Cascade strand displacement reaction-assisted aptamer-based highly sensitive detection of ochratoxin A

A CRISPR/Cas12a-based competitive aptasensor for ochratoxin A detection

The serious contamination of ochratoxin A (OTA) in agricultural products has promoted the development of rapid, sensitive, and selective analytical methods for OTA monitoring. We demonstrated a competitive aptasensor for OTA detection using CRISPR/Cas12a as an effective signal amplifier. OTA competes with complementary DNA of the aptamer on the microplate to bind to the aptamer. Streptavidin bridges the biotinylated aptamer and biotinylated activator to convert the OTA input into Cas12a activation, which cleaves fluorescent DNA reporters. Under optimized experimental conditions, the aptasensor was demonstrated to work well for sensitive detection of OTA, with a linear range from 0.5 nM to 62.5 nM and a detection limit of 0.5 nM. Moreover, our method not only exhibits high selectivity, but also has satisfactory anti-interference ability against complex sample matrices. Taken together, the CRISPR/Cas12a-based competitive aptasensor offers a simple and sensitive platform for OTA detection, and it holds great promise for food security monitoring.

A fluorescent Aptasensor based on magnetic-separation strategy with gold nanoclusters for Deoxynivalenol (DON) detection

A highly sensitive method based on MBs-cDNA@Apt-AuNCs519 was developed for deoxynivalenol (DON) detection in wheat. The MBs-cDNA@Apt-AuNCs519 was established using green emission gold nanoclusters (AuNCs519) with aggregation-induced emission properties as signal probes and combining amino-modified DON-aptamer (Apt), biotin-modified DNA strand (the partially complementary to Apt (cDNA)), and streptavidin-modified magnetic beads (MBs). The Apt-AuNCs519 were well connected with MBs-cDNA without DON but dissociated from MBs-cDNA@Apt-AuNCs519 with the addition of DON, leading to a noticeable reduction in the fluorescent intensity of the aptasensor. Moreover, this fluorescence aptasensor showed two linear relationships in the concentration range of 0.1-50 ng/mL and 50-5000 ng/mL with a limit of detection of 3.73 pg/mL with good stability, reproducibility and specificity. The results were consistent with high-performance liquid chromatography and enzyme-linked immunosorbent assay methods, further indicating the potential of this method for accurate trace detection of DON in wheat.

Exo I-based cyclic digestion coupled with synergistic enhancement strategy for integrating dual-mode optical aptasensor platform

The improvement of dual-mode techniques was of particular interest to researchers, which might enhance the detection performance and applicability. Here, a dual-mode optical aptasensor (DO-aptasensor) platform based on exonuclease I (Exo I) cyclic digestion and synergistic enhancement strategy had proposed for zearalenone (ZEN). Following the preparation of dumbbell-shaped signal probe, the Exo I-based cyclic digestion amplification performed, and then the synergistic enhancement effect carried out to achieve the Poly-HRP-based colorimetry and FAM-SGI-based fluorescence. The efficient homogeneous system realized through the magnetic separation, while the signal interference further eliminated by the graphene oxide (GO). The LOD values were as low as 0.067 ng mL-1 for colorimetry mode and 0.009 ng mL-1 for fluorescence mode, which reduced 23-fold and 172-fold than ELASA by same ZEN-Apt. This promising platform gave rise to a dual-mode optical readout, improved sensitivity and positively correlated detection. Meanwhile, the DO-aptasensor also exhibited the acceptable specificity, desirable reliability and excellent practicability. This novel avenue of aptasensor platform hold great potential for dual-mode optical monitoring of other targets, which can further expand the application scope of Exo I-based signal amplification and synergistic enhancement effect.

Establishment of a Dual-Signal Enhanced Fluorescent Aptasensor for Highly Sensitive Detection of Ochratoxin A

A robust and versatile dual-signal enhanced fluorescent aptasensor was developed for ochratoxin A (OTA) detection based on fluorescence resonance energy transfer between 5-carboxyfluorescein (FAM) and Super Green I (SG) fluorophores as the donor and graphene oxide (GO) nanosheet as the acceptor. Abundant SG probes were adsorbed into the FAM-complementary DNA (cDNA)-aptamer double-stranded structure to achieve remarkably enhanced fluorescence responses. Without OTA, the FAM-cDNA-SG conjugates coexisted with GO nanosheets, exhibiting strong fluorescence signals. In the presence of OTA, it was captured by the aptamers to release cDNA-FAM and SG probes, which were adsorbed by GO, leading to OTA-dependent fluorescence quenching. The changed fluorescence intensity was measured for accurate quantitation of OTA. Under optimum conditions, the dual-signal enhanced fluorescent aptasensor realized fascinating sensitivity with a limit of detection of 0.005 ng/mL and a wide concentration range of 0.02-20 ng/mL, as well as high selectivity for OTA over other interfering substances, excellent accuracy with average recoveries of 91.37-116.83% in the fortified malt matrices, and superior reliability and practicability in actual samples. This FAM-cDNA-aptamer-SG/GO nanosheet-based aptasensing platform could be extended to monitor other contaminants or trace molecules in food, environmental, and diagnostic fields by altering the corresponding aptamers.

Enhanced sensitivity in electrochemical detection of ochratoxin A within food samples using ferrocene- and aptamer-tethered gold nanoparticles on disposable electrodes

Ensuring food security is crucial for public health, and the presence of mycotoxins, produced by fungi in improperly stored processed or unprocessed food, poses a significant threat. This research introduces a novel approach - a disposable aptasensing platform designed for the detection of ochratoxin A (OTA). The platform employs gold-nanostructured screen-printed carbon electrodes functionalized with a ferrocene derivative, serving as an integrated faradaic transducing system, and an anti-OTA aptamer as a bioreceptor site. Detection relies on the ferrocene electrochemical signal changes induced by the aptamer folding in the presence of the target molecule. Remarkably sensitive, the platform detects OTA within the range of 0.5 to 70 ng mL-1 and a detection limit of 11 pg mL-1. This limit is approximately 200 times below the levels stipulated by the European Commission for agricultural commodities. Notably, the sensing device exhibits efficacy in detecting OTA in complex media, such as roasted coffee beans and wine, without the need for sample pretreatment, yielding accurate recoveries. Furthermore, while label-free electrochemical aptasensors have proliferated, this study addresses a gap in understanding the binding mechanisms of some aptasensors. To enhance the experimental findings, a theoretical study was conducted to underscore the specificity of the anti-OTA aptamer as a donor for OTA detection. The molecular docking technique was employed to unveil the key binding region of the aptamer, providing valuable insights into the aptasensor specificity.

Silver nanocluster-based aptasensor for the label-free and enzyme-free detection of ochratoxin A

Mycotoxin contamination in cereal is a global concern, threatening food safety and human health, necessitating the development of rapid on-site methods. Here, a label- and enzyme-free biosensor was developed based on aptamer-regulated DNA-silver nanoclusters (AgNCs) for rapid detection of ochratoxin A (OTA). A novel DNA-templated AgNCs emitting strong red fluorescence was designed and synthesized in this study. The partial sequence of the DNA template was selected from the complementary OTA aptamer (Apt-OTA) sequence, which can quench fluorescence from the AgNCs via hybridization in the absence of OTA. In the presence of OTA, the high OTA-Aptamer affinity prevented the Apt-OTA from quenching the AgNCs, resulting in "turn on" of the fluorescence. This biosensor eliminated the use of costly reagents, complex pretreatments, and sophisticated equipment, which could realize the point-of-care testing (POCT) of OTA with a limit of detection (LOD) of 1.3 nM and a detection time of 45 min.

Structure-switching aptasensors for sensitive detection of ochratoxin A

Ochratoxin A (OTA) is a toxic metabolite commonly found in various foods and feedstuffs. Accurate and sensitive detection of OTA is needed for food safety and human health. Based on a common OTA-binding aptamer (OTABA), two structure-switching OTABAs, namely OTABA4 and OTABA3, were designed by configuring a split G-quadruplex and a split G-triplex, respectively, at the two ends of OTABA to construct aptasensors for the detection of OTA. The OTABA, G-quadruplex, and G-triplex all can capture the thioflavin T (ThT) probe, thereby enhancing the fluorescence intensity of ThT. Bonding with OTA could change the conformations of OTABA and G-quadruplex or G-triplex regions, resulting in the release of the captured ThT and diminution of its fluorescence intensity. Dual conformation changes in structure-switching OTABA synergistically amplified the fluorescence signal and improved the sensitivity of the aptasensor, especially for that with OTABA3. The detection limits of the OTABA4-ThT and OTABA3-ThT systems for OTA were 0.28 and 0.059 ng ml-1 , with a 1.4-fold and 6.7-fold higher sensitivity than that of the original OTABA-ThT system, respectively. They performed well in corn and peanut samples and met the requirements of the food safety inspections.

A label-free fluorescent aptasensor based on a novel exponential rolling circle amplification for highly sensitive ochratoxin A detection

Rapid and sensitive analysis of ochratoxin A (OTA) plays an important role in food safety. Here, an aptasensor based on novel exponential rolling circle amplification (ERCA) was proposed for ultrasensitive and label-free fluorescence detection of OTA. The attachment of OTA to its aptamer could release H and rapidly hybridize with CT to initiate rolling circle amplification (RCA). The amplicons could further displace H from APH to initiate recycled RCA, achieving exponential growth of amplification products that contained G4 dimers for lighting up ThT. Benefiting from the exponential amplification efficiency of the ERCA strategy and the high fluorescence quantum yield of G4 dimer/ThT, this strategy exhibited a wide linear range from 10 fg/mL to 10 ng/mL with a detection limit of 4.3 fg/mL. In addition, the aptasensor displayed satisfactory recoveries in real sample analysis. We believe that this novel aptasensor possesses promising application prospects in food safety and medicine detection.

Targeted Selection of Aptamer Complementary Elements toward Rapid Development of Aptamer Transducers

Biosensing using aptamers has been a recent interest for their versatility in detecting many different analytes across a wide range of applications, including medical and environmental applications. In our last work, we introduced a customizable aptamer transducer (AT) that could successfully feed-forward many different output domains to target a variety of reporters and amplification reaction networks. In this paper, we explore the kinetic behavior and performance of novel ATs by modifying the aptamer complementary element (ACE) chosen based on a technique for exploring the ligand-binding landscape of duplexed aptamers. Using published data, we selected and constructed several modified ATs that contain ACEs with varying length, position of the start sites, and position of single mismatches, whose kinetic responses were tracked with a simple fluorescence reporter. A kinetic model for ATs was derived and used to extract the strand-displacement reaction constant k₁ and the effective aptamer dissociation constant K_d,eff, allowing us to calculate a relative performance metric, k₁/K_d,eff. Comparing our results with the predictions based on the literature data, we provide useful insight into the dynamics of the adenosine AT's duplexed aptamer domain and suggest a high-throughput approach for future ATs to be developed with improved sensitivity. The performance of our ATs showed a moderate correlation to those predicted by the ACE scan method. Here, we find that predicted performance based on our ACE selection method was moderately correlated to our AT's performance.

A Novel Fluorescent Aptasensor Based on Dual-labeled DNA Nanostructure for Simultaneous Detection of Ochratoxin A and Aflatoxin B1

Based on DNA strand replacement reaction and aptamer-specific recognition, a simple dual-labeled DNA nanostructure is designed for the simultaneous detection of Ochratoxin A (OTA) and aflatoxin B1 (AFB₁). C1 is labeled with Cy3 and Cy5, while C2 and C3 are labeled with BHQ2. The fluorescence intensity of DNA nanostructure composed of C1, C2 and C3 is weak because of fluorescence resonance energy transfer. When OTA Aptamer (OTA-Apt) and AFB1 Aptamer (AFB₁-Apt) are added to the homogeneous system at the same time, C1 can be replaced with the help of toehold strand displacement, resulting in fluorescence enhancement. In the presence of both OTA and AFB₁, the toehold strand displacement reaction is inhibited due to preferential binding between the target and their corresponding aptamers. The limit of detection of OTA was 0.007 ng/mL and that of AFB₁ was 0.03 ng/mL. The recoveries of OTA and AFB₁ were 96%-101% and 97%-101% in the corn sample, and 99%-101% and 92%-106% in the wine sample. Compared with other sensors, the preparation of this aptasensor needs simpler experimental steps and a shorter total-preparing time, confirming the convenient, rapid, and time-saving operation process.

Dual-signal output fluorescent aptasensor based on DNA programmability and gold nanoflowers for multiple mycotoxins detection

Herein, a dual-signal output fluorescent aptamer sensor was constructed for the simultaneous detection of aflatoxin B₁ (AFB₁) and ochratoxin A (OTA) using the specific recognition ability of aptamers and the programmability of DNA. A functional capture probe (cDNA) was designed with the black hole quenching motif BHQ1 labeled at the 5' end and biotin (bio) labeled at the 3' end. The fluorescent dye Cy3-labeled aflatoxin B1 aptamer (AFB₁-Apt) and the carboxyfluorescein FAM-labeled ochratoxin A aptamer (OTA-Apt) were used as two fluorescent probes. The cDNA is anchored to the quenching material gold nanoflowers (AuNFs) by the action of streptavidin (SA) and biotin. Its ends can be complementarily paired with two fluorescent probe bases to form a double-stranded structure. The fluorescence of Cy3 was quenched by AuNFs, and the fluorescence of FAM was quenched by BHQ1 through the fluorescence energy resonance transfer (FRET) effect, forming a fluorescence quenching system. Due to the high affinity of the target and the aptamer, the structure of the aptamer probe changes and detaches from the sensor when AFB₁ and OTA are present, resulting in enhanced fluorescence. Under optimal conditions, the linear range of AFB₁ was 0.1-100 ng/mL (R² = 0.996), the limit of detection (LOD) was as low as 0.014 ng/mL, and the limit of quantification (LOQ) was 0.046 ng/mL. The linear range of OTA was 0.1-100 ng/mL (R² = 0.995), the limit of detection (LOD) was as low as 0.027 ng/mL, and the limit of quantification (LOQ) was 0.089 ng/mL. The sensor had high accuracy in detecting both AFB₁ and OTA in real sample analysis. The results of the t test show that there is no significant difference between the results of this study and the high-performance liquid phase (HPLC) method, indicating that the prepared sensor can be used as a potential platform for multiple mycotoxins detection.

A Novel Fluorescent Aptasensor Based on Real-Time Fluorescence and Strand Displacement Amplification for the Detection of Ochratoxin A

It is urgently necessary to develop convenient, reliable, ultrasensitive and specific methods of ochratoxin A determination in food safety owing to its high toxicity. In the present study, an ultrasensitive and labeled-free fluorescent aptamer sensor combining real-time fluorescence with strand displacement amplification (SDA) was fabricated for the determination of OTA. In the presence of OTA, the OTA–aptamer combines with OTA, thus opening hairpins. Then, SDA primers specifically bind to the hairpin stem, which is used for subsequent amplification as a template. SDA amplification is initiated under the action of Bst DNA polymerase and nicking endonuclease. The amplified products (ssDNA) are dyed with SYBR Green II and detected with real-time fluorescence. The method has good linearity in the range of 0.01–50 ng mL⁻¹, with the lowest limit of detection of 0.01 ng mL⁻¹. Additionally, the fluorescent aptamer sensor shows outstanding specificity and reproducibility. Furthermore, the sensor shows excellent analytical performance in the artificial labeled detection of wheat and oat samples, with a recovery rate of 96.1~100%. The results suggest that the developed sensor has a promising potential application for the ultrasensitive detection of contaminants in food.

A Systematic Mapping Study of Coffee Quality throughout the Production-to-Consumer Chain

Coffee is one of the most consumed beverages in the world and is crucial in the economy of many developing countries. The search to improve coffee quality comes from many fronts, as do the many ways to measure quality and the factors that affect it. Several techniques are used to measure the different metrics to assess coffee quality, across different types of coffee samples and species, and throughout the entire process from farm to cup. In this work, we conducted a systematic mapping study of 1,470 articles to identify the aspects of quality that are the most important in the scientific literature to evaluate coffee throughout the processing chain. The study revealed that cup quality and biochemical composition are the most researched quality attributes. The main objective of the reviewed studies is the correlation between different quality measurements. The most used techniques are the analytical chemistry methods. The most studied species is Coffea arabica. The most used sample presentation is green coffee. The postharvest stage is the most researched, in which quality control receives more attention. In the preharvest stage, management practices stand out. Finally, the most used type of research was the evaluation research.

Eco-friendly 'ochratoxin A' control in stored licorice roots - quality assurance perspective

According to toxicity data, ochratoxin A (OTA) is the second most important mycotoxin and is produced by Aspergillus and Penicillium. As a natural antifungal agent, clove essential oil (CEO) is a substance generally recognised as safe (GRAS) and shows strong activity against fungal pathogens. Here, we aimed to investigate the control efficacy of CEO in nano-emulsions (CEN) against OTA production in licorice roots and rhizomes during storage. The experiments were performed under simulated conditions of all four seasons (i.e. Spring, Summer, Autumn and Winter). Relative humidity (RH) and temperature were simulated in desiccators along with various salt solutions in incubators. Fresh licorice roots were immersed in CEN at various concentrations (150, 300, 600, 1200 and 2400 µl/l). Before utilising the nano-emulsions, we measured their polydispersity index and mean droplet size by the dynamic light scattering (DLS) technique. Also, the chemical composition of the CEO was determined using GC and GC-MS analyses. Sampling was carried out to monitor OTA once every five days. The samples were dried immediately and analysed by high-performance liquid chromatography (HPLC). Results showed that various concentrations of CEN inhibited the growth of fungi and OTA production. The most effective CEN concentrations were 1200 and 2400 µl/l, which reduced OTA production to 19 and 20 ppb under Winter and Autumn conditions, respectively. These results suggest an effective eco-friendly method for the storage of licorice to reduce postharvest fungal decay.

Construction of a fluorescence biosensor for ochratoxin A based on magnetic beads and exonuclease III-assisted DNA cycling signal amplification

Specific and sensitive detection of hazardous mycotoxins in agricultural crops is one of the most important goals of food safety. A fluorescence biosensor for sensitive detection of ochratoxin A (OTA) was constructed via magnetic beads and the exonuclease III (Exo III)-assisted trigger DNA circle amplification approach. Exo III-assisted trigger DNA circle amplification can be utilized as an effective strategy for the sensitive detection of OTA. The employment of streptavidin labeled magnetic beads offers a manner for the accumulation and separation of the hairpin signal probe sDNA-FAM in solution. After target specific recognition, the aptamers combined with OTA were released and the remaining block DNA (bDNA) probes captured the signal probes on magnetic bead modified fluorophores. Subsequently, the enzyme digestion reaction leads to the fluorophore free solution. Exo III-assisted DNA circle amplification contributed to the high sensitivity of the presented OTA fluorescence aptasensor. The experimental results demonstrate that the aptasensor is sensitive with the limit of detection as low as 0.28 ng mL^-1 for OTA, which was lower than that of the proposed aptasensors reported by the other literature on fluorescence methods. Additionally, the developed aptasensor with the diverse aptamer sequence shows promising potential applications in food monitoring.

Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases

Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.

Application of the Dimeric G-Quadruplex and toehold-mediated strand displacement reaction for fluorescence biosensing of ochratoxin A

Ochratoxin A (OTA) is one of the most toxic mycotoxins that exists in various agro-products and foods. Here, a non-label and enzyme-free fluorescence biosensor for highly specific detection of OTA has been developed by the combination of toehold-mediated strand displacement reaction (TMSD) and G-quadruplex dimer/ThT (G-dimer/ThT). The DNA duplex (aptamer-IP) is composed of the anti-OTA aptamer and a single stranded initiation probe (IP). In the presence of OTA, the attachment of target to aptamer leads to the liberation of the IP, which activates the cycle TMSD amplifications of two hairpin probes (H1 and H2) accompanied by the production of numerous H1-H2 assemblies. This double-stranded H1-H2 structure results in the proximity between the 5'-end overhang tail of H1 and the 3'-end stem of H2 to liberate the pre-blocked G-dimer sequence for lighting up ThT. In addition, the method displayed a stable fluorescence emission in the high-salt media. It was successfully applied to analyze OTA in real food samples. Hence, the constructed fluorescence biosensing platform might provide a new way for OTA and other toxin analysis detection.

Aptasensors for mycotoxin detection: A review

Mycotoxins are toxic compounds produced by fungi, which represent a risk to the food and feed supply chain, having an impact on health and economies. A high percentage of feed samples have been reported to be contaminated with more than one type of mycotoxin. Systematic, cost-effective and simple tools for testing are critical to achieve a rapid and accurate screening of food and feed quality. In this review, we describe the various aptamers that have been selected against mycotoxins and their incorporation into optical and electrochemical aptasensors, outlining the strategies exploited, highlighting the advantages and disadvantages of each approach. The review also discusses the different materials used and the immobilization methods employed, with the aim of achieving the highest sensitivity and selectivity.

DNAzyme Amplified Aptasensing Platform for Ochratoxin A Detection Using a Personal Glucose Meter

Aptamer-based sensors have emerged as a major platform for detecting small-molecular targets, because aptamers can be selected to bind these small molecules with higher affinity and selectivity than other receptors such as antibodies. However, portable, accurate, sensitive, and affordable detection of these targets remains a challenge. In this work, we developed an aptasensing platform incorporating magnetic beads and a DNAzyme for signal amplification, resulting in high sensitivity. The biosensing platform was constructed by conjugating a biotin-labeled aptamer probe of small-molecular targets such as toxins and a biotin-labeled substrate strand on magnetic beads, and the DNAzyme strand hybridized with the aptamer probe to block the substrate cleavage activity. The specific binding of the small-molecular target by the aptamer probe can replace the DNAzyme strand and then induce the hybridization between the DNAzyme strand and substrate strand, and the iterative signal amplification reaction of hydrolysis and cleavage of the substrate chain occurs in the presence of a metal ion cofactor. Using invertase to label the substrate strand, the detection of small molecules of the toxin is successfully transformed into the measurement of glucose, and the sensitive analysis of small molecules such as toxins can be realized by using the household portable glucose meter as a readout. This platform is shown to detect ochratoxin, a common toxin in food, with a linear detection range of 5 orders of magnitude, a low detection limit of 0.88 pg/mL, and good selectivity. The platform is easy to operate and can be used as a potential choice for quantitative analysis of small molecules, at home or under point-of-care settings. Moreover, by changing and designing the aptamer probe and the arm of DNAzyme strand, it can be used for the analysis of other analytes.

A novel colorimetric immunoassay for sensitive monitoring of ochratoxin A based on an enzyme-controlled citrate-iron(iii) chelating system

Schematic illustration of an enzyme-controlled citrate-iron(iii) chelating system-based colorimetric immunoassay for sensitive determination of ochratoxin A.