Primer remodeling amplification-activated multisite-catalytic hairpin assembly enabling the concurrent formation of Y-shaped DNA nanotorches for the fluorescence assay of ochratoxin A

Strategy of functional nucleic acids-mediated isothermal amplification for detection of foodborne microbial contaminants: A review

Foodborne microbial contamination (FMC) is the leading cause of food poisoning and foodborne illness. The foodborne microbial detection methods based on isothermal amplification have high sensitivity and short detection time, and functional nucleic acids (FNAs) could extend the detectable object of isothermal amplification to mycotoxins. Therefore, the strategy of FNAs-mediated isothermal amplification has been emergingly applied in biosensors for foodborne microbial contaminants detection, making biosensors more sensitive with lower cost and less dependent on nanomaterials for signal output. Here, the mechanism of six isothermal amplification technologies and their application in detecting FMC is firstly introduced. Then the strategy of FNAs-mediated isothermal amplification is systematically discussed from perspectives of FNAs' versatility including recognition elements (Aptamer, DNAzyme), programming tools (DNA tweezer, DNA walker and CRISPR-Cas) and signal units (G-quadruplex, FNAs-based nanomaterials). Finally, challenges and prospects are presented in terms of addressing the issue of nonspecific amplification reaction, developing better FNAs-based sensing elements and eliminating food matrix effects.

Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection

Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.

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.

Recent Progress in Rapid Determination of Mycotoxins Based on Emerging Biorecognition Molecules: A Review

Mycotoxins are secondary metabolites produced by fungal species, which pose significant risk to humans and livestock. The mycotoxins which are produced from Aspergillus, Penicillium, and Fusarium are considered most important and therefore regulated in food- and feedstuffs. Analyses are predominantly performed by official laboratory methods in centralized labs by expert technicians. There is an urgent demand for new low-cost, easy-to-use, and portable analytical devices for rapid on-site determination. Most significant advances were realized in the field bioanalytical techniques based on molecular recognition. This review aims to discuss recent progress in the generation of native biomolecules and new bioinspired materials towards mycotoxins for the development of reliable bioreceptor-based analytical methods. After brief presentation of basic knowledge regarding characteristics of most important mycotoxins, the generation, benefits, and limitations of present and emerging biorecognition molecules, such as polyclonal (pAb), monoclonal (mAb), recombinant antibodies (rAb), aptamers, short peptides, and molecularly imprinted polymers (MIPs), are discussed. Hereinafter, the use of binders in different areas of application, including sample preparation, microplate- and tube-based assays, lateral flow devices, and biosensors, is highlighted. Special focus, on a global scale, is placed on commercial availability of single receptor molecules, test-kits, and biosensor platforms using multiplexed bead-based suspension assays and planar biochip arrays. Future outlook is given with special emphasis on new challenges, such as increasing use of rAb based on synthetic and naïve antibody libraries to renounce animal immunization, multiple-analyte test-kits and high-throughput multiplexing, and determination of masked mycotoxins, including stereoisomeric degradation products.

Signal enhancing strategies in aptasensors for the detection of small molecular contaminants by nanomaterials and nucleic acid amplification

Small molecular contaminants (such as mycotoxins, antibiotics, pesticide residues, etc.) in food and environment have given rise to many biological and ecological toxicities, which has attracted worldwide attention in recent years. Meanwhile, due to the advantages of aptamers such as high specificity and stability, easy synthesis and modification, as well as low cost and immunogenicity, various aptasensors for the detection of small molecular contaminants have been flourishing. An aptasensor as a whole is composed of an aptamer-based target recognizer and a signal transducer, which are fields of concentrated research. In the practical detection applications, in order to achieve the quantitative detection of small molecular contaminants at low abundance in real samples, a large number of signal enhancing strategies have been utilized in the development of aptasensors. Recent years is a vintage period for efficient signal enhancing strategies of aptasensors by the aid of nanomaterials and nucleic acid amplification that are applied in the elements for target recognition and signal conversion. Therefore, this paper meticulously reviews the signal enhancing strategies based on nanomaterials (including the (quasi-)zero-dimensional, one-dimensional, two-dimensional and three-dimensional nanomaterials) and nucleic acid amplification (including enzyme-assisted nucleic acid amplification and enzyme-free nucleic acid amplification). Furthermore, the challenges and future trends of the abovementioned signal enhancing strategies for application are also discussed in order to inspire the practitioners in the research and development of aptasensors for small molecular contaminants.

Ultrasensitive electrochemical aptasensor based on palindromic sequence mediated bidirectional SDA and a DNAzyme walker for kanamycin detection

An electrochemical biosensing platform for kanamycin analysis based on SDA and a DNA walker.

Functional nucleic acid biosensors utilizing rolling circle amplification

Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.

Target-Dependent Protection of DNA Aptamers against Nucleolytic Digestion Enables Signal-On Biosensing with Toehold-Mediated Rolling Circle Amplification

We report a generalizable strategy for biosensing that takes advantage of the resistance of DNA aptamers against nuclease digestion when bound with their targets, coupled with toehold mediated strand displacement (TMSD) and rolling circle amplification (RCA). A DNA aptamer containing a toehold extension at its 5'-end protects it from 3'-exonuclease digestion by phi29 DNA polymerase (phi29 DP) in a concentration-dependent manner. The protected aptamer can participate in RCA in the presence of a circular template that is designed to free the aptamer from its target via TMSD. The absence of the target leads to aptamer digestion, and thus no RCA product is produced, resulting in a turn-on sensor. Using two different DNA aptamers, we demonstrate rapid and quantitative real-time fluorescence detection of two human proteins: platelet-derived growth factor (PDGF) and thrombin. Sensitive detection of PDGF was also achieved in human serum and human plasma, demonstrating the selectivity of the assay.

Target-Mediated 5'-Exonuclease Digestion of DNA Aptamers with RecJ to Modulate Rolling Circle Amplification for Biosensing

We report a new method for biosensing based on the target-mediated resistance of DNA aptamers against 5'-exonuclease digestion, allowing them to act as primers for rolling circle amplification (RCA). A target-bound DNA strand containing an aptamer region on the 5'-end and a primer region on the 3'-end is protected from 5'-exonuclease digestion by RecJ exonuclease in a target-dependent manner. As the protected aptamer is at the 5'-end, the exposed primer on the 3'-end can participate in RCA in the presence of a circular template to generate a turn-on sensor. Without target, RecJ digests the primer and prevents RCA from occurring, allowing quantitative fluorescence detection of both thrombin, a protein, and ochratoxin A (OTA), a small molecule, at picomolar concentrations.

A novel electrochemical aptasensor for ochratoxin a sensing in spiked food using strand-displacement polymerase reaction

Herein, an aptasensor is presented for electrochemical determination of ochratoxin A (OTA) based on nontarget-triggered production of rolling circular amplification (RCA). The surface of gold electrode is modified with thiolated complementary strand of aptamer (CS) as both capture probe and primer and OTA aptamer (Apt) as both sensing molecule and padlock probe (PLP). Following the addition of OTA, Apt/OTA conjugate is formed and detached from the electrode surface. Therefore, no RCA is produced after incubation of the modified electrode with T4 DNA ligase and phi29 DNA polymerase and a sharp current signal occurs. The analytical response ranged from 30 pM to 120 nM with detection limit of 5 pM. The designed aptasensor showed superior analytical performance in comparison with other approaches for OTA detection. Also, the approach exhibited good performance for OTA determination in spiked grape juice samples. The technique presented in this study, can be applied to develop sensors for detecting different toxins by replacing the relevant aptamers and complementary strands.

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.

Ultrasensitive detection of ochratoxin A based on biomimetic nanochannel and catalytic hairpin assembly signal amplification

In this paper, an ultrasensitive nanochannel sensor has been proposed for label-free Ochratoxin A (OTA) assay in combination with graphene oxide (GO) and catalyzed hairpin assembly (CHA). The high-performance sensor is segmented into two parts. One is composed of graphene oxide (GO) and DNA probes. In the presence of target OTA, OTA works as a catalyst to trigger the self-assembly pathway of the two probes and initiate the cycling of CHA circuits, which results in numerous double-stranded DNAs (dsDNA) in solution. The excess ssDNA probes are removed by GO. The other part is composed of biomimetic nanochannel coated with polyethyleneimine (PEI) and Zr⁴⁺, which can quantify the concentration of OTA by detecting the dsDNA in solution. The nanofluidic device has a detection limit of as low as 6.2 pM with an excellent selectivity. The nanochannel based assay was used to analyse food samples (red wine) with satisfied results. Thus, the proposed analytical method will provide a new approach the detection of OTA and can be applied for quality control to ensure food safety.

An LC-MS/MS method for protein detection based on a mass barcode and dual-target recognition strategy

A mass barcode mediated signal amplification strategy was developed and applied to the determination of protein. A new compound, N'-((2-aminopyridin-3-yl)methylene)-5-(1,2-dithiolan-3-yl)pentanehydrazide (TAPA), was synthesized from the linker and the signal barcode, and used as the bonding barcode. For the realization of signal transduction, TAPAs and the target catcher aptamers, were both modified on gold nanoparticles (AuNPs) to establish the relationship between TAPAs and the target. Owing to the fact that the amount of TAPAs was much greater than the target, the signal of the target was not only transduced to the signal of the mass barcodes, but also amplified greatly. Thrombin, an important biomarker for coagulation abnormality diseases, was selected as a model analyte. Two kinds of thrombin recognition aptamers, aptamer 29 (apt29) and aptamer 15 (apt15), were modified onto the magnetic beads (MBs) and AuNPs, respectively. The modified AuNPs were further functionalized with lots of TAPA and formed apt15-AuNPs-TAPA. MBs-apt29 and apt15-AuNPs-TAPA could both recognize the target thrombin and form the sandwich complex (MBs-apt29/thrombin/apt15-AuNPs-TAPA). After the complex was separated by an extra magnetic field, NaClO oxidant solution was added to release the signal barcodes, 2-Amino-3-pyridinecarboxaldehyde (APA), which were then collected after centrifuging and analyzed by LC-MS/MS. Under optimized conditions, the mass response intensity was proportional to thrombin concentration in the range of 0.05-10 nM, with a 0.007 nM detection limit. This method was applied to the determination of thrombin in spiked serum samples, and the average recoveries ranged from 89.6% to 110.4%, which confirmed the applicability of this method.

Progress on Structured Biosensors for Monitoring Aflatoxin B1 From Biofilms: A Review

Aspergillus exists commonly in many crops and any process of crop growth, harvest, storage, and processing can be polluted by this fungus. Once it forms a biofilm, Aspergillus can produce many toxins, such as aflatoxin B1 (AFB1), ochratoxin, zearalenone, fumonisin, and patulin. Among these toxins, AFB1 possesses the highest toxicity and is labeled as a group I carcinogen in humans and animals. Consequently, the proper control of AFB1 produced from biofilms in food and feed has long been recognized. Moreover, many biosensors have been applied to monitor AFB1 in biofilms in food. Additionally, in recent years, novel molecular recognition elements and transducer elements have been introduced for the detection of AFB1. This review presents an outline of recent progress made in the development of biosensors capable of determining AFB1 in biofilms, such as aptasensors, immunosensors, and molecularly imprinted polymer (MIP) biosensors. In addition, the current feasibility, shortcomings, and future challenges of AFB1 determination and analysis are addressed.

Simultaneous electrochemical determination of ochratoxin A and fumonisin B1 with an aptasensor based on the use of a Y-shaped DNA structure on gold nanorods

A complementary DNA (cDNA) was designed to simultaneously hybridize with the ochratoxin A (OTA) aptamer and the fumonisin B1 (FB1) aptamer to form a unique Y-shaped DNA structure and to achieve simultaneous detection. Gold nanorods (AuNRs) were used to immobilize thionine (Th), thiolated ferrocene (Fc), thiolated OTA aptamer (Apt1), and thiolated FB1 aptamer (Apt2), to form an amplified signal element and a recognition element. The Apt1-AuNRs-Th complex and the Apt2-AuNRs-Fc complex hybridize with cDNA to form a unique Y-DNA structure on a gold electrode. This produces two initial electrochemical signals [with 177 μΑ cm^-2 near -0.2 V, and 3121 μΑ cm^-2 near +0.46 V (vs. Ag/AgCl)] by differential pulse voltammetry. Upon addition of 0.1 ng mL^-1 OTA and 0.1 ng mL^-1 FB1, the aptamers bind the two toxins. This results in the release of Apt1-AuNRs-Th and Apt2-AuNRs-Fc, so the peak currents densities decrease to 115 μΑ cm^-2 and 209 μΑ cm^-2. The assay allows simultaneous determination of OTA and FB1 in the 1.0 pg·mL^-1 to 100 ng·mL^-1 concentration ranges, with LODs of 0.47 and 0.26 pg·mL^-1. The assay is reproducible, stable and specific. It was applied to the determination of OTA and FB1 in spiked beer, with recoveries between 89.0% and 102.0%. Graphical abstractSchematic representation of OTA and FB₁ detection based on Apt₂-AuNRs-Fc/Apt₁-AuNRs-Th/cDNA/AuE. (AuNRs: Gold nanorods; Th: thionine; Fc: ferrocene; SH: thiol; BSA: Bovine serum albumin; cDNA: Complementary DNA; Apt₁: Aptamer1; Apt₂: Aptamer2; OTA: Ochratoxin A; FB₁: Fumonisin B₁).

Hybridization chain reaction-enhanced enzyme biomineralization for ultrasensitive colorimetric biosensing of a protein biomarker

By employment of an aptamer-initiated hybridization chain reaction (HCR) to enhance the enzyme biomineralization of cupric subcarbonate, this work develops a novel colorimetric biosensing method for protein analysis. The HCR product was used to specifically attach a large amount of urease-functionalized gold nanoparticles (Au NPs) for the preparation of a gold nanoprobe. After the sandwich biorecognition reactions, this nanoprobe could be quantitatively captured onto the antibody-functionalized magnetic bead (MB) platform. Then, numerous copper ions would be enriched onto the MB surface through the urease-induced biomineralization of cupric subcarbonate. Based on the complete release of Cu2+ ions for the sensitive copper chromogenic reaction, convenient colorimetric signal transduction was thus achieved for the quantitative analysis of the target analyte of the carcinoembryonic antigen. The HCR product provides a large number of biotin sites for the attachment of Au NP nanotags. The biomineralization reaction of high-content urease loaded onto Au NPs leads to highly efficient Cu2+ enrichment for signal amplification. So this method features excellent performance including a very wide linear range and a low detection limit down to 0.071 pg mL-1. In addition, the satisfactory results of real sample experiments reveal that this method possesses huge potential for practical applications.

N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA

N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect - high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules (e.g. ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.

Ultrasensitive electrochemical detection of ochratoxin A based on signal amplification by one-pot synthesized flower-like PEDOT-AuNFs supported on a graphene oxide sponge

To enhance the sensitivity of an aptasensor, a novel strategy was designed to develop an electrochemical aptasensor based on poly(3,4-ethylenedioxy thiophene)-gold nanoflower (PEDOT-AuNF) composites supported on a three-dimensional graphene oxide sponge (GOS). GOS with a three-dimensional sponge-like porous structure, exhibiting excellent electrical conductivity and a large surface area, provided the first amplification of the electrochemical signal for ochratoxin A (OTA) detection. PEDOT-AuNFs, synthesized by an ionic liquid-assisted one-pot method, presented a peculiar hierarchical flower-like structure, a high electroactive surface area, and more binding sites for immobilizing the aptamer molecules by the Au-S bonds. When PEDOT-AuNFs were supported on the surface of GOS by the interaction of the π-π packing between PEDOT and graphene oxide, a synergistic effect was produced to provide the second amplification for the aptasensor. PEDOT-AuNFs/GOS provided an ultrasensitive detection technique by multiple signal amplification for the electrochemical sensing of OTA. Consequently, this strategy not only endowed the aptasensor with high sensitivity but also needed no complicated signal amplification. The electrochemical sensor was fabricated successfully on a glassy carbon electrode to detect OTA with a linear response in the range of 0.01-20 ng L^-1 and a limit of detection of 4.9 pg L^-1. Moreover, it displayed good specificity, reproducibility and stability. The utilization of the proposed aptasensor for the quantitative determination of OTA in wine indicates that it can find promising applications in detecting OTA and even other mycotoxins in foodstuffs.

A multiplexed FRET aptasensor for the simultaneous detection of mycotoxins with magnetically controlled graphene oxide/Fe3O4 as a single energy acceptor

A multiplexed FRET aptasensor was developed for the simultaneous detection of AFB1 and FB1 with magnetically controlled GO/Fe₃O₄ as a single energy acceptor.