Bio-Layer Interferometry-Based SELEX and Label-Free Detection of Patulin Using Generated Aptamer

Current developments of SELEX technologies and prospects in the aptamer selection with clinical applications

Aptamers are single-stranded oligonucleotide sequences capable of binding to specific ligands with high affinity. In this manner, they are like antibodies but have advantages such as lower manufacturing costs, lower immunogenicity, fewer batch-to-batch differences, a longer shelf life, high tolerance to different molecular milieus, and a greater number of potential targets. Due to their special features, they have been used in drug delivery, biosensor technology, therapy, and diagnostics. The methodology that allowed its production was the "Systematic Evolution of Ligands by Exponential enrichment" (SELEX). Unfortunately, the traditional protocol is time-consuming and laborious. Therefore, numerous variants with considerable optimization steps have been developed, nonetheless, there are still challenges to achieving real applications in the clinical field. Among them, are control of in vivo activities, fast renal filtration, degradation by nucleases and toxicity testing. This review focuses on current technologies based on SELEX, the critical factors for successful aptamer selection, and its upcoming biomedical and biotechnological applications.

Active Discovery of the Allosteric Inhibitor Targeting Botrytis cinerea Chitinase Based on Neural Relational Inference for Food Preservation

Currently, allosteric inhibitors have emerged as an effective strategy in the development of preservatives against the drug-resistant Botrytis cinerea (B. cinerea). However, their passively driven development efficiency has proven challenging to meet the practical demands. Here, leveraging the deep learning Neural Relational Inference (NRI) framework, we actively identified an allosteric inhibitor targeting B. cinerea Chitinase, namely, 2-acetonaphthone. 2-Acetonaphthone binds to the crucial domain of Chitinase, forming the strong interaction with the allosteric sites. Throughout the interaction process, 2-acetonaphthone diminished the overall connectivity of the protein, inducing conformational changes. These findings align with the results obtained from Chitinase activity experiments, revealing an IC50 value of 67.6 μg/mL. Moreover, 2-acetonaphthone exhibited outstanding anti-B. cinerea activity by inhibiting Chitinase. In the gray mold infection model, 2-acetonaphthone significantly extended the preservation time of cherry tomatoes, positioning it as a promising preservative for fruit storage.

Screening biotoxin aptamer and their application of optical aptasensor in food stuff: a review

Biotoxins are ranges of toxic substances produced by animals, plants, and microorganisms, which could contaminate foods during their production, processing, transportation, or storage, thus leading to foodborne illness, even food terrorism. Therefore, proposing simple, rapid, and effective detection methods for ensuring food free from biotoxin contamination shows a highly realistic demand. Aptamers are single-stranded oligonucleotides obtained from the systematic evolution of ligands by performing exponential enrichment (SELEX). They can specifically bind to wide ranges of targets with high affinity; thus, they have become important recognizing units in safety monitoring in food control and anti-terrorism. In this paper, we reviewed the technical points and difficulties of typical aptamer screening processes for biotoxins. For promoting the understanding of food control in the food supply chain, the latest progresses in rapid optical detection of biotoxins based on aptamers were summarized. In the end, we outlined some challenges and prospects in this field. We hope this paper could stimulate widespread interest in developing advanced sensing systems for ensuring food safety.

A Redox Mediator-Free Highly Selective and Sensitive Electrochemical Aptasensor for Patulin Mycotoxin Detection in Apple Juice Using Ni-NiO Pseudocapacitive Nanomaterials

Pseudocapacitive nanomaterials have recently gained significant attention in electrochemical biosensors due to their rapid response, long cycle life, high surface area, biomolecule compatibility, and superior energy storage capabilities. In our study, we introduce the potential of using Ni-NiO nanofilm's pseudocapacitive traits as transducer signals in electrochemical aptasensors. Capitalizing on the innate affinity between histidine and nickel, we immobilized histidine-tagged streptavidin (HTS) onto Ni-NiO-modified electrodes. Additionally, we employed a biolayer interferometry-based SELEX to generate biotinylated patulin aptamers. These aptamers, when placed on Ni-NiO-HTS surfaces, make a suitable biosensing platform for rapid patulin mycotoxin detection in apple juice using electrochemical amperometry in microseconds. The novelty lies in optimizing pseudocapacitive nanomaterials structurally and electrochemically, offering the potential for redox mediator-free electrochemical aptasensors. Proof-of-concept is conducted by applying this surface for the ultrasensitive detection of a model analyte, patulin mycotoxin. The aptamer-functionalized bioelectrode showed an excellent linear response (10-106 fg/mL) and an impressive detection limit (1.65 fg/mL, +3σ of blank signal). Furthermore, reproducibility tests yielded a low relative standard deviation of 0.51%, indicating the good performance of the developed biosensor. Real sample analysis in freshly prepared apple juice revealed no significant difference (P < 0.05) in current intensity between spiked and real samples. The sensor interface maintained excellent stability for up to 2 weeks (signal retention 96.45%). The excellent selectivity, stability, and sensitivity of the electrochemical aptasensor exemplify the potential for using nickel-based pseudocapacitive nanomaterials for a wide variety of electrochemical sensing applications.

Label-Free Biochemical Sensing Using Processed Optical Fiber Interferometry: A Review

Over the last 20 years, optical fiber-based devices have been exploited extensively in the field of biochemical sensing, with applications in many specific areas such as the food processing industry, environmental monitoring, health diagnosis, bioengineering, disease diagnosis, and the drug industry due to their compact, label-free, and highly sensitive detection. The selective and accurate detection of biochemicals is an essential part of biosensing devices, which is to be done through effective functionalization of highly specific recognition agents, such as enzymes, DNA, receptors, etc., over the transducing surface. Among many optical fiber-based sensing technologies, optical fiber interferometry-based biosensors are one of the broadly used methods with the advantages of biocompatibility, compact size, high sensitivity, high-resolution sensing, lower detection limits, operating wavelength tunability, etc. This Review provides a comprehensive review of the fundamentals as well as the current advances in developing optical fiber interferometry-based biochemical sensors. In the beginning, a generic biosensor and its several components are introduced, followed by the fundamentals and state-of-art technology behind developing a variety of interferometry-based fiber optic sensors. These include the Mach-Zehnder interferometer, the Michelson interferometer, the Fabry-Perot interferometer, the Sagnac interferometer, and biolayer interferometry (BLI). Further, several technical reports are comprehensively reviewed and compared in a tabulated form for better comparison along with their advantages and disadvantages. Further, the limitations and possible solutions for these sensors are discussed to transform these in-lab devices into commercial industry applications. At the end, in conclusion, comments on the prospects of field development toward the commercialization of sensor technology are also provided. The Review targets a broad range of audiences including beginners and also motivates the experts helping to solve the real issues for developing an industry-oriented sensing device.

Magnetic nanoparticle-based immunosensors and aptasensors for mycotoxin detection in foodstuffs: An update

Mycotoxin contamination of food crops is a global challenge due to their unpredictable occurrence and severe adverse health effects on humans. Therefore, it is of great importance to develop effective tools to prevent the accumulation of mycotoxins through the food chain. The use of magnetic nanoparticle (MNP)-assisted biosensors for detecting mycotoxin in complex foodstuffs has garnered great interest due to the significantly enhanced sensitivity and accuracy. Within such a context, this review includes the fundamentals and recent advances (2020-2023) in the area of mycotoxin monitoring in food matrices using MNP-based aptasensors and immunosensors. In this review, we start by providing a comprehensive introduction to the design of immunosensors (natural antibody or nanobody, random or site-oriented immobilization) and aptasensors (techniques for aptamer selection, characterization, and truncation). Meanwhile, special attention is paid to the multifunctionalities of MNPs (recoverable adsorbent, versatile carrier, and signal indicator) in preparing mycotoxin-specific biosensors. Further, the contribution of MNPs to the multiplexing determination of various mycotoxins is summarized. Finally, challenges and future perspectives for the practical applications of MNP-assisted biosensors are also discussed. The progress and updates of MNP-based biosensors shown in this review are expected to offer readers valuable insights about the design of MNP-based tools for the effective detection of mycotoxins in practical applications.

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.

Improvement of the sensitivity of lateral flow systems for detecting mycotoxins: Up-to-date strategies and future perspectives

Mycotoxins are dangerous human and animal health-threatening secondary fungal metabolites that can be found in various food and agricultural products. Several countries have established regulations to restrict their presence in food and agricultural products destined for human and animal consumption. Consequently, the need to develop highly sensitive and smart detection systems was recognized worldwide. Lateral flow assay possesses the advantages of easy operation, rapidity, stability, accuracy, and specificity, and it plays an important role in the detection of mycotoxins. Nevertheless, strategies to comprehensively improve the sensitivity of lateral flow assay to mycotoxins in food have rarely been highlighted and discussed. In this article, a comprehensive overview was presented on the application of lateral flow assay in mycotoxin detection in food samples by highlighting the principle of lateral flow assay, presenting a detailed discussion on various analytical performance-improvement strategies, such as the development of high-affinity recognition reagents, immunogen immobilization methods, and signal amplification. Additionally, a detailed discussion on the various signal analyzers and interpretation approaches was provided. Finally, current hurdles and future perspectives on the application of lateral flow assay in the detection of mycotoxins were discussed.

Highly-efficient selection of aptamers for detecting various HPV subtypes in clinical samples

Nucleic acid aptamers are of great potentials in diagnostic and therapeutic applications because of their unique molecular recognition capabilities. However, satisfactory aptamers with high affinity and specificity are still in short supply. Herein, we have developed new selection methods allowing the free interactions between the targets and potential aptamers in solution. In our selection system, the protein targets (biotinylated randomly or site-specifically) were first incubated with the random DNA library, followed by the pull-down with the streptavidin magnetic beads or biolayer-interferometry (BLI) sensors. By comparing the two biotinylation strategies (random or site-specific) and two states of the targets (free or immobilized), we have found that the combination of the site-specific biotinylation and free-target strategies was most successful. Based on these highly-efficient selection strategies, HPV L1 aptamers were obtained. By designing the sandwich aptasensor assisted with RCA and CRISPR/Cas12a, we have diagnosed various HPV subtypes in clinical samples, such as easily-collected urine samples. In summary, our new strategy can allow efficient selection of aptamers with high affinity and specificity for clinical applications.

Development of a novel fluorescent aptasensor based on the interaction between hexagonal β-Co(OH)2 nanoplates and nitrogen-doped carbon dots for ultrasensitive detection of patulin

There is an urgent need to develop an economical and convenient method for the ultrasensitive detection of patulin (PAT), a mycotoxin that can potentially harm human health when it is found in fruits and their derivatives. In this study, we have developed a novel fluorescent aptasensor that utilizes nitrogen-doped carbon dots (N-CDs) as the fluorescent donor and hexagonal β-Co(OH)2 nanoplates as the fluorescent acceptor. N-CDs were synthesized through the hydrothermal method, resulting in spherical particles with a diameter of 7.6 nm. These nanoparticles exhibited excellent water solubility and displayed a vibrant blue emission at 448 nm when excited at 360 nm. Cobalt hydroxide nanoplates with a beta crystal structure [β-Co(OH)2] were synthesized using a simple co-precipitation method, exhibiting hexagonal plate-like shapes with uniform lateral sizes of 4-5 μm. The fluorescence of N-CDs can be efficiently quenched by hexagonal β-Co(OH)2 nanoplates through Förster resonance energy transfer mechanism. The maximum quenching-recovery capability can be achieved when the concentrations of N-CDs-Apt and β-Co(OH)2 nanoplates are 150 nmol/L and 100 μg/mL, respectively. The pH of the TE buffer should be 8.0, and the incubation time should be 10 min at 25 °C. The developed fluorescent aptasensor displayed an excellent selectivity for PAT determination with a detection limit of 0.57 pg/mL in the linear range of 1.25 pg/mL-100 ng/mL. The rapid PAT determination in fruit juice samples was realized with good recoveries (96.9-105.8%). The developed fluorescent aptasensor based on the interaction between N-CDs and hexagonal β-Co(OH)2 nanoplates can be a promising method for the rapid and ultrasensitive detection of PAT in agricultural products.

Rational design of a ratiometric fluorescent aptasensor for patulin in traditional Chinese medicine through the studies of the interaction mechanism between its DNA aptamer and the target molecule

Patulin (PAT) is a kind of mycotoxin which must be monitored for the sake of quality and safety in traditional Chinese medicine (TCM) owing to its harm to human health. On this account, a rationally designed ratiometric fluorescent aptasensor was developed based on the studies of the interaction mechanism between PAT and its aptamer (PAT-APT). First, CD spectroscopy, molecular docking, and molecular dynamic simulation were applied to investigate the details on how PAT-APT binds with its target molecule. The results indicated that the structure of PAT-APT changed to a certain extent and was stabilized after binding with PAT. C-11, C-37 and C-38 were the key sites for the recognition and interaction between PAT-APT and its target. Second, based on these results, a ratiometric aptasensor was designed using fluorescence resonance energy transfer (FRET) and synchronous fluorescence spectroscopy. A complementary sequence (cDNA) to the aptamer with an appropriate length and hybridization position was obtained through rational design and optimization. Both PAT-APT and cDNA were labeled using a pair of fluorophores, which could generate FRET when the two single-stranded oligonucleotides hybridized. The accurate detection of PAT could be realized according to the change ratio of the fluorescence intensity at the corresponding wavelengths of the two fluorophores before and after the assay. The aptasensor achieved an ultralow limit of detection of 0.16 nM, perfect selectivity, and satisfactory practicability in complex TCM samples. To our knowledge, this is the first aptasensor for PAT designed through the interaction mechanism between its aptamer and the target molecule. Moreover, the assay for PAT is cost-effective, does not need complicated pretreatment and only takes less than an hour. In summary, this study makes a contribution to the safety control of TCM and provides a thinking mode from mechanism to rational design to conquer the problem of sensitive aptasensing of one component in a complex system.

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

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

Aptamer recognition-promoted hybridization chain reaction for amplified label-free and enzyme-free fluorescence analysis of pesticide

Development of high-performance fluorescence sensors for pesticide is highly urgent but remains a grand challenge. It is due to that most of known fluorescence sensors detect pesticides based on enzyme-inhibited strategy, which requires high-price cholinesterase, suffers from serious interference of reductive materials, and can't difference pesticides with each other; the known aptamer-based fluorescence ones entail tool enzymes or nanomaterials to transducer/amplify the signal and demand signalers to be tagged in nucleic acid, which are expensive and intricate. Herein, we develop a novel aptamer-based fluorescence system for label-free, enzyme-free and highly sensitive detection of pesticide (profenofos) based on target-initiated hybridization chain reaction (HCR)-assisted signal amplification and specific intercalation of N-methylmesoporphyrin IX (NMM) in G-quadruplex DNA. Hairpin probe ON1 recognizes profenofos to generate profenofos@ON1 complex, which switches the HCR to yield multiple G-quadruplex DNA, consequently making large numbers of NMM be locked. In comparison with profenofos absence, a sharply improved fluorescence signal was recorded and it was dependent on profenofos dose. Hence, label-free, enzyme-free and highly sensitive detection of profenofos is achieved with limit of detection of 0.085 nM, which compared favorably with or superior to those of known fluorescence methods. Furthermore, the present method was applied to determine the profenofos residue in rice with agreeable result, and will provide more valuable information for guaranteeing the pesticide-related food safety.

Screening of a Sialyllactose-Specific Aptamer and Engineering a Pair of Recognition Elements with Unique Fluorescent Characteristics for Sensitive Detection of Sialyllactose

A single-stranded DNA (ssDNA) aptamer specific for 6'-sialyllactose (6'-SL) was screened through magnetic separation-based SELEX and post-SELEX truncation and used to construct unique aptamer bio-dots for sensitive detection of 6'-SL. Eighteen rounds of screening were conducted during the SELEX process. The ssDNA aptamer Apt9 (K_d = 152.3 nM) with a length of 79 nucleotides (nt) was demonstrated as the optimal aptamer candidate after affinity and specificity evaluation. Then, Apt9 was truncated and optimized according to secondary structure and molecular docking. A 35 nt truncated aptamer Apt9-1 (K_d = 91.75 nM) with higher affinity than Apt9 was finally obtained. Furthermore, Apt9-1 was used to synthesize bio-dots as a new recognition element of 6'-SL, and the aminobenzene boric acid functionalized carbon dots were employed as the other recognition element. With the respective fluorescent characteristics, the two quantum dots (QDs) were made a pair to construct a 6'-SL fluorescent biosensor. The linear detection range of the biosensor is 10 μM to 5 mM, and the detection limit is 0.9 μM. With the advantages of time-saving, high efficiency, and simplicity in the actual sample detection, the screened aptamer and dual-QD-based biosensor have broad application prospects in 6'-SL detection.

Advances in Aptamers-Based Applications in Breast Cancer: Drug Delivery, Therapeutics, and Diagnostics

Aptamers are synthetic single-stranded oligonucleotides (such as RNA and DNA) evolved in vitro using Systematic Evolution of Ligands through Exponential enrichment (SELEX) techniques. Aptamers are evolved to have high affinity and specificity to targets; hence, they have a great potential for use in therapeutics as delivery agents and/or in treatment strategies. Aptamers can be chemically synthesized and modified in a cost-effective manner and are easy to hybridize to a variety of nano-particles and other agents which has paved a way for targeted therapy and diagnostics applications such as in breast tumors. In this review, we systematically explain different aptamer adoption approaches to therapeutic or diagnostic uses when addressing breast tumors. We summarize the current therapeutic techniques to address breast tumors including aptamer-base approaches. We discuss the next aptamer-based therapeutic and diagnostic approaches targeting breast tumors. Finally, we provide a perspective on the future of aptamer-based sensors for breast therapeutics and diagnostics. In this section, the therapeutic applications of aptamers will be discussed for the targeting therapy of breast cancer.