Direct fluorescence anisotropy approach for aflatoxin B1 detection and affinity binding study by using single tetramethylrhodamine labeled aptamer

Polycations as Aptamer-Binding Modulators for Sensitive Fluorescence Anisotropy Assay of Aflatoxin B1

Fluorescence induced by the excitation of a fluorophore with plane-polarized light has a different polarization depending on the size of the fluorophore-containing reagent and the rate of its rotation. Based on this effect, many analytical systems have been implemented in which an analyte contained in a sample and labeled with a fluorophore (usually fluorescein) competes to bind to antibodies. Replacing antibodies in such assays with aptamers, low-cost and stable oligonucleotide receptors, is complicated because binding a fluorophore to them causes a less significant change in the polarization of emissions. This work proposes and characterizes the compounds of the reaction medium that improve analyte binding and reduce the mobility of the aptamer-fluorophore complex, providing a higher analytical signal and a lower detection limit. This study was conducted on aflatoxin B1 (AFB1), a ubiquitous toxicant contaminating foods of plant origins. Eight aptamers specific to AFB1 with the same binding site and different regions stabilizing their structures were compared for affinity, based on which the aptamer with 38 nucleotides in length was selected. The polymers that interact reversibly with oligonucleotides, such as poly-L-lysine and polyethylene glycol, were tested. It was found that they provide the desired reduction in the depolarization of emitted light as well as high concentrations of magnesium cations. In the selected optimal medium, AFB1 detection reached a limit of 1 ng/mL, which was 12 times lower than in the tris buffer commonly used for anti-AFB1 aptamers. The assay time was 30 min. This method is suitable for controlling almond samples according to the maximum permissible levels of their contamination by AFB1. The proposed approach could be applied to improve other aptamer-based analytical systems.

A Highly Sensitive and Group-Specific Enzyme-Linked Immunosorbent Assay (ELISA) for the Detection of AFB1 in Agriculture and Aquiculture Products

Aflatoxins (AFs) including AFB1, AFB2, AFG1 and AFG2 are widely found in agriculture products, and AFB1 is considered one of the most toxic and harmful mycotoxins. Herein, a highly sensitive (at the pg mL-1 level) and group-specific enzyme-linked immunosorbent assay (ELISA) for the detection of AFB1 in agricultural and aquiculture products was developed. The AFB1 derivative containing a carboxylic group was synthesized and covalently linked to bovine serum albumin (BSA). The AFB1-BSA conjugate was used as an immunogen to immunize mice. A high-quality monoclonal antibody (mAb) against AFB1 was produced by hybridoma technology, and the mAb-based ELISA for AFB1 was established. IC50 and limit of detection (LOD) of the ELISA for AFB1 were 90 pg mL-1 and 18 pg mL-1, respectively. The cross-reactivities (CRs) of the assay with AFB2, AFG1, and AFG2 were 23.6%, 42.5%, and 1.9%, respectively, revealing some degree of group specificity. Corn flour, wheat flour, and crab roe samples spiked with different contents of AFB1 were subjected to ELISA procedures. The recoveries and relative standard deviation (RSD) of the ELISA for AFB1 in spiked samples were 78.3-116.6% and 1.49-13.21% (n = 3), respectively. Wheat flour samples spiked with the mixed AF (AFB1, AFB2, AFG1, AFG2) standard solution were measured by ELISA and LC-MS/MS simultaneously. It was demonstrated that the proposed ELISA can be used as a screening method for evaluation of AFs (AFB1, AFB2, AFG1, AFG2) in wheat flour samples.

Noncompetitive Determination of Small Analytes by Sandwich-Type Lateral Flow Assay Based on an Aptamer Kissing Complex

Here, we present the proof-of-concept of a lateral flow assay (LFA) that is capable of detecting small-molecule targets in a noncompetitive manner by deploying a sandwich-type format based on the aptamer kissing complex (AKC) strategy. A fluorescently labeled hairpin aptamer served as the signaling agent, while a specific RNA hairpin grafted onto the strip served as the capture element. The hairpin aptamer switched from an unfolded to a folded form in the presence of the target, resulting in kissing interactions between the loops of the reporter and the capture agents. This design triggered a target-dependent fluorescent signal at the test line. The AKC-based LFA was developed for the detection of adenosine, achieving a detection limit in the micromolar range. The assay revealed the presence of the same analyte in urine. The method also proved effective with another small molecule (theophylline). We believe that the AKC-based LFA approach could overcome many of the shortcomings associated with conventional signal-off methods and competitive processes.

An electrochemical aptasensor for methylamphetamine rapid detection by single-on mode based on competition with complementary DNA

A simple and rapid electrochemical sensing method with high sensitivity and specificity of aptamers was developed for the detection of methylamphetamine (MAMP). A short anti-MAMP thiolated aptamer (Apt) with a methylene blue (MB) probe at 3'-end was immobilized on the surface of a gold electrode (MB-Apt-S/GE). The electrochemical signal appeared when MAMP presenting in the sample solution competed with cDNA for binding with MB-Apt-S. Under optimized conditions, the liner range of this signal-on electrochemical aptasensor for the detection of MAMP achieved from 1.0 to 10.0 nmol/L and 10.0-400 nmol/L. LOD 0.88 nmol/L were obtained. Satisfactory spiked recoveries of saliva and urine were also obtained. In this method, only 5 min were needed to incubate before the square wave voltammetry (SWV) analysis, which was much more rapid than other electrochemical sensors, leading to a bright and broad prospect for the detection of MAMP in biological sample. This method can be used for on-site rapid detection on special occasions, such as drug driving scenes, entertainment venues suspected of drug use, etc.

Recent Progress of Electrochemical Aptasensors toward AFB1 Detection (2018-2023)

Food contaminants represent possible threats to humans and animals as severe food safety hazards. Prolonged exposure to contaminated food often leads to chronic diseases such as cancer, kidney or liver failure, immunosuppression, or genotoxicity. Aflatoxins are naturally produced by strains of the fungi species Aspergillus, which is one of the most critical and poisonous food contaminants worldwide. Given the high percentage of contaminated food products, traditional detection methods often prove inadequate. Thus, it becomes imperative to develop fast, accurate, and easy-to-use analytical methods to enable safe food products and good practices policies. Focusing on the recent progress (2018-2023) of electrochemical aptasensors for aflatoxin B1 (AFB1) detection in food and beverage samples, without pretending to be exhaustive, we present an overview of the most important label-free and labeled sensing strategies. Simultaneous and competitive aptamer-based strategies are also discussed. The aptasensors are summarized in tabular format according to the detection mode. Sample treatments performed prior analysis are discussed. Emphasis was placed on the nanomaterials used in the aptasensors' design for aptamer-tailored immobilization and/or signal amplification. The advantages and limitations of AFB1 electrochemical aptasensors for field detection are presented.

A Fluorescence Resonance Energy Transfer Aptasensor for Aflatoxin B1 Based on Ligand-Induced ssDNA Displacement

In this study, a fluorescence resonance energy transfer (FRET)-based aptasensor for the detection of aflatoxin B1 (AFB1) was designed using a carboxyfluorescein (FAM)-labeled aptamer and short complementary DNA (cDNA) labeled with low molecular quencher RTQ1. The sensing principle was based on the detection of restored FAM-aptamer fluorescence due to the ligand-induced displacement of cDNA in the presence of AFB1, leading to the destruction of the aptamer/cDNA duplex and preventing the convergence of FAM and RTQ1 at the effective FRET distance. Under optimal sensing conditions, a linear correlation was obtained between the fluorescence intensity of the FAM-aptamer and the AFB1 concentration in the range of 2.5-208.3 ng/mL with the detection limit of the assay equal to 0.2 ng/mL. The assay time was 30 min. The proposed FRET aptasensor has been successfully validated by analyzing white wine and corn flour samples, with recovery ranging from 76.7% to 91.9% and 84.0% to 86.5%, respectively. This work demonstrates the possibilities of labeled cDNA as an effective and easily accessible tool for sensitive AFB1 detection. The homogeneous FRET aptasensor is an appropriate choice for contaminant screening in complex matrices.

A Dynamic and Pseudo-Homogeneous MBs-icELISA for the Early Detection of Aflatoxin B1 in Food and Feed

Aflatoxin B1 (AFB1) is one of the most toxic and harmful fungal toxins to humans and animals, and the fundamental way to prevent its entry into humans is to detect its presence in advance. In this paper, the monoclonal antibody mAbA2-2 was obtained via three-step sample amplification and multi-concentration standard detection using a subcloning method based on the limited dilution method with AFB1 as the target. A dynamic and pseucdo-homogeneous magnetic beads enzyme-linked immunosorbent assay (MBs-icELISA) was established using the prepared antibody as the recognition element and immunomagnetic beads as the antigen carrier. The MBs-icELISA showed good linear correlation in the concentration range of 0.004-10 ng/mL with R2 = 0.99396. The limit of detection (LOD) of the MBs-icELISA for AFB1 was 0.0013 ng/mL. This new ELISA strategy significantly shortened AFB1 detection time through improved sensitivity compared to the conventional ELISA method.

Rapid and sensitive point-of-care PTS-CRISPR assay for food safety monitoring of aflatoxin B1

Food safety is crucial for human health, but its effective on-site monitoring remains a challenge. Pregnancy test strip (PTS) is the successful point-of-care testing (POCT) product of the highest market share in the world, with the cost as low as $0.10 per test. Herein, combined with the CRISPR (clustered regularly interspaced short palindromic repeats) system, PTS-CRISPR was for the first time introduced into food safety monitoring, for rapid and sensitive POCT of aflatoxin B1. The low-cost, easy-to-operate PTS-CRISPR is expected to bring security to the grassroots food market.

Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer

The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.

Aflatoxin detection technologies: recent advances and future prospects

Aflatoxins have posed serious threat to food safety and human health. Therefore, it is important to detect aflatoxins in samples rapidly and accurately. In this review, various technologies to detect aflatoxins in food are discussed, including conventional ones such as thin-layer chromatography (TLC), high performance liquid chromatography (HPLC), enzyme linked immunosorbent assay (ELISA), colloidal gold immunochromatographic assay (GICA), radioimmunoassay (RIA), fluorescence spectroscopy (FS), as well as emerging ones (e.g., biosensors, molecular imprinting technology, surface plasmon resonance). Critical challenges of these technologies include high cost, complex processing procedures and long processing time, low stability, low repeatability, low accuracy, poor portability, and so on. Critical discussion is provided on the trade-off relationship between detection speed and detection accuracy, as well as the application scenario and sustainability of different technologies. Especially, the prospect of combining different technologies is discussed. Future research is necessary to develop more convenient, more accurate, faster, and cost-effective technologies to detect aflatoxins.

Fluorescence-based aptasensors for small molecular food contaminants: From energy transfer to optical polarization

Small molecular food contaminants, such as mycotoxins, pesticide residues and antibiotics, are highly probable to be passively introduced in food at all stages of its processing, including planting, harvest, production, transportation and storage. Owing to the high risks caused by the unknowing intake and accumulation in human, there is an urgent need to develop rapid, sensitive and efficient methods to monitor them. Fluorescence-based aptasensors provide a promising platform for this area owing to its simple operation, high sensitivity, wide application range and economical practicability. In this paper, the common sorts of small molecular contaminants in foods, namely mycotoxins, pesticides, antibiotics, etc, are briefly introduced. Then, we make a comprehensive review, from fluorescence resonance energy transfer (in turn-on, turn-off, and ratiometric mode, as well as energy upconversion) to fluorescence polarization, of the fluorescence-based aptasensors for the determination of these food contaminants reported in the last five years. The principle of signal generation, the advances of each sort of fluorescent aptasensors, as well as their applications are introduced in detail. Additionally, we also discussed the challenges and perspectives of the fluorescent aptasensors for small molecular food contaminants. This work will offer systematic overview and inspiration for amateurs, researchers and developers of fluorescence-based aptasensors for the detection of small molecules.

Programming Non-Nucleic Acid Molecules into Computational Nucleic Acid Systems

Nucleic acid (NA) computation has been widely developed in the past years to solve kinds of logic and mathematic issues in both information technologies and biomedical analysis. However, the difficulty to integrate non-NA molecules limits its power as a universal platform for molecular computation. Here, we report a versatile prototype of hybridized computation integrated with both nucleic acids and non-NA molecules. Employing the conformationally controlled ligand converters, we demonstrate that non-NA molecules, including both small molecules and proteins, can be computed as nucleic acid strands to construct the circuitry with increased complexity and scalability, and can be even programmed to solve arithmetical calculations within the computational nucleic acid system. This study opens a new door for molecular computation in which all-NA circuits can be expanded with integration of various ligands, and meanwhile, ligands can be precisely programmed by the nuclei acid computation.

Amplification of fluorescence polarization signal based on specific recognition of aptamers combined with quantum quenching effect for ultrasensitive and simple detection of PCB-77

Here, we report a novel aptasensor based on decahedral silver nanoparticles (Ag₁₀NPs) enhanced fluorescence polarization (FP) for detecting PCB-77. Using aptamer modified Ag₁₀NPs hybridized with DNA sequence labeled fluorescent group as an analytical probe, polychlorinated biphenyls (PCB-77) could be detected with high sensitivity and selectivity. The linear range of determination was 0.02 ng/L to 390 ng/L and the limit of detection was 5 pg/L. In addition, through the optimization of the experiment condition and signal probe DNA (pDNA), we found that the maximum FP signal could be generated when the distance between fluorescein and the surface of Ag₁₀NPs was 3 nm. When the aptamer was immobilized on the surface of Ag₁₀NPs could be strengthened the anti-interference performance of aptamer nanoprobe and further improved the detection ability. At the same time, we also compared the detection performance of the traditional FP signal enhancer streptavidin (SA) analysis system. The fluorescence polarization aptasensor could detect PCB-77 samples efficiently in complex environmental water, which shows a good application prospect.

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.

Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations

Understanding aptamer-ligand interactions is necessary to rationally design aptamer-based systems. Commonly used in silico tools have proven to be accurate to predict RNA and DNA oligonucleotide tertiary structures. However, given the complexity of nucleic acids, the most thermodynamically stable conformation is not necessarily the one with the highest affinity for a specific ligand. Because many metastable states may coexist, it remains challenging to predict binding sites through molecular docking simulations using available computational pipelines. In this study, we used independent simulations to broaden the conformational diversity sampled from DNA initial models of distinct stability and assessed the binding affinity of selected metastable representative structures. In our results, utilizing multiple metastable conformations for molecular docking analysis helped identify structures favorable for ligand binding and accurately predict the binding sites. Our workflow was able to correctly identify the binding sites of the characterized adenosine monophosphate and l-argininamide aptamers. Additionally, we demonstrated that our pipeline can be used to aid the design of competition assays that are conducive to aptasensing strategies using an uncharacterized aflatoxin B1 aptamer. We foresee that this approach may help rationally design effective and truncated aptamer sequences interacting with protein biomarkers or small molecules of interest for drug design and sensor applications.

A Simple Structure-Switch Aptasensor Using Label-Free Aptamer for Fluorescence Detection of Aflatoxin B1

Aflatoxin B1 (AFB1) is one of the mycotoxins produced by Aspergillus flavus and Aspergillus parasiticus, and it causes contamination in foods and great risk to human health. Simple sensitive detection of AFB1 is important and demanded for food safety and quality control. Aptamers can specifically bind to targets with high affinity, showing advantages in affinity assays and biosensors. We reported an aptamer structure-switch for fluorescent detection of aflatoxin B1 (AFB1), using a label-free aptamer, a fluorescein (FAM)-labeled complementary strand (FDNA), and a quencher (BHQ1)-labeled complementary strand (QDNA). When AFB1 is absent, these three strands assemble into a duplex DNA structure through DNA hybridization, making FAM close to BHQ1, and fluorescence quenching occurs. In the presence of AFB1, the aptamer binds with AFB1, instead of hybridizing with QDNA. Thus, FAM is apart from BHQ1, and fluorescence increases with the addition of AFB1. This assay allowed detection of AFB1 with a detection limit of 61 pM AFB1 and a dynamic concentration range of 61 pM to 4 μM. This aptamer-based method enabled detection of AFB1 in complex sample matrix (e.g., beer and corn flour samples).

Selection, truncation and fluorescence polarization based aptasensor for Weissella viridescens detection

Weissella viridescens is a spoilage bacterium commonly found in low-temperature meat products. In this work, after fifteen rounds including three counter selection rounds of whole-cell systemic evolution of ligands by exponential enrichment (SELEX) in vitro, a novel aptamer L3 that can specifically recognize W. viridescens was obtained with a dissociation constant (K_d) value of 68.25 ± 5.32 nM. The sequence of aptamer L3 was optimized by truncation and a new aptamer sequence TL43 was obtained with a lower K_d value of 32.11 ± 3.01 nM. Finally, a simple and rapid fluorescence polarization (FP) platform was constructed to detect W. viridescens, in which FAM-labeled complementary sequence (FAM-cDNA) was employed to generate FP signal and streptavidin was used to amplify FP signal. In the presence of target bacteria, FP value decreased owning to the dissociation of FAM-cDNA from streptavidin/biotin-TL43/FAM-cDNA complex. Under optimal conditions, the concentration of W. viridescens and FP value displayed a good linear relationship with the detection range from 10² to 10⁶ cfu/mL. Moreover, the designed detection system had a good recovery rate of 90.6%-107.7% in smoked ham samples compared with classical plate counting method, indicating the great potential of the selected and truncated aptamer in practical biosensing applications.

Aptamer fluorescence anisotropy assays for detection of aflatoxin B1 and adenosine triphosphate using antibody to amplify signal change

Fluorescence polarization/anisotropy (FP/FA) is an attractive technology for determining small molecules in homogeneous solution based on rotation changes of a fluorescent reporter. Binding induced conformation change is a specific property of aptamers. This property has been integrated into aptamer based FA assays for small molecules. In this work, we reported aptamer FA assays for aflatoxin B1 (AFB1) and adenosine triphosphate (ATP) by using antibody conjugated complementary DNA at the 3′ end and a fluorescein (FAM)-labeled aptamer at the 5′ end. The hybridization of aptamer and cDNA induced a FAM label close to the large-sized antibody, which restricts the local rotation of FAM and gives high FA signal. With the addition of target, the aptamer probe binds with the target, and the aptamer–cDNA duplex is inhibited, causing FA signal decreases. This method achieved detection of 25 pM AFB1 and 1 μM ATP, respectively. The assay is promising for application.

Aptamer fluorescence anisotropy assays for small molecules (aflatoxin B1 and ATP) using antibody to amplify signal change.

Utilizing the DNA Aptamer to Determine Lethal α-Amanitin in Mushroom Samples and Urine by Magnetic Bead-ELISA (MELISA)

Amanita poisoning is one of the most deadly types of mushroom poisoning. α-Amanitin is the main lethal toxin in amanita, and the human-lethal dose is about 0.1 mg/kg. Most of the commonly used detection techniques for α-amanitin require expensive instruments. In this study, the α-amanitin aptamer was selected as the research object, and the stem-loop structure of the original aptamer was not damaged by truncating the redundant bases, in order to improve the affinity and specificity of the aptamer. The specificity and affinity of the truncated aptamers were determined using isothermal titration calorimetry (ITC) and gold nanoparticles (AuNPs), and the affinity and specificity of the aptamers decreased after truncation. Therefore, the original aptamer was selected to establish a simple and specific magnetic bead-based enzyme linked immunoassay (MELISA) method for α-amanitin. The detection limit was 0.369 μg/mL, while, in mushroom it was 0.372 μg/mL and in urine 0.337 μg/mL. Recovery studies were performed by spiking urine and mushroom samples with α-amanitin, and these confirmed the desirable accuracy and practical applicability of our method. The α-amanitin and aptamer recognition sites and binding pockets were investigated in an in vitro molecular docking environment, and the main binding bases of both were T3, G4, C5, T6, T7, C67, and A68. This study truncated the α-amanitin aptamer and proposes a method of detecting α-amanitin.

Label free structure-switching fluorescence polarization detection of chloramphenicol with truncated aptamer

In this study, the original chloramphenicol aptamer containing 80 bases was truncated to 30 bases with high affinity by the SYBR Green I assay. It was found that the ionic strength and type affect the recognition of aptamers, especially magnesium ion played a vital role in the binding process. Furthermore, the binding performance of aptamer, including binding mode, key binding sites and conformational changes were further investigated by circular dichroism spectroscopy, UV-vis absorption spectrum and molecular docking. Based on these research data, we inferred that chloramphenicol bound to the minor groove region in the aptamer double helix. Finally, the optimized aptamer LLR10 was used to develop a novel label free fluorescence polarization assay to detect chloramphenicol within SYBR Green I as the source of fluorescence polarization signal. Under optimal conditions, the designed method showed a linear detection range of 0.1-10 nM with a detection limit of 0.06 nM. Additionally, the aptasensor exhibited a high accuracy to the detection of chloramphenicol in milk samples with a recovery rate from 93.7% to 98.4%. Therefore, the developed label free fluorescence polarization aptasensor provides a new idea for the rapid, reliable and sensitive detection of chloramphenicol, which can be applied to food safety control.

Polystyrene Microsphere-Based Immunochromatographic Assay for Detection of Aflatoxin B1 in Maize

Aflatoxin B1 (AFB1), a mycotoxin, is hepatotoxic, carcinogenic, and nephrotoxic in humans and animals, and contaminate a wide range of maize. In this study, an immunochromatographic assay (ICA) based on polystyrene microspheres (PMs) was developed for sensitive and quantitative detection of AFB1 in maize. The amounts of PMs, the condition for activating carboxyl groups of PMs, the amount of monoclonal antibody (mAb), and the volume of the immune probe were optimized to enhance the performance PMs-ICA for point-of-care testing of AFB1 in maize. The PMs-ICA showed the cut-off value of 1 ng/mL in phosphate buffer (PB) and 6 µg/kg in maize samples, respectively. The quantitative limit of detection (qLOD) was 0.27 and 1.43 µg/kg in PB and maize samples, respectively. The accuracy and precision of the PMs-ICA were evaluated by analysis of spiked maize samples with recoveries of 96.0% to 107.6% with coefficients of variation below 10%. In addition, the reliability of PMs-ICA was confirmed by the liquid chromatography-tandem mass spectrometry method. The results indicated that the PMs-ICA could be used as a sensitive, simple, rapid point-of-care testing of AFB1 in maize.

Self-replicating catalyzed hairpin assembly for rapid aflatoxin B1 detection

Herein, a rapid signal amplified aflatoxin B1 (AFB1) detection system based on self-replicating catalyzed hairpin assembly (SRCHA) has been constructed. In this SRCHA system, trigger DNA was initially blocked and two split trigger DNA sequences were integrated into two hairpin auxiliary probes, H1 and H2, respectively. In the presence of AFB1, the aptamer sequence was recognized by AFB1 and trigger DNA was released, which can initiate a CHA reaction and lead to the formation of a helix DNA H1-H2 complex. Then this complex can dissociate double-stranded probe DNA (F-Q) and the fluorescence signal was recovered. Meanwhile, the two split trigger DNA sequences came into close-enough proximity and a trigger DNA replica was formed. Then the obtained replicas can trigger an additional CHA reaction, leading to the rapid and significant enhancement of the fluorescence signal, and AFB1 can be detected within 15 min with a detection limit of 0.13 ng mL-1. This AFB1 detection system exhibits potential application in the on-site rapid detection of AFB1.

Fluorescence Polarization-Based Bioassays: New Horizons

Fluorescence polarization holds considerable promise for bioanalytical systems because it allows the detection of selective interactions in real time and a choice of fluorophores, the detection of which the biosample matrix does not influence; thus, their choice simplifies and accelerates the preparation of samples. For decades, these possibilities were successfully applied in fluorescence polarization immunoassays based on differences in the polarization of fluorophore emissions excited by plane-polarized light, whether in a free state or as part of an immune complex. However, the results of recent studies demonstrate the efficacy of fluorescence polarization as a detected signal in many bioanalytical methods. This review summarizes and comparatively characterizes these developments. It considers the integration of fluorescence polarization with the use of alternative receptor molecules and various fluorophores; different schemes for the formation of detectable complexes and the amplification of the signals generated by them. New techniques for the detection of metal ions, nucleic acids, and enzymatic reactions based on fluorescence polarization are also considered.

Low Temperature Greatly Enhancing Responses of Aptamer Electrochemical Sensor for Aflatoxin B1 Using Aptamer with Short Stem

Aflatoxin B1 (AFB1), one of the most toxic mycotoxins, poses great health risks. Rapid and sensitive detection of AFB1 is important for food safety, environment monitoring, and health risk assessment. We report here the development of a simple and reusable electrochemical aptasensor for rapid and sensitive detection of AFB1. Main improvements were achieved through engineering an aptamer containing a short stem-loop structure and enhancing the binding affinity at a lower temperature. The DNA aptamer with a methylene blue (MB) label at one end was immobilized on a gold electrode. Upon AFB1 binding, the aptamer folded into a stem-loop structure and brought MB close to the electrode surface, resulting in increases in electric current. The aptamer having a shorter stem (2-4 bp) underwent a larger conformation change upon target binding. The sensors built with the aptamer containing a 2 bp stem generated much higher signal-on responses to AFB1 at 4 °C than at room temperature (25 °C). The improvements resulted in a detection limit of 6 pM, enabling the determination of trace AFB1 in a complex sample matrix. This study demonstrates that low temperature greatly enhances the performance of aptamer electrochemical sensors. This aptasensor is simple to construct and readily regenerated by washing with deionized water for reuse. This aptasensor strategy could be applied to the development of an electrochemical aptasensor for other targets.

A reagentless electrochemical sensor for aflatoxin B1 with sensitive signal-on responses using aptamer with methylene blue label at specific internal thymine

Aptamer electrochemical sensors using immobilized aptamers with redox tag rely on the target binding-induced changes of current signal on electrode, offering advantages in operation convenience, no separation, rapidity, and sensitivity. Usually, the redox tag is placed on aptamer terminal, however, sometimes the terminal label may be insensitive to target-binding and fail to generate sensitive responses. The redox tag methylene blue (MB) labeled on different sites of aptamer may experience distinct changes in local environment, distance to electrode, or interactions with aptamer bases during affinity binding, which affect the current signal. Thus, it is possible to construct aptamer electrochemical sensors with sensitive and significant responses to targets by screening a series of sites (e.g., internal thymine T) of the aptamer and placing MB tag on a specific site of the aptamer. With this strategy, we successfully fabricated an electrochemical sensor on gold electrode for rapid, reagentless, and sensitive detection of aflatoxin B1 (AFB1), an important mycotoxin causing great health risks, by using a 26-mer DNA aptamer with MB on an internal T site (e.g., 18th T) and a thiol moiety at 5' terminal. This sensor generated remarkable signal-on responses to AFB1, allowed a detection limit of 6 pM, and enabled detection of AFB1 in wine, milk and corn flour samples. This sensor can be well regenerated by rinsing with deionized water and reused, and shows good stability. This sensor and the demonstrated strategy are promising in wide applications.

Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects

Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.

Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review

Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.

A Lateral Flow Strip Based on a Truncated Aptamer-Complementary Strand for Detection of Type-B Aflatoxins in Nuts and Dried Figs

Type-B aflatoxins (AFB1 and AFB2) frequently contaminate food, especially nuts and fried figs, and seriously threaten human health; hence, it is necessary for the newly rapid and sensitive detection methods to prevent the consumption of potentially contaminated food. Here, a lateral flow aptasensor for the detection of type-B aflatoxins was developed. It is based on the use of fluorescent dye Cy5 as a label for the aptamer, and on the competition between type-B aflatoxins and the complementary DNA of the aptamer. This is the first time that the complementary strand of the aptamer has been used as the test line (T-line) to detect type-B aflatoxins. In addition, the truncated aptamer was used to improve the affinity with type-B aflatoxins in our study. Therefore, the lengths of aptamer and cDNA probe were optimized as key parameters for higher sensitivity. In addition, binding buffer and organic solvent were investigated. The results showed that the best pair for achieving improved sensitivity and accuracy in detecting AFB1 was formed by a shorter aptamer (32 bases) coupled with the probe complementary to the AFB1 binding region of the aptamer. Under the optimal experimental conditions, the test strip showed an excellent linear relationship in the range from 0.2 to 20 ng/mL with a limit of detection of 0.16 ng/mL. This aptamer-based strip was successfully applied to the determination of type-B aflatoxins in spiked and commercial peanuts, almonds, and dried figs, and the recoveries of the spiked samples were from 93.3%-112.0%. The aptamer-complementary strand-based lateral flow test strip is a potential alternative tool for the rapid and sensitive detection of type-B aflatoxins in nuts and dried figs. It is of help for monitoring aflatoxins to avoid the consumption of unsafe food.

In silico maturation of affinity and selectivity of DNA aptamers against aflatoxin B1 for biosensor development

A high affinity and selectivity DNA aptamer for aflatoxin B₁ (AFB₁) was designed through Genetic Algorithm (GA) based in silico maturation (ISM) strategy. The sequence of a known AFB₁ aptamer (Patent: PCT/CA2010/001292, Apt1) applied as a probe in many aptasensors was modified using seven GA rounds to generate an initial library and three different generations of ss DNA oligonucleotides as new candidate aptamers. Molecular docking methodology was used to screen and analyze the best aptamer-AFB₁ complexes. Also, a new pipeline was proposed to faithfully predict the tertiary structure of all single stranded DNA sequences. By the second generation, aptamer Apt1 sequence was optimized in the local search space and five aptamers including F20, g12, C52, C32 and H1 were identified as the best aptamers for AFB₁. The selected aptamers were applied as probes in an unmodified gold nanoparticles-based aptasensor to evaluate their binding affinity to AFB₁ and their selectivity against other mycotoxins (aflatoxins B₂, G₁, G₂, M₁, ochratoxin A and zearalenone). In addition, a novel direct fluorescent anisotropy aptamer assay was developed to confirm the binding interaction of the selected aptamers over AFB_1. The ISM allowed the identification of an aptamer, F20, with up to 9.4 and 2 fold improvement in affinity and selectivity compared to the parent aptamer, respectively.

Determination of aflatoxins in milk sample with ionic liquid modified magnetic zeolitic imidazolate frameworks

The ionic liquid (IL) was introduced to the synthesis system of magnetic zeolite imidazolate framework-8 (M/ZIF-8), which was benefit to the formation of binary imidazole and the co-modification of M/ZIF-8. The morphology and textural properties of ILM/ZIF-8 were characterized by SEM, TEM, BET and BJH. The crystal structural shape and size of MZIF-8 was unvaried with the interventional of IL. The ILM/ZIF-8 was applied to the concentration and determination of aflaoxins (AFB₁, AFB₂, AFG₁ and AFG₂) in milk samples based on magnetic solid phase extraction (MSPE) coupled with ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The experimental parameters of the MSPE, including amount of ILM/ZIF-8, pH, type and amount of desorption solvent, extraction time and sample volume were investigated by a univariate method and orthogonal screening. The four AFs were concentrated from the 20 mL milk when 90 mg ILM/ZIF-8 was used as magnetic adsorbent. The extraction efficiency of AFs was higher than 80.0% within 15 min. The limits of quantitative and detection were 7.5-26.7 and 2.3-8.1 ng/L, respectively. The proposed method was applied to the determination of milk samples containing trace amounts of AFs and the recoveries ranged from 79.0% to 102.5%, with RSD below 7.7%.

A signal-on electrochemical aptasensor for rapid detection of aflatoxin B1 based on competition with complementary DNA

Aflatoxin B1 (AFB1) is the most toxic mycotoxin, causing harmful effects on human and animal health, and the rapid and sensitive detection of AFB1 is highly demanded. We developed a simple electrochemical aptasensor achieving rapid detection of aflatoxin B1 (AFB1). A short anti-AFB1 aptamer having a methylene blue (MB) redox tag at the 3'-end was immobilized on the surface of a gold electrode. In the absence of AFB1, a complementary DNA (cDNA) strand hybridized with the MB-labeled aptamer, causing MB apart from the electrode surface and low current of MB. In the presence of AFB1, AFB1 competed with the cDNA in the binding to the MB-labeled aptamer, and the aptamer-AFB1 binding caused formation of a hairpin structure, making the MB close to the electrode surface and current of MB increase. Under optimized conditions, we achieved detection of AFB1 over dynamic concentration range of 2 nM-4 μM by using this signal-on electrochemical aptasensor. This method only required a simple 5-min incubation of sample solution prior to rapid electrochemical sensing, more rapid than other electrochemical aptasensors. The sensor could be well regenerated and reused. This sensor allowed to detect AFB1 spiked in 20-fold diluted beer and 50-fold diluted white wine, respectively. It shows potential for detection of AFB1 in wide applications.

An aptamer assay for aflatoxin B1 detection using Mg2+ mediated free zone capillary electrophoresis coupled with laser induced fluorescence

We described an aptamer based and Mg²⁺ mediated free zone capillary electrophoresis-laser induced fluorescence (CE-LIF) assay for aflatoxin B1 (AFB1) detection. This CE-LIF assay applied an anti-AFB1 aptamer with a single fluorescein (FAM) label at 5' end and a short complementary DNA (cDNA). In the absence of AFB1, the cDNA hybridized with the aptamer probe and formed a duplex DNA. The use of running buffer containing MgCl₂ allowed good isolation of the duplex DNA from the single stranded DNA in CE. We found introducing a biotin label on the cDNA further improved the isolation. When AFB1 existed in sample solution, the aptamer probe bound with AFB1, dissociating from the duplex DNA. Thus, the duplex DNA peak decreased, while the aptamer probe peak increased during CE-LIF analysis. We achieved detection of AFB1 by measuring the aptamer probe peak. The length of cDNA, the ratio of aptamer to cDNA, and the concentration of MgCl₂ in sample buffer and separation buffer had great effect on the aptamer based CE-LIF assay. Under optimized conditions, the detection limit of AFB1 was 0.2 nM, and the dynamic range was from 0.2 nM to 500 nM. Limit of quantitation was 0.5 nM. This CE-LIF assay enabled detection of AFB1 spiked in diluted human serum, diluted human urine, and corn flour samples. This assay exhibits potential for wide application as it integrates the rapidity, high sensitivity, low sample consumption of CE-LIF analysis and the strengths of aptamer.

Systematic truncating of aptamers to create high-performance graphene oxide (GO)-based aptasensors for the multiplex detection of mycotoxins

Graphene oxide (GO)-based aptasensors are currently one of the most popular sensing platforms for the simple and rapid detection of various targets. Unfortunately, the GO-based aptasensors with long aptamer strands typically show unsatisfactory performance resulting from insignificant structural transformations upon target binding. We report herein the utilization of an aptamer-truncating strategy to combat such a challenge. Taking a pre-selected anti-aflatoxin B1 (AFB1) aptamer (P-AFB1-50) as a trial system, we sequentially remove the extraneous nucleotides within the aptamer by means of circular dichroism (CD) spectroscopy and binding affinity analysis. Particularly, the ratio of the quenching constants between the GO sheets and the truncated aptamers (labelled with fluorophores) in the absence and presence of the target was determined for each of the truncated aptamers to evaluate the optimal sequence. As a result, the truncated aptamer comprising 40 nucleotides was confirmed to show the highest FL output and the best detection limit upon conjugation with GO sheets. More importantly, we demonstrated that this truncating strategy is versatile, i.e., it can be easily extended to other aptamer systems (anti-ochratoxin A (OTA) aptamer, P-OTA-61, as an example) for extraneous nucleotide identification. Impressively, the two optimal truncated aptamers can work together on GO sheets to achieve a simultaneous detection of two different mycotoxins (i.e., AFB1 and OTA) in one single test. Essentially, this research opens a new avenue for the design and testing of aptamer-/GO-based-sensing platforms for rapid, low-cost and multiplex quantification of analytical targets of interest.

GO-amplified fluorescence polarization assay for high-sensitivity detection of aflatoxin B1 with low dosage aptamer probe

Aflatoxin B₁ (AFB₁) is the most toxic mycotoxin of the aflatoxins (AFs) and shows carcinogenic, teratogenic and mutagenic effects in humans and animals. AFB₁ is widely seen in cereal products such as rice and wheat. This research proposed a low-cost, high-sensitivity fluorescence polarization (FP) assay for detection of AFB₁ using aptamer biosensors based on graphene oxide (GO). The aptamers labelled with fluorescein amidite (FAM) were adsorbed on the surface of GO through π-π stacking and electrostatic interaction, thus forming aptamer/GO macromolecular complexes. Under these conditions, the local rotation of fluorophores was limited and the system had a high FP value. When there was AFB₁ in the system, aptamers were dissociated from the GO surface and combined with AFB₁ owing to their specificity to form aptamer/AFB₁ complexes. As a result, large changes were observed in the molecular weights of aptamers before, and after, the combination, therefore leading to the apparent changes in FP value. The results showed that when only 10 nM of aptamer was used, the changes in FP and the AFB₁ concentration had a favourable linear relationship within 0.05 to 5 nM of AFB₁, and the lowest detection limit (LOD) was 0.05 nM. In addition, the recoveries of rice sample extract ranged from 89.2% to 112%. The method is simple, highly sensitive, cost-efficient and shows potential application prospects.

Isolation of Aflatoxin B1 from Moldy Foods by Solid-Phase Extraction Combined with Bifunctional Ionic Liquid-Based Silicas

A solid-phase extraction method was developed by using new bifunctional ionic liquid-based silicas as sorbents to isolate aflatoxin B1 from moldy corn and peanut. Firstly, according to the adsorption efficiency, two sorbents imidazolium chloride-butylimidazolium chloride-based silica (Sil@BIm-Im) and imidazolium chloride-hexylimidazolium chloride-based silica (Sil@HIm-Im) were selected. The RSM was introduced to optimize adsorption conditions such as methanol/water ratio, time, and pH. Sil@HIm-Im, which had the highest adsorption efficiency, was used in SPE as a sorbent. After 2.0 mL of loading samples, washing solvents were optimized as 6.0 mL and 4.0 mL of water for corn and peanut, 2.0 mL of acetonitrile, and 3.0 mL of methanol. 3.0 mL of methanol/acetic acid (2.0% vol.) was investigated as an elution solvent. Finally, 0.009 μg/g and 0.023 μg/g of aflatoxin B1 were obtained in corn and peanut extract with recoveries of 80.0%-103.3% and RSDs of 2.37%-6.58%.