Fluorometric aptamer-based determination of ochratoxin A based on the use of graphene oxide and RNase H-aided amplification

Nanomaterial-based aptamer biosensors for ochratoxin A detection: a review

Ochratoxin A (OTA) is a widely distributed mycotoxin that often contaminates food, grains and animal feed. It poses a serious threat to human health because of its high toxicity and persistence. Therefore, the development of an inexpensive, highly sensitive, accurate and rapid method for OTA detection is imperative. In recent years, various nanomaterials used in the establishment of aptasensors have attracted great attention due to their large surface-to-volume ratio, good stability and facile preparation. This review summarizes the development of nanomaterial-based aptasensors for OTA determination and sample treatment over the past 5 years. The nanomaterials used in OTA aptasensors include metal, carbon, luminescent, magnetic and other nanomaterials. Finally, the limitations and future challenges in the development of nanomaterial-based OTA aptasensors are reviewed and discussed.

Aptamers-Diagnostic and Therapeutic Solution in SARS-CoV-2

The SARS-CoV-2 virus is currently the most serious challenge to global public health. Its emergence has severely disrupted the functioning of health services and the economic and social situation worldwide. Therefore, new diagnostic and therapeutic tools are urgently needed to allow for the early detection of the SARS-CoV-2 virus and appropriate treatment, which is crucial for the effective control of the COVID-19 disease. The ideal solution seems to be the use of aptamers—short fragments of nucleic acids, DNA or RNA—that can bind selected proteins with high specificity and affinity. They can be used in methods that base the reading of the test result on fluorescence phenomena, chemiluminescence, and electrochemical changes. Exploiting the properties of aptamers will enable the introduction of rapid, sensitive, specific, and low-cost tests for the routine diagnosis of SARS-CoV-2. Aptamers are excellent candidates for the development of point-of-care diagnostic devices and are potential therapeutic tools for the treatment of COVID-19. They can effectively block coronavirus activity in multiple fields by binding viral proteins and acting as carriers of therapeutic substances. In this review, we present recent developments in the design of various types of aptasensors to detect and treat the SARS-CoV-2 infection.

Carbon-Based Nanocomposite Smart Sensors for the Rapid Detection of Mycotoxins

Carbon-based nanomaterials have become the subject of intensive interest because their intriguing physical and chemical properties are different from those of their bulk counterparts, leading to novel applications in smart sensors. Mycotoxins are secondary metabolites with different structures and toxic effects produced by fungi. Mycotoxins have low molecular weights and highly diverse molecular structures, which can induce a spectrum of biological effects in humans and animals even at low concentrations. A tremendous amount of biosensor platforms based on various carbon nanocomposites have been developed for the determination of mycotoxins. Therefore, the contents of this review are based on a balanced combination of our own studies and selected research studies performed by academic groups worldwide. We first address the vital preparation methods of biorecognition unit (antibodies, aptamers, molecularly imprinted polymers)-functionalized carbon-based nanomaterials for sensing mycotoxins. Then, we summarize various types of smart sensors for the detection of mycotoxins. We expect future research on smart sensors to show a significant impact on the detection of mycotoxins in food products.

Electrochemical Biosensors in Food Safety: Challenges and Perspectives

Safety and quality are key issues for the food industry. Consequently, there is growing demand to preserve the food chain and products against substances toxic, harmful to human health, such as contaminants, allergens, toxins, or pathogens. For this reason, it is mandatory to develop highly sensitive, reliable, rapid, and cost-effective sensing systems/devices, such as electrochemical sensors/biosensors. Generally, conventional techniques are limited by long analyses, expensive and complex procedures, and skilled personnel. Therefore, developing performant electrochemical biosensors can significantly support the screening of food chains and products. Here, we report some of the recent developments in this area and analyze the contributions produced by electrochemical biosensors in food screening and their challenges.

Two-color, ultra-sensitive fluorescent strategy for Ochratoxin A detection based on hybridization chain reaction and DNA tweezers

A two-color fluorescent DNA tweezers was developed for ultrasensitive detection of Ochratoxin A (OTA) based on hairpin-locked aptamer and hybridization chain reaction (HCR) amplification strategy. OTA can bind with hairpin-locked aptamer and then trigger the HCR reaction to produce a long double-strand DNA. The side-chains of the long duplex can separately hybridize with the two locker sequences of DNA tweezer, causing the opening of DNA tweezer and the recovery of two-color fluorescent signals. It shows a good linear range from 0.02 to 0.8 ppb with limit of detection of 0.006 ppb for FAM and 0.014 ppb for Cy5, which is beyond the requirement of actual application. In addition, the two-color fluorescent strategy can greatly reduce the false positive rate. It shows excellent performance for detection of OTA in practical food sample.

Advances in detection of infectious agents by aptamer-based technologies

Infectious diseases still remain one of the biggest challenges for human health. Accurate and early detection of infectious pathogens are crucial for transmission control, clinical diagnosis, and therapy. For a traditional reason, most immunological and microbiological laboratories are equipped with instruments designated for antibody-based assays in detection of infectious pathogens or clinical diagnosis. Emerging aptamer-based technologies have pushed a shift from antibody-based to aptamer-based assays due to equal specificity, even better sensitivity, lower manufacturing cost and more flexibility in amending for chemiluminescent, electrochemical or fluorescent detection in a multifaceted and high throughput fashion in comparison of aptamer-based to antibody-based assays. The nature of aptamer-based technologies is particularly suitable for point-of-care testing in remote areas at warm or hot atmosphere, and mass screening for potential infection in pandemic of emerging infectious agents, such as SARS-CoV or SARS-CoV-2 in an epicentre or other regions. This review intends to summarize currently available aptamer-based technologies in detection of bacterial, viral, and protozoan pathogens for research and clinical application. It is anticipated that potential technologies will be further optimized and validated for clinical translation in meeting increasing demands for prompt, precise, and reliable detection of specific pathogens in various atmospheric conditions.

Dual Triple Helix-Aptamer Probes for Mix-and-Read Detecting Antibiotics in Fish and Milk

Antibiotic abuse in agricultural products leads to serious food safety issues. To this end, we proposed a mix-and-read and enzyme-free amplified assay for antibiotics based on a dual triple helix-aptamer probe, potentially applicable for on-site monitoring of antibiotic residues. A dual triple helix-aptamer probe can leverage the response toward target molecules without enzyme-based amplification, rendering it sensitive and robust for profiling target molecules. The proposed assay allowed mix-and-read detection of chloramphenicol with a detection limit of 0.18 nM. Besides, it accommodated for specifically resolving chloramphenicol among other antibiotics. Chloramphenicol residual in aquatic products in fish and milk can be precisely determined. Thus, the aptamer probe deems to enrich the toolbox for managing antibiotic use.

A Non-Enzyme and Non-Label Sensitive Fluorescent Aptasensor Based on Simulation-Assisted and Target-Triggered Hairpin Probe Self-Assembly for Ochratoxin a Detection

The monitoring and control of mycotoxins has caused widespread concern due to their adverse effects on human health. In this research, a simple, sensitive and non-label fluorescent aptasensor has been reported for mycotoxin ochratoxin A (OTA) detection based on high selectivity of aptamers and amplification of non-enzyme hybridization chain reaction (HCR). After the introduction of OTA, the aptamer portion of hairpin probe H1 will combine with OTA to form OTA-aptamer complexes. Subsequently, the remainder of the opened H1 will act as an initiator for the HCR between the two hairpin probes, causing H1 and H2 to be sequentially opened and assembled into continuous DNA duplexes embedded with numerous G-quadruplexes, leading to a significant enhancement in fluorescence signal after binding with N-methyl-mesoporphyrin IX (NMM). The proposed sensing strategy can detect OTA with concentration as low as 4.9 pM. Besides, satisfactory results have also been obtained in the tests of actual samples. More importantly, the thermodynamic properties of nucleic acid chains in the monitoring platform were analyzed and the reaction processes and conditions were simulated before carrying out biological experiments, which theoretically proved the feasibility and simplified subsequent experimental operations. Therefore, the proposed method possess a certain application value in terms of monitoring mycotoxins in food samples and improving the quality control of food security.

Engineering Multivalence Aptamer Probes for Amplified and Label-Free Detection of Antibiotics in Aquatic Products

Excessive use of antibiotics in aquatic products is a serious problem for food safety and human health, and on-site detection of antibiotics is highly demanded. Herein, we proposed multivalence aptamer probes, allowing sensitive, label-free, and homogeneous detection of antibiotics in different aquatic products. Compared to commonly used aptamers, multivalence aptamer probes can provide multiple binding sites and a higher affinity for target molecules, and the iterative binding on different binding sites contributes to an amplified recognition effect, sharply increasing the response and sensitivity of aptamer probes. The 2-valence aptamer probes conferred a limit of detection of 0.097 nM for kanamycin detection, where it is estimated that their sensitivity is enhanced 12 times compared to 1-valence aptamer probes. Meanwhile, multivalence aptamer probes allowed us to specifically identify kanamycin among other antibiotics. It could detect kanamycin residual in aquatic products including river eel and puffer fish, as well as tap water with high precision. A multivalence design strategy of aptamer probes would significantly improve the detection performance of aptamers, facilitating the translation of aptamer for food safety control.

A novel fluorescent assay based on DNAzyme-assisted detection of prostate specific antigen for signal amplification

Prostate specific antigen (PSA) is one of the most common biomarkers for the management of prostate cancer. However, it still remains urgent to develop highly sensitive, cost-effective and selective strategies for PSA assay. In this paper, we developed a low-cost, highly sensitive and specific analytical strategy for the detection of PSA by using a fluorescence sensor based on Pb²⁺-dependent DNAzyme. We designed a DNA sequence called cmMB with a hairpin structure, containing PSA-specific aptamers and Pb²⁺-dependent DNAzyme chains. Also, a fluorophore-labelled DNA sequence called Sub-FAM, which contains a cleavage site of Pb²⁺-dependent DNAzyme and serves as substrate, is also designed for the signal generation. In the presence of PSA, interaction between aptamer and PSA blocks the hairpin structure of cmMB, resulting in the formation of Pb²⁺-dependent DNAzyme with Pb²⁺. Then, Pb²⁺-dependent DNAzyme can cleavage Sub-FAM and produce a high fluorescence. In the absence of PSA, since Sub-FAM remains to be ssDNA and can be absorbed by GO, only low fluorescence can be detected. Under optimal experimental conditions, a good linear relationship in the range of 1-100 pg mL^-1 was exhibited, with a limit of detection (LOD) of 0.76 pg mL^-1. In addition, the proposed method has potential value in the diagnosis and monitoring of prostate cancer because of its good selectivity and practical application in biological samples.

A fluorometric aptamer-based assay for ochratoxin A by using exonuclease III-assisted recycling amplification

A fluorometric assay is described for ochratoxin A (OTA) using an aptamer. The method is based on exonuclease-assisted recycling amplification. The OTA-binding aptamer partially hybridizes with complementary DNA (cDNA) that is released when the aptamer recognizes OTA. Then, cDNA hybridizes with a specifically designed hairpin DNA. Next, short ssDNA and cDNA are, respectively, released by exonuclease III catalyzed hydrolysis of the dsDNA. The cDNA induces the next ring opening and digestion. The short ssDNA captures the sDNA that is labeled with fluorescent FAM and is absorbed on graphene oxide (GO). The green fluorescence of the sDNA/GO system is quenched but is recovered if the sDNA is released from GO. This assay is high sensitive, works in the 5 nM to 200 nM OTA concentration range and has a 0.96 nM lower detection limit. It was applied to the quantitation of OTA in spiked wine and coffee samples. Graphical abstractSchematic of a fluorometric assay based on exonuclease-assisted recycling amplification for quantitative monitoring of OTA without the need of sample separation and multiple washing steps.

A review on recent developments in optical and electrochemical aptamer-based assays for mycotoxins using advanced nanomaterials

This review (with 163 refs) covers the recent developments of nanomaterial-based optical and electrochemical sensors for mycotoxins. The review starts with a brief discussion on occurrence, distribution, toxicity of mycotoxins and the legislations in monitoring their levels. It further outlines the research methods, various recognition matrices and the strategies involved in the development of highly sensitive and selective sensor systems. It also points out the salient features and importance of aptasensors in the detection of mycotoxins along with the different immobilization methods of aptamers. The review meticulously discusses the performance of different optical and electrochemical sensors fabricated using aptamers coupled with nanomaterials (CNT, graphene, metal nanoparticles and metal oxide nanoparticles). The review addresses the limitations in the current developments as well as the future challenges involved in the successful construction of aptasensors with the functionalized nanomaterials. Graphical abstract Recent developments in nanomaterial based aptasensors for mycotoxins are summarized. Specifically, the efficiency of the nanomaterial coupled aptasensors (such as CNT, graphene, metal nanoparticles and metal oxide nanoparticles) in optical and electrochemical methods are discussed.

Exonuclease III-assisted fluorometric aptasensor for the carcinoembryonic antigen using graphene oxide and 2-aminopurine

A reliable fluorometric assay is described for the determination carcinoembryonic antigen (CEA) using exonuclease III (Exo III) and a 2-aminopurine binding aptamer. In the absence of CEA, dsDNA is degraded by Exo III, and free 2-AP (which has a blue fluorescence with excitation/emission maxima of 310/365 nm) is released. Strong fluorescence is generated after addition of graphene oxide (GO) to the solution. However, the 2-AP modified DNA (T2) cannot be degraded in the presence of CEA by Exo III due to the interaction between CEA and aptamer T1. Hence, only weak fluorescence can be detected after addition of GO. In this system, CEA can be quantified in the 0.05 - 2 ng·mL^-1 concentration range with a detection limit of 30 pg·mL^-1 (at S/N = 3). The method was successfully applied to analyze serum samples for CEA. Graphical Abstract An exonuclease III-assisted fluorometric aptasensor has been developed for the detection of carcinoembryonic antigen using graphene oxide and 2-aminopurine.

An exonuclease-assisted fluorescence sensor for assaying alkaline phosphatase based on SYBR Green I

In this report, we propose a fast, reliable and convenient approach to determine the alkaline phosphatase (ALP) activity based on a label-free fluorescence strategy. Upon catalysis of ALP, dephosphorylated dsDNA hampers the λ exonuclease (λexo) cleavage, shows high affinity to SYBR Green I (SG I), resulting in a strong fluorescence emission peak at 520 nm. In the absence of ALP, the dsDNA with 5'-phosphoryl-termini could be employed as a substrate of λexo. After cleavage, a weak fluorescence emission peaks at 520 nm could be observed. The assay was both selective and sensitive, and the detection limit was found to be as low as 3 U/L. This method was utilized to evaluate Na₃VO₄ as ALP inhibitor. The method was successfully applied to the determination of the activity of ALP in spiked human serum samples.

Fluorescent Method for the Detection of Biothiols Using an Ag⁺-Mediated Conformational Switch

In this work, a novel, simple, and time-saving fluorescence approach for the detection of biothiols (glutathione and cysteine) was developed by employing a DNA probe labeled with 2-aminopurine. As an adenine analogue, 2-aminopurine exhibits high fluorescence intensity that can be rapidly quenched in the presence of DNA. In the presence of Ag⁺, the fluorescence increased significantly, which was a result of the formation of cytosine–Ag⁺–cytosine base pairs and the release of 2-aminopurine. Upon addition of either glutathione or cysteine, the structure of cytosine–Ag⁺–cytosine was disrupted, a product of the stronger affinity between biothiols and Ag⁺. As a result, the 2-aminopurine-labeled DNA probe returned to its former structure, and the fluorescence signal was quenched accordingly. The detection limit for glutathione and cysteine was 3 nM and 5 nM, respectively. Furthermore, the determination of biothiols in human blood serum provided a potential application for the probe as a diagnostic tool in clinical practice.

Aptamer-Based Fluorometric Ochratoxin A Assay Based on Photoinduced Electron Transfer

This study describes a novel quencher-free fluorescent method for ochratoxin A (OTA) detection based on the photoinduced electron transfer (PIET) between guanine and fluorophore. In the absence of OTA, carboxyfluorescein (FAM)-labeled aptamer can partly hybridize with the complementary strand of OTA aptamer (OTA-cAPT), which contains four guanines at its 3′-end. As a result, the fluorescence of FAM is quenched due to PIET and stacked guanines. In the presence of OTA, FAM-labeled OTA aptamer can bind specifically to OTA, and thereby the high fluorescence intensity of the dye can be maintained. Under the optimal conditions, the method had a detection limit of 1.3 nM. In addition, the method we proposed is highly sensitive and specific for OTA. Furthermore, the method was proven to be reliable based on its successful application in the detection of OTA in red wine samples. Therefore, this promising, facile, and quencher-free method may be applied to detect other toxins by using other appropriate aptamers.

Fluorometric determination of the activity of uracil-DNA glycosylase by using graphene oxide and exonuclease I assisted signal amplification

The base-excision repair enzyme uracil-DNA glycosylase (UDG) plays a crucial role in the maintenance of genome integrity. The authors describe a fluorometric method for the detection of the activity of UDG. It is making use of (a) a 3'-FAM-labeled hairpin DNA probe with two uracil deoxyribonucleotides in the self-complementary duplex region of its hairpin structure, (b) exonuclease I (Exo I) that catalyzes the release of FAM from the UDG-induced stretched ssDNA probe, and (c) graphene oxide that quenches the green FAM fluorescence of the intact hairpin DNA probe in the absence of UDG. If Exo I causes the release of FAM from the hairpin DNA probe, the fluorescence peaking at 517 nm is turned off in the absence of UDG but turned on in its presence. The resulting assay has a wide linear range (0.008 to 1 U·mL^-1) and a detection limit as low as 0.005 U·mL^-1. It has good specificity for UDG over potentially interfering enzymes and gave satisfactory results when applied to biological samples. Conceivably, the method may be used in a wide range of applications such as in diagnosis, drug screening, and in studying the repair of DNA lesions. Graphical abstract Schematic presentation of a fluorometric strategy for detection of the activity of uracil-DNA glycosylase by using on graphene oxide and exonuclease I assisted signal amplification.

A sensitive cyclic signal amplification fluorescence strategy for determination of methyltransferase activity based on graphene oxide and RNase H

A sensitive fluorometric method for DNA methyltransferase activity detection based on graphene oxide and RNase H-assisted signal amplification.

Facile combination of beta-cyclodextrin host-guest recognition with exonuclease-assistant signal amplification for sensitive electrochemical assay of ochratoxin A

Smartly coupling exonuclease-induced target recycling signal amplifications with β-cyclodextrin host-guest recognition, a novel "signal-on" aptamer sensor for sensitive determination of ochratoxin A (OTA) was proposed for the first time. Firstly, the formation of double-strand DNA (dsDNA) was occurred by hybridizing OTA aptamer with its complementary DNA (cDNA) and as the probe DNA the cDNA at its 3' terminal was labeled with methylene blue (MB). Next, when OTA was present, the aptamer tended to form aptamer-OTA complex with conformation of G-quadruplex instead of aptamer-cDNA duplex, leading to thus the probe DNA separating from dsDNA complex. Then the RecJf exonuclease was added, demolishing partially G-quadruplex structure and releasing a certain number of OTA. Sequentially, those released OTA would continue to react with the rest of aptamer in dsDNA, drawn into development of a new round of G-quadruplex complex, where the target cycling was realized. Meanwhile, as a signal molecule, MB modified on cDNA was liberated along with the cDNA being digested into monoucleotides by RecJf exonuclease, capable of diffusing onto the electrode surface due to host-guest recognition with β-cyclodextrin, whereupon the signal was enriched and yielded. In this way, cycles of target with continuous output of signal indicators were undergone, in which the detection of target was in return fulfilled with signal amplification owing to the joint endeavor of exonuclease and β-cyclodextrin. Under the optimal conditions, the raising signal maintained a linear relation with the logarithm of the target concentrations ranging from 10 pg/mL to 10.0 ng/mL and the detection limit reached as low as 3 pg/mL. This brand-new strategy was simple and low-cost but satisfactory in terms of detection limit, range and sensitivity, in all possibility to be applied extensively for diverse targets detection by easily alternating the corresponding aptamers.

A Label-Free Fluorescent Assay for the Rapid and Sensitive Detection of Adenosine Deaminase Activity and Inhibition

Adenosine deaminase (ADA), able to catalyze the irreversible deamination of adenosine into inosine, can be found in almost all tissues and plays an important role in several diseases. In this work, we developed a label-free fluorescence method for the detection of adenosine deaminase activity and inhibition. In the presence of ADA, ATP has been shown to be hydrolyzed. The ATP aptamer was shown to form a G-quadruplex/thioflavin T (ThT) complex with ThT and exhibited an obvious fluorescence signal. However, the ATP aptamer could bind with ATP and exhibited a low fluorescence signal because of the absence of ADA. This assay showed high sensitivity to ADA with a detection limit of 1 U/L based on an SNR of 3 and got a good linear relationship within the range of 1–100 U/L with R² = 0.9909. The LOD is lower than ADA cutoff value (4 U/L) in the clinical requirement and more sensitive than most of the reported methods. This technique exhibited high selectivity for ADA against hoGG I, UDG, RNase H and λexo. Moreover, this strategy was successfully applied for assaying the inhibition of ADA using erythro-9-(2-hydroxy-3-nonyl) adenine (EHNA) and, as such, demonstrated great potential for the future use in the diagnosis of ADA-relevant diseases, particularly in advanced drug development.