as fluorescent probes for direct quantitative analysis of S. typhimurium in milk. The optimized parameters were determined, and specificity and sensitivity were validated in phosphate-buffered saline (PBS) and milk. The results demonstrated a wide dynamic detection range for S. typhimurium (103-108 colony forming units [CFU]/mL), with the limit of detection in PBS and milk at 234 and 346 CFU/mL, respectively. The results of nano-FSIA were consistent with those of plate counts and enzyme-linked immunosorbent assays, providing an effective and promising single-bacterium counting method for the rapid detection of Salmonella.

Recent progress of SELEX methods for screening nucleic acid aptamers

Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.

Electrochemical aptasensors for pathogenic detection toward point-of-care diagnostics

A biosensor system refers to a biomedical device, which detects biological, chemical, or biochemical components by converting those signals to an electrical signal by utilizing and uniting physical or chemical transducer with biorecognition elements. An electrochemical biosensor is generally based on the reaction of either production or consumption of electrons under a three-electrode system. Biosensor systems are exploited in a wide range of areas, such as medicine, agriculture, husbandry, food, industry, environment protection, quality control, waste disposal, and the military. Pathogenic infections are the third leading cause of death worldwide after cardiovascular diseases and cancer. Therefore, there is an urgent need for effective diagnostic tools to control food, water, and soil contamination result in protecting human life and health. Aptamers are peptide or oligonucleotide-based molecules that show very high affinity to their targets that are produced from large pools of random amino acid or oligonucleotide sequences. Generally, aptamers have been utilized for fundamental sciences and clinical implementations for their target-specific affinity and have been intensely exploited for different kinds of biosensor applications for approximately 30 years. The convergence of aptamers with biosensor systems enabled the construction of voltammetric, amperometric, and impedimetric biosensors for the detection of specific pathogens. In this review, electrochemical aptamer biosensors were evaluated by discussing the definition, types, and production techniques of aptamers, the advantages of aptamers as a biological recognition element against their alternatives, and a wide range of aptasensor examples from literature in the detection of specific pathogens.

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.

Aptamers for Viral Detection and Inhibition

Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.

Selection and identification of high-affinity aptamer of Kunitz trypsin inhibitor and their application in rapid and specific detection

Kunitz trypsin inhibitor (KTI), a harmful protein, seriously affects food hygiene and safety. Therefore, a sensitive, efficient, and rapid method for KTI detection is urgently needed. Aptamers are short and single-stranded (ss) DNA that recognize target molecules with high affinity. This work used graphene oxide-SELEX (GO-SELEX) to screen KTI aptamers. The positive and reverse screening was designed to ensure the high specificity and affinity of the selected aptamers. After 10 rounds of screening, multiple nucleic acid chains were obtained, and the chains were sequenced. Three aptamers with better affinity were obtained, and the values of the dissociation constant (K d) were calculated to be 52.6 nM, 22.7 nM, and 67.9 nM, respectively. Finally, a colorimetric aptamer biosensor based on gold nanoparticles (AuNPs) was constructed. The biosensor exhibited a broader linear range of 30-750 ng/ml, with a lower detection limit of 18 ng/ml, and the spiked recovery rate was between 98.2% and 103.3%. This experiment preliminary demonstrated the potential of the application of KTI aptamer in the real sample tests.

Effectively Selecting Aptamers for Targeting Aromatic Biogenic Amines and Their Application in Aptasensing Establishment

It is necessary to detect the biogenic amine (BA) content in food due to their toxicological effects and their role as an index of freshness for protein-rich foods. Aptamer-based techniques have the potential to provide alternative methods for sensitive and efficient monitoring of BAs. Herein, we described the selection and characterization of DNA aptamers for tyramine (TYR) and β-phenethylamine (PHE) using a one-pot coupled with separate selection strategy. During the selection process, melting curve analysis was developed to monitor the enrichment of the aptamer species, and a saturation of the selection was found at the 14th round. Based on the fluorescence assay, aptamers TYR-2 and PHE-2 showed high affinity to TYR and PHE with the dissociation constant values of 64.28 ± 10.4 and 71.64 ± 11.47 nM, respectively. The circular dichromatic and molecular docking technologies were employed for the preliminary binding mechanism analysis. The obtained aptamers TYR-2 and PHE-2 were used in a fluorescence method for the TYR and PHE determination with limits of detection of 0.34 and 0.39 ng/mL, respectively. In addition, the developed aptasensor was further applied to the TYR and PHE detection in pork and beer samples, and the recovery rate was between 95.6 and 104.2%. It was demonstrated that the selected aptamers had enormous potential as a molecular probe for the identification and determination of BAs.

Regenerative Flexible Upconversion-Luminescence Biosensor for Visual Detection of Diethylstilbestrol Based on Smartphone Imaging

Diethylstilbestrol (DES), an endocrine disrupting chemical, has been linked to serious health problems in humans. In this work, a regenerative flexible upconversion-fluorescence biosensor was designed for the detection of DES in foodstuffs and environmental samples. Herein, amino-functionalized upconversion nanoparticles (UCNPs) were synthesized and immobilized on the surface of a flexible polydimethylsiloxane substrate, which was further modified with complementary DNA and dabcyl-labeled DES aptamer. The fluorescence resonance energy transfer (FRET) system was established for DES detection between dabcyl and UCNPs as the acceptor and donor pairs, respectively, which resulted in the quenching of the upconversion luminescence intensity. In the presence of a target, the FRET system was destroyed and upconversion fluorescence was restored due to the stronger affinity of the aptamer toward DES. The designed biosensor was also implemented in a dual-mode signal readout based on images from a smartphone and spectra from a spectrometer. Under the optimized experimental conditions, good linear relationships were achieved based on imaging (y = 53.055x + 36.175, R² = 0.9851) and spectral data (y = 1.1582x + 1.9561, R² = 0.9897). The designed biosensor revealed great practicability with a spiked recovery rate of 77.91-97.95% for DES detection in real environment and foodstuff samples. Furthermore, the proposed biosensor was regenerated seven times with an accuracy threshold of 80% demonstrating its durability and reusability. Thus, this biosensor is expected to be applied to point-of-care and on-site detection based on the developed portable smartphone device and android application.

Aptasensors for mycotoxins in foods: Recent advances and future trends

Mycotoxin contamination in foods has posed serious threat to public health and raised worldwide concern. The development of simple, rapid, facile, and cost-effective methods for mycotoxin detection is of urgent need. Aptamer-based sensors, abbreviated as aptasensors, with excellent recognition capacity to a wide variety of mycotoxins have attracted ever-increasing interest of researchers because of their simple fabrication, rapid response, high sensitivity, low cost, and easy adaptability for in situ measurement. The past few decades have witnessed the rapid advances of aptasensors for mycotoxin detection in foods. Therefore, this review first summarizes the reported aptamer sequences specific for mycotoxins. Then, the recent 5-year advancements in various newly developed aptasensors, which, according to the signal output mode, are divided into electrochemical, optical and photoelectrochemical categories, for mycotoxin detection are comprehensively discussed. A special attention is taken on their strengths and limitations in real-world application. Finally, the current challenges and future perspectives for developing novel highly reliable aptasensors for mycotoxin detection are highlighted, which is expected to provide powerful references for their thorough research and extended applications. Owing to their unique advantages, aptasensors display a fascinating prospect in food field for safety inspection and risk assessment.

Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications

Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.

Overview of Rapid Detection Methods for Salmonella in Foods: Progress and Challenges

Salmonella contamination in food production and processing is a serious threat to consumer health. More and more rapid detection methods have been proposed to compensate for the inefficiency of traditional bacterial cultures to suppress the high prevalence of Salmonella more efficiently. The contamination of Salmonella in foods can be identified by recognition elements and screened using rapid detection methods with different measurable signals (optical, electrical, etc.). Therefore, the different signal transduction mechanisms and Salmonella recognition elements are the key of the sensitivity, accuracy and specificity for the rapid detection methods. In this review, the bioreceptors for Salmonella were firstly summarized and described, then the current promising Salmonella rapid detection methods in foodstuffs with different signal transduction were objectively summarized and evaluated. Moreover, the challenges faced by these methods in practical monitoring and the development prospect were also emphasized to shed light on a new perspective for the Salmonella rapid detection methods applications.

Rapid exposure monitoring of six bisphenols and diethylstilbestrol in human urine using fabric phase sorptive extraction followed by high performance liquid chromatography - photodiode array analysis

A novel fabric phase sorptive extraction protocol is developed for rapid exposure monitoring of six bisphenol analogues, including bisphenol A, bisphenol S, bisphenol F, bisphenol E, bisphenol B, bisphenol C, and diethylstilbestrol (DES) from human urine prior to high-performance liquid chromatography-photodiode array analysis. FPSE sample pretreatment protocol ensures the harmonization of the proposed method with the principles of Green Analytical Chemistry (GAC). Among eighteen evaluated FPSE membranes, sol-gel poly (ethylene glycol) (PEG) coated cellulose FPSE membrane resulted in the most efficient extraction. This polar FPSE membrane effectively exploits a number of advantageous features inherent to FPSE including sponge-like porous architecture of the sol-gel sorbent coating, favorable surface chemistry, flexibility and built-in permeability of cellulose fabric substrate, high primary contact surface area for rapid sorbent-analyte interaction, expanded pH, solvent and thermal stability as well as reusability of the FPSE membrane. Optimization was centered on the evaluation of critical parameters, namely the size of the FPSE membrane, the elution solvent mixture, the volume of the sample, the extraction time, the elution time, the kind of the external agitation mechanical stimulus, the ionic strength and the pH of the sample. The chromatographic separation was achieved on a Spherisorb C18 column and a gradient elution program with mobile phase consisted of 0.05 ammonium acetate solution and acetonitrile. The total analysis time was 17.4 min. The developed method was validated in terms of linearity, sensitivity, selectivity, precision, accuracy, stability, and ruggedness. The limits of detection and quantification varied from 0.26-0.62 ng/mL and 0.8-1.9 ng/mL, respectively. The relative recoveries were calculated between 90.6 and 108.8%, while the RSD values were <10% in all cases. The effectiveness of the proposed method was confirmed by its successful implementation in the bioanalysis of real urine samples.

Recent Advances in Conventional Methods and Electrochemical Aptasensors for Mycotoxin Detection

The presence of mycotoxins in foodstuffs and feedstuffs is a serious concern for human health. The detection of mycotoxins is therefore necessary as a preventive action to avoid the harmful contamination of foodstuffs and animal feed. In comparison with the considerable expense of treating contaminated foodstuffs, early detection is a cost-effective way to ensure food safety. The high affinity of bio-recognition molecules to mycotoxins has led to the development of affinity columns for sample pre-treatment and the development of biosensors for the quantitative analysis of mycotoxins. Aptamers are a very attractive class of biological receptors that are currently in great demand for the development of new biosensors. In this review, the improvement in the materials and methodology, and the working principles and performance of both conventional and recently developed methods are discussed. The key features and applications of the fundamental recognition elements, such as antibodies and aptamers are addressed. Recent advances in aptasensors that are based on different electrochemical (EC) transducers are reviewed in detail, especially from the perspective of the diagnostic mechanism; in addition, a brief introduction of some commercially available mycotoxin detection kits is provided.

An integrated actuating and sensing system for light-addressable potentiometric sensor (LAPS) and light-actuated AC electroosmosis (LACE) operation

To develop a lab on a chip (LOC) integrated with both sensor and actuator functions, a novel two-in-one system based on optical-driven manipulation and sensing in a microfluidics setup based on a hydrogenated amorphous silicon (a-Si:H) layer on an indium tin oxide/glass is first realized. A high-intensity discharge xenon lamp functioned as the light source, a chopper functioned as the modulated illumination for a certain frequency, and a self-designed optical path projected on the digital micromirror device controlled by the digital light processing module was established as the illumination input signal with the ability of dynamic movement of projected patterns. For light-addressable potentiometric sensor (LAPS) operation, alternating current (AC)-modulated illumination with a frequency of 800 Hz can be generated by the rotation speed of the chopper for photocurrent vs bias voltage characterization. The pH sensitivity, drift coefficient, and hysteresis width of the Si₃N₄ LAPS are 52.8 mV/pH, -3.2 mV/h, and 10.5 mV, respectively, which are comparable to the results from the conventional setup. With an identical two-in-one system, direct current illumination without chopper rotation and an AC bias voltage can be provided to an a-Si:H chip with a manipulation speed of 20 μm/s for magnetic beads with a diameter of 1 μm. The collection of magnetic beads by this light-actuated AC electroosmosis (LACE) operation at a frequency of 10 kHz can be easily realized. A fully customized design of an illumination path with less decay can be suggested to obtain a high efficiency of manipulation and a high signal-to-noise ratio of sensing. With this proposed setup, a potential LOC system based on LACE and LAPS is verified with the integration of a sensor and an actuator in a microfluidics setup for future point-of-care testing applications.