Aptamer-DNAzyme hairpins for biosensing of Ochratoxin A

Recent advances in DNAzymes for bioimaging, biosensing and cancer therapy

DNAzymes, a class of single-stranded catalytic DNA with good stability, high catalytic activity, and easy synthesis, functionalization and modification properties, have garnered significant interest in the realm of biosensing and bioimaging. Their integration with fluorescent dyes or chemiluminescent moieties has led to remarkable bioimaging outcomes, while DNAzyme-based biosensors have demonstrated robust sensitivity and selectivity in detecting metal ions, nucleic acids, proteins, enzyme activities, exosomes, bacteria and microorganisms. In addition, by delivering DNAzymes into tumor cells, the mRNA therein can be cleaved to regulate the expression of corresponding proteins, which has further propelled the application of DNAzymes in cancer gene therapy and synergistic therapy. This paper reviews the strategies for screening attractive DNAzymes such as SELEX and high-throughput sequencing, and briefly describes the amplification strategies of DNAzymes, which mainly include catalytic hairpin assembly (CHA), DNA walker, hybridization chain reaction (HCR), DNA origami, CRISPR-Cas12a, rolling circle amplification (RCA), and aptamers. In addition, applications of DNAzymes in bioimaging, biosensing, and cancer therapy are also highlighted. Subsequently, the possible challenges of these DNAzymes in practical applications are further pointed out, and future research directions are suggested.

Advances in Aptamer-Based Conjugate Recognition Techniques for the Detection of Small Molecules in Food

Small molecules are significant risk factors for causing food safety issues, posing serious threats to human health. Sensitive screening for hazards is beneficial for enhancing public security. However, traditional detection methods are unable to meet the requirements for the field screening of small molecules. Therefore, it is necessary to develop applicable methods with high levels of sensitivity and specificity to identify the small molecules. Aptamers are short-chain nucleic acids that can specifically bind to small molecules. By utilizing aptamers to enhance the performance of recognition technology, it is possible to achieve high selectivity and sensitivity levels when detecting small molecules. There have been several varieties of aptamer target recognition techniques developed to improve the ability to detect small molecules in recent years. This review focuses on the principles of detection platforms, classifies the conjugating methods between small molecules and aptamers, summarizes advancements in aptamer-based conjugate recognition techniques for the detection of small molecules in food, and seeks to provide emerging powerful tools in the field of point-of-care diagnostics.

Mg2+- or Ca2+-regulated aptamer adsorption on polydopamine-coated magnetic nanoparticles for fluorescence detection of ochratoxin A

It has been observed that polyvalent metal ions can mediate the adsorption of DNA on polydopamine (PDA) surfaces. Exploiting this, we used two divalent metal ions (Mg2+ or Ca2+) to promote the adsorption of fluorescence-labelled ochratoxin A (OTA) aptamers on PDA-coated magnetic nanoparticles (Fe3O4@PDA). Based on the different adsorption affinities of free aptamers and OTA-bound aptamers, a facile assay method was established for OTA detection. The aptamers adsorbed on Fe3O4@PDA were removed via simple magnetic separation, and the remaining aptamers in the supernatant exhibited a positive correlation with the OTA concentration. The concentrations of Mg2+ and Ca2+ were finely tuned to attain the optimal adsorption affinity and sensitivity for OTA detection. In addition, other factors, including the Fe3O4@PDA dosage, pH, mixing order, and incubation time, were studied. Finally, under optimized conditions, a detection limit (3σ/s) of 1.26 ng/mL was achieved for OTA. Real samples of spiked red wine were analysed with this aptamer-based method. This is the first report of regulating aptamer adsorption on the PDA surface with polyvalent metal ions for OTA detection. By changing the aptamers, the method can be easily extended to other target analytes.

Aptasensors Based on Non-Enzymatic Peroxidase Mimics: Current Progress and Challenges

Immunoassays based on antibodies as recognizing elements and enzymes as signal-generating modules are extensively used now in clinical lab diagnostics, food, and environmental analyses. However, the application of natural enzymes and antibodies has some drawbacks, such as relatively high manufacturing costs, thermal instability, and lot-to-lot variations that lower the reproducibility of results. Oligonucleotide aptamers are able to specifically bind their targets with high affinity and selectivity, so they represent a prospective alternative to protein antibodies for analyte recognition. Their main advantages include thermal stability and long shelf life, cost-efficient chemical synthesis, and negligible batch-to-batch variations. At the same time, a wide variety of non-protein peroxidase mimics are now available that show strong potential to replace protein enzymes. Here, we review and analyze non-protein biosensors that represent a nexus of these two concepts: aptamer-based sensors (aptasensors) with optical detection (colorimetric, luminescent, or fluorescent) based on different peroxidase mimics, such as DNAzymes, nanoparticles, or metal-organic frameworks.

RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy

Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.

Design of a Quencher-Free Fluorescent Aptasensor for Ochratoxin A Detection in Red Wine Based on the Guanine-Quenching Ability

This study describes a quencher-free fluorescent aptasensor for ochratoxin A (OTA) detection using the specific quenching ability of guanine for fluorescein (FAM) molecules based on photo-induced electron transfer (PIET). In this strategy, OTA is detected by monitoring the fluorescence change induced by the conformational change of the aptamer after target binding. A new shorter OTA aptamer compromising three guanine bases at the 5' end was used in this study. This new aptamer, named G3-OTAapt1-FAM (F1), was labeled with FAM on the 3' end as a fluorophore. In order to increase the binding affinity of the aptamer and OTA, G3-OTAapt2-FAM (F2) was designed; this added a pair of complementary bases at the end compared with F1. To prevent the strong self-quenching of F2, a complementary chain, A13, was added. Although the F1 aptasensor was simpler to implement, the sensitivity of the F2 aptasensor with A13 was better than that of F1. The proposed F1 and F2 sensors can detect OTA with a concentration as low as 0.69 nmol/L and 0.36 nmol/L, respectively.

A Sensitive Aptasensor Using Biotin-Streptavidin System for Patulin Detection in Apple Juice

Patulin contamination in fruits, vegetables, and their products is considered a serious health risk factor for food safety and human health. Thus, a rapid, simple detection method for patulin is becoming important, which could provide a tool for routine screening and food surveys. The objective of this study was to develop a sensitive aptamer-based lateral flow assay (FLA) using Streptavidin functionalized gold nanoparticles for sensitive patulin detection. An excellent dynamic range for patulin detection was obtained (2.7~139.8 ng/mL in the buffer and 7.07~359.5 ng/mL in the sample) with no affinity for other mycotoxins such as zearalenone (ZEN), ochratoxin A (OTA), aflatoxin B₁ (AFB₁), citrinin or tenuazonic acid (TEA). The limit of detection was 0.19 ng/mL in the buffer and 0.36 ng/mL in the real sample. The recoveries were 83.3% to 107.1%, with a satisfactory RSD value from 6.5% to 7.5%. Hence the established LFA could be used as a rapid, simple, on-site screening tool for PAT determination in apple juice.

Analyzing Criteria Affecting the Functionality of G-Quadruplex-Based DNA Aptazymes as Colorimetric Biosensors and Development of Quinine-Binding Aptazymes

A DNA aptazyme consists of an aptamer domain and a DNAzyme module, in which the DNAzyme activity can be regulated by the aptamer-target interaction. The complex of G-quadruplex (GQ) and hemin is a peroxidase-mimicking DNAzyme and has become increasingly popular as a reporter system for biosensing applications. The development of GQ-based aptazymes is of high interest as they can be used as label-free biosensors for the real-time detection of pathogens. Herein, we rationally designed ca. 200 GQ-based aptazyme candidates and evaluated the suitability of 14 aptamers targeting quinine, Protein A, Staphylococcus enterotoxin B, and ATP for this detection concept. As a result, six novel aptazymes were developed for the specific detection of quinine based on two quinine-binding aptamers. The rest of designed probes, however, hardly showed significant functionality. To uncover the reasons, we performed enzyme-linked oligonucleotide assays to find how the affinity of aptamers is affected once conjugated to the DNAzyme sequence or upon integration into the aptazyme probe. Furthermore, we investigated the impact of the structure-switching functionality in the parent aptamer and the effect of the reaction matrix on the efficiency of probes.

Recent Advances in Aptamer Sensors

Recently, aptamers have attracted attention in the biosensing field as signal recognition elements because of their high binding affinity toward specific targets such as proteins, cells, small molecules, and even metal ions, antibodies for which are difficult to obtain. Aptamers are single oligonucleotides generated by in vitro selection mechanisms via the systematic evolution of ligand exponential enrichment (SELEX) process. In addition to their high binding affinity, aptamers can be easily functionalized and engineered, providing several signaling modes such as colorimetric, fluorometric, and electrochemical, in what are known as aptasensors. In this review, recent advances in aptasensors as powerful biosensor probes that could be used in different fields, including environmental monitoring, clinical diagnosis, and drug monitoring, are described. Advances in aptamer-based colorimetric, fluorometric, and electrochemical aptasensing with their advantages and disadvantages are summarized and critically discussed. Additionally, future prospects are pointed out to facilitate the development of aptasensor technology for different targets.

Recent Progress and Development of G-Quadruplex-Based Luminescent Assays for Ochratoxin A Detection

Ochratoxin A (OTA) is a mycotoxin that is widespread throughout the world. It contaminates foods such as vegetables, fruits, and rice. It harms human health and has potential carcinogenic effects. The G-quadruplex (G4) is a tetraplexed DNA structure generated from guanine-rich DNA that has found emerging use in aptamer-based sensing systems. This review outlines the status of OTA contamination and conventional detection methods for OTA. Various G4-based methods to detect OTA developed in recent years are summarized along with their advantages and disadvantages compared to existing approaches.

Dual Aptamer-DNAzyme based colorimetric assay for the detection of AFB1 from food and environmental samples

In the present study, a colorimetric biosensor strategy is devised in combination with apta-magnetic separation assisted with DNAzyme based colorimetric detection of Aflatoxin B1 (AFB1). The optimized analytical procedures consisted of the capture of AFB1 by biotinylated aptamer conjugated to streptavidin magnetic beads and detection by a colorimetric signal from a DNAzyme modified aptamer in presence hemin and H2O2/TMB (3', 3', 5, 5'- tetramethylbenzidine). The DNA concentration, incubation time, hemin, and NaCl concentrations were evaluated and optimized. The visual optical signal thus generated could determine the presence of AFB1 in the given sample. The selectivity of the method with other mycotoxins was evaluated. The linear range of AFB1 from 0 to 200 ppb was assessed and detected as low as 40 ppb visually. The absorbance of blue color generated by the catalytic reaction was in a linear correlation with AFB1 concentrations and was able to detect as low as 22.6 ppb (LOD). The suitability of the assay for AFB1 quantification in sorghum and natural samples was also evaluated. Thus, the developed assay could be a reliable, inexpensive, alternative tool for possible use as a screening method for aflatoxins and other mycotoxins.

Label-Free Quantifications of Multiplexed Mycotoxins by G-Quadruplex Based on Photonic Barcodes

Multiplexed quantification of mycotoxins is of great significance in food safety. Here, novel photonic crystal (PhC) barcodes with G-quadruplex aptamer encapsulated for label-free multiplex mycotoxins quantification are developed. The probes are immobilized on PhC barcodes to form a molecular beacon (MB), which contains the sequences of mycotoxin aptamers and a G-quadruplex. In the presence of the target, the hairpin structure of MB would open and the region of the G-quadruplex is exposed, which subsequently combines with Thioflavin T (ThT) to produce fluorescence. The relative fluorescence intensity increased as the mycotoxins concentration increased in a linear range from 1.0 pg/mL to 100 ng/mL. Moreover, the multiplexed mycotoxins quantification could be achieved by tuning the structural color of the PhC barcodes. We demonstrate that this method with high accuracy and specificity for multiplexed detection of mycotoxins, with the sensitivity of the detection as low as 0.70 pg/mL. Our results show that G-quadruplex-encapsulated PhC barcodes offer a novel simple and label-free pathway toward the multiplex screen assay of mycotoxins for food safety.

A potential reusable fluorescent aptasensor based on magnetic nanoparticles for ochratoxin A analysis

An aptasensor for the detection of ochratoxin A (OTA) in environmental samples was developed. It displayed high sensitivity and good selectivity. Factors such as specific binding between a FAM (5-carboxyfluorescein)-labeled aptamer (f-RP) and OTA, and a magnetic property of a streptavidin magbeads-modified capture probe (bm-CP) resulted in aptasensor’s linear relationship between fluorescence intensity and the concentration of OTA. This characteristic is present at the OTA concentration ranges from 0.100 μM to 25.00 μM with a LOD (limit of detection) of 0.0690 μM. The bm-CP can be reused through melting, washing and magnetic separation, which contributes to cost reduction. In addition, the proposed method is simple and detection process is fast. The aptasensor can be used in real samples.

Aptamer assisted ultrafiltration cleanup with high performance liquid chromatography-fluorescence detector for the determination of OTA in green coffee

One of the most common mycotoxin contaminating feed and foodstuffs is Ochratoxin A (OTA). OTA has a chronic toxic effect and proved to be mutagenic, nephrotoxic, teratogenic, immunosuppressive, and carcinogenic. Aptamer with their specific affinity for OTA was used in this paper to create an analytical technique. Several methods have been reported for the determination of OTA in foods. However, most of these methods could not be applied to a complex food as green coffee because the interfering native fluorescent products made the quantification very difficult. In this work, we mixed two separations based techniques to identify and quantify OTA in green coffee. Aptamer assisted ultrafiltration as separation technique based on the size of molecules was applied to separate the free OTA, the quantification of OTA was established by a high-performance liquid chromatography (HPLC-FD) with a limit of detection (LOD) of 0.05 ng/mL for OTA. Artificially contaminated green coffee displayed a good range of OTA recoveries up to 97.7%. This method can be applied to the quantitative determination of OTA in green coffee at levels below the maximum levels proposed by the European Commission for green coffee. It also confirm that aptamers can be used as biorecognition element in diagnostic assays with commercial application for mycotoxin analysis.

Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges

DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.

Shape Coding Microhydrogel for a Real-Time Mycotoxin Detection System Based on Smartphones

How to create a portable and quick way to detect multiple coexisting toxins is closely related to everyone's health. In this paper, we have established a real-time mycotoxin detection system that combined shape-encoded hydrogel particle preparation technology and image processing technology with smartphone portable devices. First, hydrogel microparticles containing a specific recognition toxin aptamer were programmable synthesized by stop-flow lithography. The hydrogel particles prepared by us had clear, variable signals and high coding capacity. Then, the indirect competitive detection based on aptamers was simple and rapid; the total reaction time was no more than 1 h 45 min and the image processing process was no more than 10 s. Finally, images could be captured by cameras on portable devices and smartphones. The self-built Android app that used the image recognition program installed on the smartphone would analyze the image and return the results in real time. The results showed that the detection limit reached 0.1 ng/mL, which was lower than the standard. In summary, this platform provides a fast, portable, high-throughput detection solution for real-time detection of mycotoxins, with excellent application prospects.

Dual flow immunochromatographic assay for rapid and simultaneous quantitative detection of ochratoxin A and zearalenone in corn, wheat, and feed samples

A one-step dual flow immunochromatographic assay (DICGA), based on a competitive format, was developed for simultaneous quantification of ochratoxin A (OTA) and zearalenone (ZEN) in corn, wheat, and feed samples. The limit of detection for OTA was 0.32 ng/ml with a detection range of 0.53‒12.16 ng/ml, while for ZEN it was 0.58 ng/ml with a detection range of 1.06‒39.72 ng/ml. The recovery rates in corn, wheat, and feed samples ranged from 77.3% to 106.3% with the coefficient of variation lower than 15%. Naturally contaminated corn, wheat, and feed samples were analyzed using both DICGA and liquid chromatography-tandem mass spectrometry (LC-MS/MS) and the correlation between the two methods was evaluated using a regression analysis. The DICGA method shows great potential for simple, rapid, sensitive, and cost-effective quantitative detection of OTA and ZEN in food safety control.

Sensitive colorimetric detection of ochratoxin A by a dual-functional Au/Fe3O4 nanohybrid-based aptasensor

A novel colorimetric aptasensor based on a Au/Fe₃O₄ nanohybrid was developed to detect ochratoxin A (OTA). The aptasensor is composed of a free OTA aptamer, a Au/Fe₃O₄ nanohybrid coated with biotinylated complementary DNA of the OTA aptamer (biotin-cDNA-Au/Fe₃O₄), and free alkaline-phosphatase-labeled streptavidin (SA-ALP). The Au/Fe₃O₄ nanohybrid not only immobilizes biotin-cDNA but also magnetically separates SA-ALP from the sample solution. One part of the OTA aptamer sequence hybridizes with biotin-cDNA immobilized on Au/Fe₃O₄, and the left part of the OTA aptamer sequence covers the biotin and blocks the specific interaction between biotin and SA-ALP. OTA can interrupt the interaction of OTA aptamer binding to biotin-cDNA-Au/Fe₃O₄ and can inhibit the shielding effect of the OTA aptamer on biotin. The amount of SA-ALP that can be captured by biotin-cDNA-Au/Fe₃O₄ thus increases with increasing OTA concentration. Through a simple magnetic separation, the collected SA-ALP-linked Au/Fe₃O₄ can produce a yellow-colored solution in the presence of p-nitrophenyl phosphate (p-NPP). This colorimetric aptasensor can detect OTA as low as 1.15 ng mL⁻¹ with high specificity.

A novel colorimetric aptasensor based on a Au/Fe₃O₄ nanohybrid was developed to detect ochratoxin A (OTA).

Sensitive aptamer-based fluorescene assay for ochratoxin A based on RNase H signal amplification

A new assay for the selective and sensitive aptamer-based fluorescent biosensor for ochratoxin A (OTA) detection is proposed. It consists of a ribonuclease H (RNase H)-assisted cycle response that leads to a significant amplification of the signal, which allow for a low limit of detection (LOD) of 0.08 ng/mL. By using this technique, a high selectivity for OTA against ochratoxin B and aflatoxin B₁ (AFB₁) was noticed. The quantitative determination in real samples has been verified using red wine samples spiked with a series of OTA concentrations (0.4, 4, and 12 ng/mL), and the recoveries ranged from 96.1 to 107.5%. This aptasensor has great practical applications in food industry and moreover, can be extended for the detection of other toxins by replacing the sequence of the recognition aptamer.

Ultrasensitive and green electrochemical immunosensor for mycotoxin ochratoxin A based on phage displayed mimotope peptide

Here, we demonstrated a new approach for development of an ultrasensitive and green electrochemical immunosensor for Ochratoxin A (OTA). Phage displayed mimotope peptide of OTA was used as mimics of conventional competing antigen, which is chemical synthesized with toxic mycotoxins OTA as raw material, in a competitive sensing platform. The working electrode was modified by polyethylene glycol (PEG) for the purpose of immobilizing antibody effectively. Under the optimized test condition, the limit of detection (LOD) of the established immunosensor was 2.04 fg/mL, and the linear range was 7.17-548.76 fg/mL. Specific measurement of this established method was conducted by testing cross-reactivity of other common mycotoxins, the result showed that mimotope peptide-based immunosensor has negligible cross-reactivity with other mycotoxins. Furthermore, the novel concept of phage displayed mimotope peptide-based immunosensor may provide a potential application in general method for the ultrasensitive detection of various toxic small molecules in food.

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

The authors describe a fluorometric assay for ochratoxin A (OTA) that is based on the use of graphene oxide and RNase H-aided amplification. On addition of OTA, cAPT is replaced from the APT/cAPT hybridization complex and then hybridizes with RNA labeled with a fluorophore at the 5'-end. Eventually, the fluorophore is released by RNase H cleavage. As the concentration of OTA increases, more cAPTs are displaced, this leading to fluorescence enhancement (best measured at excitation/emission wavelengths of 495/515 nm). This RNase H-assisted cycle response results in strong signal amplification. The limit of detection, calculated on the basis of a signal to noise ratio of 3, is 0.08 ng·mL^-1. Response is linear in the 0.08-200 ng·mL^-1 OTA concentration range. The method is highly selective for OTA over ochratoxin B and aflatoxin B₁. It was applied to the determination of OTA in red wine samples spiked at levels of 1, 7, and 50 ng·mL^-1, and the recoveries ranged from 90.9 to 112%. Graphical abstract Schematic of a novel fluorometric aptasensor for ochratoxin A based on the use of graphene oxide and RNase H-aided amplification.

Affinity Biosensors for Detection of Mycotoxins in Food

This chapter reviews recent achievements in methods of detection of mycotoxins in food. Special focus is on the biosensor technology that utilizes antibodies and nucleic acid aptamers as receptors. Development of biosensors is based on the immobilization of antibodies or aptamers onto various conventional supports like gold layer, but also on nanomaterials such as graphene oxide, carbon nanotubes, and quantum dots that provide an effective platform for achieving high sensitivity of detection using various physical methods, including electrochemical, mass sensitive, and optical. The biosensors developed so far demonstrate high sensitivity typically in subnanomolar limit of detection. Several biosensors have been validated in real samples. The sensitivity of biosensors is similar and, in some cases, even better than traditional analytical methods such as ELISA or chromatography. We believe that future trends will be focused on improving biosensor properties toward practical application in food industry.

Exonuclease-assisted multicolor aptasensor for visual detection of ochratoxin A based on G-quadruplex-hemin DNAzyme-mediated etching of gold nanorod

An exonuclease-assisted multicolor aptasensor was developed for the visual detection of ochratoxin A (OTA). It is based on the etching of gold nanorods (AuNRs) mediated by a G-quadruplex-hemin DNAzyme. A DNA sequence (AG4-OTA) was designed that comprises a hemin aptamer and an OTA aptamer. OTA binds to AG4-OTA to form an antiparallel G-quadruplex, which halts its digestion by exonuclease I (Exo I) from the 3'-end of AG4-OTA. Thus, the retained hemin aptamer can bind to hemin to form a G-quadruplex-hemin DNAzyme. This DNAzyme has peroxidase-like activity that catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H₂O₂ to produce its diimine derivative (TMB²⁺) in acidic solution. TMB²⁺ can etch the AuNRs by oxidizing Au(0) into Au(I). This results in the generation of rainbow-like colors and provides a multicolor platform for the visual detection of OTA. The assay is based on the use of a single isolated aptamer and possesses obvious advantages such as multi-color visual inspection, relatively high sensitivity and accuracy. It can be used to detect as little as 30 nM concentrations of OTA by visual observation and even 10 nM concentrations by spectrophotometry. The method was successfully applied to the determination of OTA in spiked beer where it gave recoveries of 101-108%, with a relative standard deviation (RSD, n = 5) of <5%. Graphical abstract Schematic of an exonuclease-assisted multicolor bioassay based on the G-quadruplex-hemin DNAzyme-mediated etching of gold nanorods (AuNRs). It enables visual detection of ochratoxin A (OTA) with a detection limit of 30 nM.

Nucleic acid aptamer-based methods for diagnosis of infections

Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.

Fluorescence method for quickly detecting ochratoxin A in flour and beer using nitrogen doped carbon dots and silver nanoparticles

In this paper, a FRET (Forster resonance energy transfer) based fluorescence method was developed for the quickly detection of ochratoxin A (OTA) in agricultural products (e.g., flour and beer). A highly fluorescent nitrogen doped carbon dots (CD) were served as energy donor, the DNA and MCH (6-mercapto-1-hexanol) modified Ag nanoparticles were served as energy acceptor in the FRET system. OTA can be detected in a concentration range between 10 and 5000 nM, the limit of detection is 8.7 nM. This method has three advantages: (1) an enhanced fluorescent intensity can be acquired by utilizing the nitrogen doped CD synthesized by one-step approach without sophisticated modification of nanoparticles; (2) OTA detection was accomplished quickly (less than 30 min) by using MCH as assistant molecule; (3) an extended OTA detection linear range was acquired, which may facilitate the OTA detection in real agricultural samples, and is helpful for solving food safety problems.

Label-free electrochemical biosensors based on 3,3',5,5'-tetramethylbenzidine responsive isoporous silica-micelle membrane

3,3',5,5'-Tetramethylbenzidine (TMB) has been frequently used as an indicator in G-quadruplex/hemin DNAzyme (G4zyme)-based chemical and biochemical analysis, and its oxidation products are usually monitored by electrochemical or optical methods to quantify G4zyme formation-related analytes. Herein we report a simple electrochemical approach based on isoporous silica-micelle membrane (iSMM) to measure TMB, instead of its oxidation products, in G4zyme-based detection of specific analytes. The iSMM was grown on the indium tin oxide (ITO) electrode, which was composed of highly ordered, vertically oriented silica nanochannels and cylindrical micelles of cetyltrimethylammonium. The iSMM-ITO electrode was selectively responsive to neutral TMB but not its oxidation products, thanks to the sieving and pre-concentration capacity of micellar structures in terms of molecular charge and lipophilicity. In other words, only TMB could be extracted and enriched into micelles and subsequently oxidized at the underlying ITO electrode surface (namely the micelle/ITO interface), generating an amplified anodic current. Since the depletion of TMB was catalyzed by G4zymes formed in the presence of specific analyte, the decrease of this anodic current enabled the quantitative detection of this analyte. The current variation relative to its initial value ((j₀-j)/j₀), termed as the current attenuation ratio, showed the obvious dependence on the analyte concentration. As proof-of-concept experiments, four substances, i.e., potassium cation (K⁺), adenosine triphosphate, thrombin and nucleic acid, were detected in aqueous media and the analysis of K⁺ in pre-treated human serum was also performed.

Single-Step LRET Aptasensor for Rapid Mycotoxin Detection

Contamination of foods by mycotoxins is a common yet serious problem. Owing to the increase in consumption of fresh produce, consumers have become aware of food safety issues caused by mycotoxins. Therefore, rapid and sensitive mycotoxin detection is in great demand in fields such as food safety and public health. Here we report a single-step luminescence resonance energy transfer (LRET) aptasensor for mycotoxin detection. To accomplish the single-step sensor, our sensor was constructed by linking a quencher-labeled aptamer through a linker to the surface of upconversion nanoparticles (UCNPs). Our LRET aptasensor is composed of Mn²⁺-doped NaYF₄:Yb³⁺,Er³⁺ UCNPs as the LRET donor, and black hole quencher 3 (BHQ3) as the acceptor. The maximum quenching efficiency is obtained by modulating the linker length, which controls the distance between the quencher and the UCNPs. Our distinctive design of LRET aptasensor allows detection of mycotoxins selectively in colored food samples within 10 min without multiple bioassay steps. We believe our single-step aptasensor has a significant potential for on-site detection of food contaminants, environmental pollutants, and biological metabolites.

High-Throughput Low-Background G-Quadruplex Aptamer Chemiluminescence Assay for Ochratoxin A Using a Single Photonic Crystal Microsphere

We reported a novel hemin-G-quadruplex aptamer chemiluminescence assay platform for ochratoxin A (OTA) using the single silica photonic crystal microsphere (SPCM). The oligonucleotide A sequence containing aptamer sequences of hemin and OTA is immobilized on the surface of SPCM. The other oligonucleotide B sequence containing a partially complementary sequence with one part OTA aptamer and one part hemin aptamer is used as a blocking chain. The hybridization between chain A and chain B will be influenced by the presence or absence of OTA in the system, which will affect the bioactivity of DNAzyme. Thus, the chemiluminescence signal depends on the concentration of OTA in the samples. In the single particle assay platform, the signal/noise is remarkably enhanced, and the background signal can be ignored by separating hemin from the surface of SPCM. The limit of detection of the new method reaches to the pg/mL scale, and the linear detection range is 4 orders of magnitude for OTA. The new assay platform can provide a sensitive, cost-efficient, simple, and high-throughput screening for OTA.

DNAzyme-aptamer or aptamer-DNAzyme paradigm: Biochemical approach for aflatoxin analysis

DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to differentiate between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive aflatoxin B1 DNA based biosensors.

Optimization of Aflatoxin B1 Aptasensing

Combination of aptamers with DNAzymes attracted intense attention for development of DNA-based biosensors for detection of mycotoxins. In the present study a combination of aflatoxin B1 specific aptamer and HRP- (horseradish peroxidase-) mimicking DNAzyme was optimized for detecting aflatoxin B1. Detecting approach is based on the binding affinity of aflatoxin B1 to its specific aptamer and conversion of substrate to a detectable colorimetric signal by a linked DNAzyme. Compared to conventional methods for aflatoxin B1 detection, DNA-based assay has the advantages of low cost, long-term stability, and rapid, simple, and user-friendly steps.

Design and optimization of an ultra-sensitive hairpin DNA aptasensor for Salmonella detection

A simple scheme using a hairpin DNA aptasensor was established to detectSalmonellaTyphimurium (S.Typhimurium).

Label-Free Aptasensors for the Detection of Mycotoxins

Various methodologies have been reported in the literature for the qualitative and quantitative monitoring of mycotoxins in food and feed samples. Based on their enhanced specificity, selectivity and versatility, bio-affinity assays have inspired many researchers to develop sensors by exploring bio-recognition phenomena. However, a significant problem in the fabrication of these devices is that most of the biomolecules do not generate an easily measurable signal upon binding to the target analytes, and signal-generating labels are required to perform the measurements. In this context, aptamers have been emerged as a potential and attractive bio-recognition element to design label-free aptasensors for various target analytes. Contrary to other bioreceptor-based approaches, the aptamer-based assays rely on antigen binding-induced conformational changes or oligomerization states rather than binding-assisted changes in adsorbed mass or charge. This review will focus on current designs in label-free conformational switchable design strategies, with a particular focus on applications in the detection of mycotoxins.

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.

Nuclease-aided target recycling signal amplification strategy for ochratoxin A monitoring

Ochratoxin A (OTA), a toxin produced by Aspergillus ochraceus and Penicillium verrucosum, is one of the most abundant food-contaminating mycotoxins worldwide. OTA mainly exerts nephrotoxicity, immunotoxicity, mutagenicity, carcinogenicity, teratogenicity, and neurotoxicity. This paper describes a simple and sensitive aptamer/single-walled carbon nanohorn (SWCNH)-based assay for OTA detection. SWCNHs can protect DNA from DNase I cleavage. However, aptamers can be detached from the surface of SWCNHs through specific target binding, exposing them to enzymatic cleavage and releases the target for a new cycle. Cycling of targets leads to significant signal amplification and low limit of detection (LOD), resulting in a nearly 20-fold reduction in LOD for OTA assay compared with non-target recycling under the same experimental parameters. This technique responded specifically to OTA without interference from other analogues (Ochratoxin B, Ochratoxin C, warfarin, and N-acetyl-l-phenylalanine). Moreover, the application of this technique in real sample has been verified using red wine samples spiked with a series of OTA concentrations. This aptasensor offers a great practical importance in food safety and can be widely extended for detection of other toxins by replacing the sequence of the recognition aptamer.