Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification

A double methylene blue labeled single-stranded DNA and hairpin DNA coupling biosensor for the detection of Fusarium oxysporum f. sp. cubense race 4

The DCL gene in Fusarium oxysporum f. sp. cubense Race 4 (Foc4) is a pivotal pathogenic factor causing banana fusarium wilt. Precise DCL detection is crucial for Foc4 containment. Here, we present a novel ssDNA-hDNA coupling electrochemical biosensor for highly specific DCL detection. The sensing interface was formed via electrodeposition of a composite containing reduced graphene oxide (rGO) and gold nanoparticles (AuNPs) onto a carbon screen-printed electrode (SPE), followed by thiol-modified ssDNA functionalization. Additionally, the incorporation of hDNA, with methylene blue (MB) at both ends, binds to ssDNA through base complementarity, forming an ssDNA-hDNA coupling probe with bismethylene blue. This sensing strategy relies on DCL recognition by the hDNA probe, leading to DNA hairpin unfolding and detachment of hDNA bearing two MBs from ssDNA, generating a robust "on-off" signal. Empirical results demonstrate the sensor's amplified electrical signals, reduced background currents, and an extended detection range (6.02 × 106-3.01 × 1010 copies/μL) with a limit of detection (3.01 × 106 copies/μL) for DCL identification. We applied this sensor to analyze soil, banana leaves, and fruit samples, confirming its high specificity and stability. Moreover, post-sample detection, the sensor exhibits reusability, offering a cost-effective and rapid approach for banana wilt detection.

Dual-Mode Graphene Field-Effect Transistor Biosensor with Isothermal Nucleic Acid Amplification

Despite a substantial increase in testing facilities during the pandemic, access remains a major obstacle, particularly in low-resource and remote areas. This constraint emphasizes the need for high-throughput potential point-of-care diagnostic tools in environments with limited resources. Loop-mediated isothermal amplification (LAMP) is a promising technique, but improvements in sensitivity are needed for accurate detection, especially in scenarios where the virus is present in low quantities. To achieve this objective, we present a highly sensitive detection approach of a dual-mode graphene-based field-effect transistor (G-FET) biosensor with LAMP. The G-FET biosensor, which has a transparent graphene microelectrode array on a glass substrate, detects LAMP products in less than 30 min using both observable color changes and Dirac point voltage measurements, even in samples with low viral concentrations. This dual-mode G-FET biosensor emerges as a potential alternative to conventional RT-PCR for severe acute respiratory syndrome-associated coronavirus (SARS-CoV)-2 detection or point-of-care testing, particularly in resource-constrained scenarios such as developing countries. Moreover, its capacity for colorimetric detection with the naked eye enhances its applicability in diverse settings.

A paper-embedded thermoplastic microdevice integrating additive-enhanced allele-specific amplification and silver nanoparticle-based colorimetric detection for point-of-care testing

This study introduces a thermoplastic microdevice integrated with additive-enhanced allele-specific amplification and hydrazine-induced silver nanoparticle-based detection of single nucleotide polymorphism (SNP) and opportunistic pathogens. For point-of-care testing of SNP, an allele-specific loop-mediated isothermal amplification reaction using nucleotide-mismatched primers and molecular additives was evaluated to discriminate single-nucleotide differences in the samples. The microdevice consists of purification and reaction units that enable DNA purification, amplification, and detection in a sequential manner. The purification unit enables the silica-based preparation of samples using an embedded glass fiber membrane. Hydrazine-induced silver nanoparticle formation was employed for endpoint colorimetric detection of amplicons within three min at room temperature. The versatile applicability of the microdevice was demonstrated by the successful identification of SNPs related to sickle cell anemia, genetically-induced hair loss, and Enterococcus faecium. The microdevice exhibited a detection limit of 103 copies per μL of SNP targets in serum and 102 CFU mL-1 of Enterococcus faecium in tap water within 70 min. The proposed microdevice is a promising and versatile platform for point-of-care nucleic acid testing of different samples in low-resource settings.

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.

Biosensors based on functional nucleic acids and isothermal amplification techniques

In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.

LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection

Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.

Principles and Applications of Loop-Mediated Isothermal Amplification to Point-of-Care Tests

For the identification of nucleic acids, which are important biomarkers of pathogen-mediated diseases and viruses, the gold standard for NA-based diagnostic applications is polymerase chain reaction (PCR). However, the requirements of PCR limit its application as a rapid point-of-care diagnostic technique. To address the challenges associated with regular PCR, many isothermal amplification methods have been developed to accurately detect NAs. Isothermal amplification methods enable NA amplification without changes in temperature with simple devices, as well as faster amplification times compared with regular PCR. Of the isothermal amplifications, loop-mediated isothermal amplification (LAMP) is the most studied because it amplifies NAs rapidly and specifically. This review describes the principles of LAMP, the methods used to monitor the process of LAMP, and examples of biosensors that detect the amplicons of LAMP. In addition, current trends in the application of LAMP to smartphones and self-diagnosis systems for point-of-care tests are also discussed.

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 Advances in Signal Amplification to Improve Electrochemical Biosensing for Infectious Diseases

The field of infectious disease diagnostics is burdened by inequality in access to healthcare resources. In particular, “point-of-care” (POC) diagnostics that can be utilized in non-laboratory, sub-optimal environments are appealing for disease control with limited resources. Electrochemical biosensors, which combine biorecognition elements with electrochemical readout to enable sensitive and specific sensing using inexpensive, simple equipment, are a major area of research for the development of POC diagnostics. To improve the limit of detection (LOD) and selectivity, signal amplification strategies have been applied towards these sensors. In this perspective, we review recent advances in electrochemical biosensor signal amplification strategies for infectious disease diagnostics, specifically biosensors for nucleic acids and pathogenic microbes. We classify these strategies into target-based amplification and signal-based amplification. Target-based amplification strategies improve the LOD by increasing the number of detectable analytes, while signal-based amplification strategies increase the detectable signal by modifying the transducer system and keep the number of targets static. Finally, we argue that signal amplification strategies should be designed with application location and disease target in mind, and that the resources required to produce and operate the sensor should reflect its proposed application, especially when the platform is designed to be utilized in low-resource settings. We anticipate that, based on current technologies to diagnose infectious diseases, incorporating signal-based amplification strategies will enable electrochemical POC devices to be deployed for illnesses in a wide variety of settings.

Translation of aptamers toward clinical diagnosis and commercialization

The dominance of antibodies in diagnostics has gradually changed following the discovery of aptamers in the early 1990s. Aptamers offer inherent advantages over traditional antibodies, including higher specificity, higher affinity, smaller size, greater stability, ease of manufacture, and low immunogenicity, rendering them the best candidates for point-of-care testing (POCT). In the past 20 years, the research community and pharmaceutical companies have made great efforts to promote the development of aptamer technology. Macugen® (pegaptanib) was the first aptamer drug approved by the US Food and Drug Administration (FDA), and various aptamer-based diagnostics show great promise in preclinical research and clinical trials. In this review, we introduce recent literature, ongoing clinical trials, commercial reagents of aptamer-based diagnostics, discuss the FDA regulatory mechanisms, and highlight the prospects and challenges in translating these studies into viable clinical diagnostic tools.

Development of an Innovative Quantification Assay Based on Aptamer Sandwich and Isothermal Dumbbell Exponential Amplification

Detecting blood biomarkers such as proteins with high sensitivity and specificity is of the utmost importance for early and reliable disease diagnosis. As molecular probes, aptamers are raising increasing interest for biosensor applications as an alternative to antibodies, which are used in classical enzyme-linked immuno-sorbent assays (ELISA). We have developed a sensitive and antibody-free molecular quantification assay that combines the specificity of aptamers and the sensitivity of the loop-mediated isothermal amplification (LAMP). For the proof-of-concept, we consider two types of biomarkers: (i) a model of oligonucleotide mimicking nucleic acid targets and (ii) the thrombin involved in the complex coagulation cascade as a model protein for which two relevant aptamers form a stable sandwich. The assay protocol is based on a few successive steps, similar to sandwich ELISA. First, aptamer-coated magnetic beads are added to the sample to specifically capture the targets. Then, the sandwich complex is formed by adding the second aptamer. This secondary aptamer is integrated in a larger oligonucleotide dumbbell sequence designed for LAMP detection using only two primers. After a proper rinsing step, the isothermal dumbbell exponential amplification is performed to detect and quantify a low amount of targets (limit of detection ∼ 1 pM for the oligonucleotide and ∼100 pM for thrombin). This study demonstrates that our innovative aptamero-LAMP assay could be relevant for the detection of different types of biomarkers and their quantification at physiological levels. This may also pave the way for antibody-free molecular assays.

Simple Design Concept for Dual-Channel Detection of Ochratoxin A Based on Bifunctional Metal-Organic Framework

A simple fluorescence and electrochemical dual-channel biosensor based on bifunctional Zr(IV)-based metal-organic framework (Zr-MOF) was proposed to detect Ochratoxin A (OTA). The bifunctional Zr-MOF, with photoluminescence properties and enormous electroactive ligands, was exploited to load OTA-specific aptamers for designing signal probes, greatly simplifying the probe-fabrication process and improving sensing reliability. Upon specific recognition of aptamer toward OTA, the anchored probe was released from the sensing interface into the reaction solution. In this circumstance, the increased amount of the signal probe in reaction solution led to an enhanced fluorescence response, while the decreased amount of the signal probe on the sensing interface resulted in a diminished electrochemical response. According to the dual-channel signal change with increasing OTA concentration, the visual fluorescence strategy was established for intuitive OTA detection, and meanwhile, sensitive electrochemical assay with a detection limit of 0.024 pg/mL was also achieved with the help of one-step electrodeposition as a sensing platform. Moreover, the proposed dual-channel assay has been successfully applied to determine OTA levels in corn samples with rapid response, superior accuracy, and high anti-interference capability, providing a promising method for food safety monitoring.

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.

Recent Advances in Ochratoxin A Electrochemical Biosensors: Recognition Elements, Sensitization Technologies, and Their Applications

Ochratoxin A (OTA) is a class of mycotoxin that are mainly produced by Aspergillus and Penicillium and widely found in plant origin food. OTA-contaminated foods can cause serious harm to animals and humans, while high stability of OTA makes it difficult to remove in conventional food processing. Thus, sensitive and rapid detection of OTA undoubtedly plays an important role in OTA prevention and control. In this paper, the conventional and novel methods of OTA at home and abroad are summarized and compared. The latest research progress and related applications of novel OTA electrochemical biosensors are mainly described with a new perspective. We innovatively divided the recognition element into single and combined recognition elements. Specifically, signal amplification technologies applied to the OTA electrochemical aptasensor are proposed. Furthermore, summary of the current limitations and future challenges in OTA analysis is included, which provide reference for the further research and applications.

Highly sensitive and fast Legionella spp. in situ detection based on a loop mediated isothermal amplification technique combined to an electrochemical transduction system

A rapid highly sensitive genosensor has been developed for monitoring the presence of Legionella spp. in different water systems (domestic hot water, heating/cooling systems or cooling towers) in order to avoid its spreading from the source of contamination. The genosensor integrates a loop mediated isothermal amplification (LAMP) reaction with an electrochemical transduction signal, producing a very simple, rapid to perform and cost effective method, suitable for in situ analyses. This approach detects as low as 10 fg of Legionella nucleic acid, corresponding to only 2 number copies of the bacteria. The use of an electrochemical redox-active double stranded DNA (dsDNA) intercalating molecule, known as methylen blue (MB), allows the immediate electrochemical reading during the DNA polymerization. The sensor can obtain quantitative results in 20 min with a correlation between the electrochemical data and Legionella spp. copy number (at a logarithmic scale) of r = -0.97. In conclusion, a fast, easy to use, and accurate electrochemical genosensor, with high precision, sensitivity, and specificity has been developed for in situ detection of Legionella spp. enabling real time decision making and improving significantly the current detection methods for the prevention and screening of Legionella.

A fluorescent amplification strategy for high-sensitive detection of 17 β-estradiol based on EXPAR and HCR

Environmental endocrine disruptors in the environment and food, especially 17 β-estradiol (E2), are important factors affecting the growth and development of organisms. In this research, we constructed a fluorescence strategy for two-step amplification that combined two currently popular methods, exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR). E2 competed with the complementary DNA (cDNA) to bind the aptamer modified on the magnetic beads. The free complementary strand in the supernatant was used as a trigger sequence to activate EXPAR, producing a large amount of short single-stranded DNA (ssDNA). The amplified ssDNA can trigger the second HCR amplification, producing many long double-stranded DNA (dsDNA) analogues. According to the principle of fluorescence resonance energy transfer, the carboxyfluorescein (FAM) signals in H1 and H2 hairpins were quenched by black hole quencher (BHQ-1). After the addition of E2 and initiation of amplification, the initially quenched fluorescent signal would be restored. This strategy with a detection limit of 0.37 pg mL^-1 (S/N = 3) showed a good linear relationship in the range of 0.4-800 pg mL^-1. In addition, the recovery rates of the method for milk and water samples were 98.55%-116.95% and 92.32%-107.00%, respectively. This is the first report of the combined detection of EXPAR and HCR, providing a reference for rapid and highly sensitive detection using multiple isothermal amplification methods.

Review of Electrochemical DNA Biosensors for Detecting Food Borne Pathogens

The vital importance of rapid and accurate detection of food borne pathogens has driven the development of biosensor to prevent food borne illness outbreaks. Electrochemical DNA biosensors offer such merits as rapid response, high sensitivity, low cost, and ease of use. This review covers the following three aspects: food borne pathogens and conventional detection methods, the design and fabrication of electrochemical DNA biosensors and several techniques for improving sensitivity of biosensors. We highlight the main bioreceptors and immobilizing methods on sensing interface, electrochemical techniques, electrochemical indicators, nanotechnology, and nucleic acid-based amplification. Finally, in view of the existing shortcomings of electrochemical DNA biosensors in the field of food borne pathogen detection, we also predict and prospect future research focuses from the following five aspects: specific bioreceptors (improving specificity), nanomaterials (enhancing sensitivity), microfluidic chip technology (realizing automate operation), paper-based biosensors (reducing detection cost), and smartphones or other mobile devices (simplifying signal reading devices).

Advances in biosensors for the detection of ochratoxin A: Bio-receptors, nanomaterials, and their applications

Ochratoxin A (OTA) is a class of mycotoxin mainly produced by the genera Aspergillus and Penicillium. OTA can cause various forms of kidney, liver and brain diseases in both humans and animals although trace amount of OTA is normally present in food. Therefore, development of fast and sensitive detection technique is essential for accurate diagnosis of OTA. Currently, the most commonly used detection methods are enzyme-linked immune sorbent assays (ELISA) and chromatographic techniques. These techniques are sensitive but time consuming, and require expensive equipment, highly trained operators, as well as extensive preparation steps. These drawbacks limit their wide application in OTA detection. On the contrary, biosensors hold a great potential for OTA detection at for both research and industry because they are less expensive, rapid, sensitive, specific, simple and portable. This paper aims to provide an extensive overview on biosensors for OTA detection by highlighting the main biosensing recognition elements for OTA, the most commonly used nanomaterials for fabricating the sensing interface, and their applications in different read-out types of biosensors. Current challenges and future perspectives are discussed as well.

Loop-mediated isothermal amplification-fluorescent loop primer assay for the genotyping of a single nucleotide polymorphism at position 2254 in the viral DNA polymerase gene of equid alphaherpesvirus 1

We developed a loop-mediated isothermal amplification (LAMP)-fluorescent loop primer (FLP) assay for genotyping the A/G₂₂₅₄ single nucleotide polymorphism (SNP) in the viral DNA polymerase gene of species Equid alphaherpesvirus 1 (EHV-1), which is associated with the neuropathogenic potential of this virus. In addition to the use of regular LAMP primers to amplify the target region, a 5'-FAM-labeled backward loop primer (FLB) and 3'-dabcyl-labeled quencher probe (QP) were designed for annealing curve analysis of the amplification product. The QP, which contacts the FLB, is located at the SNP site and has the A₂₂₅₄ allele. LAMP reactions were performed at 63°C for 40 min, and the subsequent annealing curve analyses were accomplished within 20 min. The LAMP-FLP assay could clearly differentiate A₂₂₅₄ and G₂₂₅₄ genotypes according to the difference in the annealing temperature of the QP between the 2 genotypes. Good agreement between the LAMP-FLP and the real-time PCR for genotyping of this SNP was observed in the detection of EHV-1 in equine clinical samples. The newly developed assay is a simple and rapid method for detecting and differentiating EHV-1 strains with A₂₂₅₄ and G₂₂₅₄ polymorphisms and would be suitable for clinical use.

Electrochemical aptamer-based sensors for food and water analysis: A review

Global food and water safety issues have prompted the development of highly sensitive, specific, and fast analytical techniques for food and water analysis. The electrochemical aptamer-based detection platform (E-aptasensor) is one of the more promising detection techniques because of its unique combination of advantages that renders these sensors ideal for detection of a wide range of target analytes. Recent research results have further demonstrated that this technique has potential for real world analysis of food and water contaminants. This review summaries the recently developed E-aptasensors for detection of analytes related to food and water safety, including bacteria, mycotoxins, algal toxins, viruses, drugs, pesticides, and metal ions. Ten different electroanalytical techniques and one opto-electroanalytical technique commonly employed with these sensors are also described. In addition to highlighting several novel sensor designs, this review also describes the strengths, limitations, and current challenges this technology faces, and future development trend.

A fluorometric aptasensor for patulin based on the use of magnetized graphene oxide and DNase I-assisted target recycling amplification

A fluorometric patulin (PAT) assay is presented that is based on the use of magnetic reduced graphene oxide (rGO) and DNase I. The fluorescence of the PAT aptamer labelled with 6-carboxyfluorescein (FAM) is quenched by magnetized reduced graphene oxide (rGO-Fe₃O₄) due to fluorescence resonance energy transfer (FRET). However, in the presence of PAT, the labelled aptamer is stripped off from rGO-Fe₃O₄. The rGO-Fe₃O₄ is then magnetically separated so that the fluorescence of free labelled PAT aptamer is restored. DNase I cannot hydrolyze the aptamer on rGO-Fe₃O₄, but it can cleave the free aptamer-PAT complex. This will release FAM and PAT which can undergo a number of additional cycles to trigger the cleavage of abundant aptamer. Recycling of DNase I-assisted target therefore leads to a strong amplification of fluorescence and consequently to an assay with low limit of detection. The detection limit for PAT is as low as 0.28 μg L^-1 which is about 13 times lower than that without using DNase I. The method offers a new approach towards rapid, sensitive and selective detection based on an aptamer. Conceivably, it has a wide scope in that it may be applied to numerous other analytes if appropriate aptamers are available. Abstract Schematic of a fluorometric assay based on the use of magnetic graphene oxide and DNase I. It was applied to the determination of patulin. DNase I was introduced for recycling amplification. The detection limit is about 13 times lower than that without using DNase I. Figure a contains poor quality of text in image. Otherwise, please provide replacement figure file.Thank you. I will provide the figure file.

Rapid Detection of Rongalite via a Sandwich Lateral Flow Strip Assay Using a Pair of Aptamers

A sandwich lateral flow strip assay (LFSA) using a couple of aptamers functionalized with gold nanoparticles (AuNPs) was designed to assess the presence of rongalite in agrifood products. More specifically, a biotin-labeled primary A09 aptamer immobilized on a streptavidin-coated membrane and a secondary B09 aptamer conjugated with AuNPs were developed as capturing and signaling probes, respectively. This system allows the successful and direct detection of rongalite in food samples with concentrations as low as 1 μg/mL, simply by observing the color change of LFSA control and test line.

Advances in aptasensors for the detection of food contaminants

Food safety is a global health objective, and foodborne diseases represent a major crisis in health. Techniques that are simple and suitable for fast screening to detect and identify pathogenic factors in the food chain are vital to ensure food safety. At present, a variety of analytical methods have been reported for the detection of pathogenic agents. Whereas the sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic bio-recognition elements, such as aptamers. Owing to the specific folding capability of aptamers in the presence of an analyte, aptasensors have substantially and successfully been exploited for the detection of a wide range of small and large molecules (e.g., toxins, antibiotics, heavy metals, bacteria, viruses) at very low concentrations. Here, we review the use of aptasensors for the development of highly sensitive and affordable detection tools for food analysis.

An ultrasensitive signal-on electrochemical aptasensor for ochratoxin A determination based on DNA controlled layer-by-layer assembly of dual gold nanoparticle conjugates

In this paper, a novel ultrasensitive signal-on electrochemical aptasensor has been proposed for Ochratoxin A (OTA) assay based on DNA controlled layer-by-layer assembly of dual gold nanoparticle (AuNP) conjugates. To construct the aptasensor, the 1^st AuNP conjugate was prepared by simultaneous immobilization of the capture probe 2 (CP2) and bridge probe (BP) onto the AuNPs. Then, OTA aptamer was loaded onto 1^st AuNPs by hybridization with CP2. The 1^st AuNP conjugate can be further immobilized onto the electrode by hybridization between BP and capture probe 1 (CP1), which was pre-immobilized on Au electrode. The 2^nd AuNP conjugate was prepared by immobilization of ferrocene (Fc) tagged SH-signal probe (SSP). Due to the recognition between aptamer on 1^st AuNP conjugate and OTA, CP2 was reformed in the ssDNA state, which can be utilized as the anchor for immobilization of 2^nd AuNP conjugate for electrochemical signal reporting. Because of the high surface-to-volume ratio and good conductivity of AuNPs, this dual AuNPs assembled nanoarchitecture finally lead to greatly improved abilities to load a large number of Fc molecules and significantly amply the electrochemical response even at a low target concentration. Both qualitative and quantitative analysis of OTA were thus realized by differential pulse voltammetry (DPV) signals, resulting in an excellent detection limit of 0.001 ppb and a wide dynamic range from 0.001 to 500 ppb over 6 orders of magnitude. Moreover, the real sample analysis towards OTA spiked wine samples was favorable, implying a great potential for practical applications. We envision that this unique dual AuNP conjugate assembly strategy would pave a new avenue for the development of versatile signal amplified electrochemical aptasensors.

A Label-Free Aptasensor for Ochratoxin a Detection Based on the Structure Switch of Aptamer

A label-free sensing platform is developed based on switching the structure of aptamer for highly sensitive and selective fluorescence detection of ochratoxin A (OTA). OTA induces the structure of aptamer, transforms into G-quadruplex and produces strong fluorescence in the presence of zinc(II)-protoporphyrin IX probe due to the specific bind to G-quadruplex. The simple method exhibits high sensitivity towards OTA with a detection limit of 0.03 nM and excellent selectivity over other mycotoxins. In addition, the successful detection of OTA in real samples represents a promising application in food safety.

Isothermal exponential amplification techniques: From basic principles to applications in electrochemical biosensors

As a conventional amplification technique, polymerase chain reaction (PCR) has been widely applied to detect a variety of analytes with exponential amplification efficiency. However, the requirement of thermocycling procedures largely limits the application of PCR-based methods. Alternatively, several isothermal amplification techniques have been developed since the early 1990s. In particular, according to the reaction kinetics, isothermal exponential amplification techniques possess higher amplification efficiency and detection sensitivity. The isothermal exponential amplification techniques can be mainly divided into two categories: enzyme-based isothermal exponential amplification and enzyme-free isothermal exponential amplification. Considering the advantages of high sensitivity and selectivity, high signal-to-noise ratio, low cost and rapid response time, exponential amplification electrochemical biosensors have attracted considerable attention. In this review, we introduce the basic principles of isothermal exponential amplification techniques and summarize their applications in electrochemical biosensors during the past five years. We also highlighted the present challenges and further perspectives of isothermal exponential amplification-based electrochemical biosensors.

Highly sensitive detection of epidermal growth factor receptor in lung cancer cells by aptamer-based target-/probe-mediated cyclic signal amplification

We develop an antibody-free fluorescence method for the epidermal growth factor receptor (EGFR) assay using aptamer-based target-/probe-mediated cyclic signal amplification. The method is highly sensitive with a detection limit of 0.16 fM, and it can be applied to detect EGFR in lung cancer cells, holding great potential in clinical diagnosis.

Two-dimensional MoS2 as a nano-binder for ssDNA: Ultrasensitive aptamer based amperometric detection of Ochratoxin A

Two-dimensional (2D) MoS₂ is found to possess different affinities for ssDNA and dsDNA. This finding is exploited in an amperometric aptamer-based method for the determination of the mycotoxin ochratoxin A (OTA). Initially, a dsDNA probe (formatted through the hybridization of OTA-aptamer with an auxiliary DNA) is self-assembled on a gold electrode. Upon introduction of OTA, it will bind to the aptamer and cause the unwinding of dsDNA, while the auxiliary DNA (with single-stranded structure) remains on the electrode. Since the affinity of 2D MoS₂ for ssDNA is considerably larger than that for dsDNA, it will be adsorbed on the electrode by binding to the auxiliary DNA. Notably, 2D MoS₂ possesses peroxidase-like activity. Hence, it can catalyze the amplification of electrochemical signal of the hydroquinone/benzoquinone redox system. Under optimal conditions, the amperometric signal (best measured at -0.2 V vs. SCE) increases with increasing OTA concentration in the range from 0.5 pg·mL^-1 to 1.0 ng·mL^-1, with a lower detection limit of 0.23 pg·mL^-1. The method was applied to the determination of OTA in spiked red wine. Graphical abstract Herein we construct a convenient electrochemical aptasensor for sensitive monitor of ochratoxin A by using 2D MoS₂ as a nano-binder to catalyze the amplification of electrochemical signal from hydroquinone/benzoquinone system.

Real-time DNA Amplification and Detection System Based on a CMOS Image Sensor

In the present study, we developed a polypropylene well-integrated complementary metal oxide semiconductor (CMOS) platform to perform the loop mediated isothermal amplification (LAMP) technique for real-time DNA amplification and detection simultaneously. An amplification-coupled detection system directly measures the photon number changes based on the generation of magnesium pyrophosphate and color changes. The photon number decreases during the amplification process. The CMOS image sensor observes the photons and converts into digital units with the aid of an analog-to-digital converter (ADC). In addition, UV-spectral studies, optical color intensity detection, pH analysis, and electrophoresis detection were carried out to prove the efficiency of the CMOS sensor based the LAMP system. Moreover, Clostridium perfringens was utilized as proof-of-concept detection for the new system. We anticipate that this CMOS image sensor-based LAMP method will enable the creation of cost-effective, label-free, optical, real-time and portable molecular diagnostic devices.

Light-Up Nonthiolated Aptasensor for Low-Mass, Soluble Amyloid-β40 Oligomers at High Salt Concentrations

Herein, a light-up nonthiolated aptasensor was developed for low-mass, soluble amyloid-β₄₀ oligomers (LS-Aβ_40-O). Au nanoparticles (AuNP) were employed as colorimetric probes, and the nonthiolated aptamers (Apt) were adsorbed on AuNP surfaces, acting as binding elements for LS-Aβ_40-O. The aggregation of AuNPs was induced when Apt-modified AuNPs (Apt@AuNPs) were under high-salt conditions. However, upon the addition of LS-Aβ_40-O into the Apt@AuNP solution, the salt tolerance of the AuNPs was greatly enhanced. Further studies confirmed that the formed LS-Aβ_40-O-Apt complex attached onto the AuNP surfaces via interactions between LS-Aβ_40-O and Au, which led to electrostatic and steric stabilization of the AuNPs under high-salt conditions. On the basis of this outcome, a sensitive light-up nonthiolated aptasensor for LS-Aβ_40-O was achieved with a detection limit of 10.0 nM and a linear range from 35.0 to 700 nM in a 175 mM NaCl solution. Cerebrospinal-fluid (CSF) samples from healthy persons and Alzheimer's disease (AD) patients were successfully distinguished by using this proposed method. The concentrations of LS-Aβ_40-O in the CSF of AD patients were of nanomolar grade, but there was no detectable LS-Aβ_40-O in those of the healthy persons. This work provides a new insight into the interaction between Apt@AuNPs and Aβ_40-O and also develops a simple, rapid, highly selective and sensitive, and applicable method for LS-Aβ_40-O detection in real CSF samples, which is significant for the diagnosis of AD.

Specific Light-Up System for Protein and Metabolite Targets Triggered by Initiation Complex Formation

Gene regulation systems are mimicked by simple quantitative detection of non-nucleic acid molecular targets such as protein and metabolite. Here, we describe a one-tube, one-step real-time quantitative detection methodology for isothermal signal amplification of those targets. Using this system, real-time quantitative detection of thrombin and streptomycin, which were used as examples for protein and metabolite targets, was successfully demonstrated with detection limits of at most 50 pM and 75 nM, respectively. Notably, the dynamic range of target concentrations could be obtained for over four orders of magnitude. Thus, our method is expected to serve as a point-of-care or on-site test for medical diagnosis and food and environmental hygiene.

Tuning the Aggregation/Disaggregation Behavior of Graphene Quantum Dots by Structure-Switching Aptamer for High-Sensitivity Fluorescent Ochratoxin A Sensor

The design of graphene quantum dots (GQDs)-aptamer bioconjugates as the new sensing platform is very important for developing high-sensitivity fluorescent biosensors; however, achieving new bioconjugates is still a great challenge. Herein, we report the development of a new high-sensitivity fluorescent aptasensor for the detection of ochratoxin A (OTA) based on tuning aggregation/disaggregation behavior of GQDs by structure-switching aptamers. The fluorescence sensing process for OTA detection involved two key steps: (1) cDNA-aptamer (cDNA, complementary to part of the OTA aptamer) hybridization induced the aggregation of GQD (fluorescence quenching) after cDNA was added into the GQDs-aptamer bioconjugate solution, and (2) the target of OTA triggered disaggregation of GQD aggregates (fluorescence recovery). Such new fluorescent sensing platform can be used to monitor OTA with a linear range of 0 to 1 ng/mL and very low detection limit of 13 pg/mL, which is among the best in all the developed fluorescent nanoparticles-based sensors. Such sensing strategy is also successful in analyzing OTA in practical red wine sample with 94.4-102.7% of recoveries and relative standard deviation in the range of 2.9-5.8%. The present works open a new way for signaling the target-aptamer binding event by tuning aggregation/disaggregation behavior of GQDs-bioconjugates.

Aptamer-based environmental biosensors for small molecule contaminants

Aptasensors are promising biosensors, which take advantage of using aptamers as a recognition element. The combination of the excellent characteristics of aptamers and the leading detection platform techniques, such as optical, electrochemical with nanomaterial-integrated, or mass-sensitive techniques with high sensitivity and specificity draws a promising view for the application of the aptasensors for the detection of harmful small toxic chemicals and real-time monitoring in the environments. In spite of attraction of aptasensors, application of them is limited to the complex environment due to the facts that how the immobilization of aptamers onto the surface affects the functions of aptamers and their structures for the detection of environmental contaminants are not clearly known. This review examines the most recent update on the selection of aptamers for small molecules, the development and application of aptasensors in the detection of small molecule contaminants in environment. Additionally, their applications to the real samples as environmental monitoring reported in the publications also are reviewed.

Magneto-controlled aptasensor for simultaneous electrochemical detection of dual mycotoxins in maize using metal sulfide quantum dots coated silica as labels

Currently there is an urgent need for multi-mycotoxin detection methods due to the co-occurrence of multiple mycotoxins in food raw materials and their augmented toxicity. Herein, a magneto-controlled aptasensor has been developed for simultaneous electrochemical detection of ochratoxin A (OTA) and fumonisin B1 (FB1), two typical mycotoxins found in food crops world-wide. This aptasensor was designed using the high specificity between the target and aptamer with heavy CdTe or PbS quantum dots (QDs) coated silica as labels and the complementary DNA functionalized magnetic beads as capture probes. In presence of targets, the aptamer preferred to form the target-aptamer binding which forced the partial release of the preloaded labels from the magnetic beads. After a one-step incubation and a simple magnetic separation, the electrochemical signals of Cd²⁺ and Pb²⁺ dissolved from the reserved labels which had negative correlation with targets contents, was measured based on the difference of peak potentials. This aptasensor provided a wide detection range of 10pgmL^-1 to 10ngmL^-1 for OTA and 50pgmL^-1 to 50ngmL^-1 for FB1, and succeeded in real maize samples. This method provides a new avenue for high throughput screen of mycotoxins due to the advantages of simple instrument, low sample consumption, short assay times, and lower detection costs per assay. Moreover, it could be readily expanded for the simultaneous detection of a large panel of mycotoxins by using different metal sulfide QDs when their specific aptamers are available.

Enzyme-assisted cycling amplification and DNA-templated in-situ deposition of silver nanoparticles for the sensitive electrochemical detection of Hg(2.)

In this work, a label-free electrochemical biosensor was developed for sensitive and selective detection of mercury (II) ions (Hg(2+)) based on in-situ deposition of silver nanoparticles (AgNPs) on terminal deoxynucleotidyl transferase (TdT) extended ssDNA for signal output and nicking endonuclease for cycling amplification. In the presence of target Hg(2+), the T-rich DNA (HP1) could partly fold into duplex-like structure (termed as output DNA) via T-Hg(2+)-T base pairs and thus exposed its sticky end. The sticky end of output DNA could then hybridize with 3'-PO4 terminated capture DNA (HP2) on electrode surface to form output DNA-HP2 hybridization complex with the sequence 5'-CCTCAGC-3'/3'-GGAGTCG-5' (the sequence could be recognized by nicking endonuclease Nt. BbvCI). With the introduction of Nt. BbvCI, output DNA existed in hybridization complex was released from electrode and participated in the next hybridization process, accompanying with the cleave of HP2 to expose substantial 3'-OH group, which could be extended into a long ssDNA nanotail with the aid of TdT and deoxyadenosine triphosphate (dATP). Since the long negatively charged ssDNA nanotail absorbed the positively charged silver ions on the DNA skeleton, the metallic silver could be in-situ deposited on electrode surface for electrochemical signal output upon addition of reduction regent sodium borohydride. Under optimal conditions, the developed electrochemical biosensor presented a good response to Hg(2+) with a detection limit of 3 pM (S/N=3). Furthermore, the biosensor exhibited good reproducibility and high selectivity towards other interfering ions. The proposed sensing system also showed a promising potential application in real sample analysis.

Establishment and application of a real-time loop-mediated isothermal amplification system for the detection of CYP2C19 polymorphisms

Single-nucleotide polymorphisms (SNPs) represent the most widespread type of genetic variation (approximately 90%) in the human genome, and the demand to overcome such variation has received more attention now than ever before. The capacity to rapidly assess SNPs that correlate with disease predisposition, drug efficacy and drug toxicity is a key step for the development of personalized medicine. In this work, a rapid one-step SNP detection method, real-time loop-mediated isothermal amplification (RT-LAMP), was first applied for CYP2C19 polymorphisms testing. The optimized method was established with specifically designed primers for target amplification by real-time detection in approximately 30 min under isothermal conditions. RT-LAMP amplified few copies of template to produce significant amounts of product and quantitatively detected human DNA with compatible specificity and sensitivity. The success in the establishment of this RT-LAMP protocol for CYP2C19 polymorphism testing is significant for the extension of this technique for the detection of other SNPs, which will further facilitate the development of personalized medicine.

Sensitive detection of bisphenol A based on a ratiometric electrochemical aptasensor

A new ratiometric electrochemical aptasensor has been developed for highly sensitive and selective detection of bisphenol A (BPA). The double-stranded DNA (dsDNA), consisting of the BPA aptamer (DNA1) and methylene blue (MB)-labeled complementary DNA (cDNA), was immobilized on a gold nanoparticle (AuNP) modified glassy carbon (GC) electrode. In the presence of BPA, the specific BPA–aptamer interaction drove the release of the MB-labeled cDNA from the electrode surface. As a result, the oxidation peak current of MB (IMB) decreased and that of BPA (IBPA) increased. The peak current ratio (IBPA/IMB) of BPA and MB was linear with the concentration of BPA in the range from 1 to 100 pmol/L with a detection limit of 0.6 pmol/L. The detection limit is much lower than that obtained by most of the reported electrochemical methods. On the other hand, the developed aptasensor possesses good selectivity, reproducibility, and stability, and the related sensing structure is very simple, showing promising practical applications in BPA assays.

An aptamer based lateral flow strip for on-site rapid detection of ochratoxin A in Astragalus membranaceus

An aptamer based lateral flow strip based on competitive format was developed for on-site rapid detection of ochratoxin A (OTA) in Astragalus membranaceus. Some crucial parameters that might influence the sensitive detection, such as the characterization of the colloidal gold, size and shape of gold nanoparticles (AuNPs), amount of AuNPs-aptamer conjugate, migration rate and the addition amount of methanol, were investigated to provide the optimum assay performance. To perform the test, 1g sample was extracted with 2.5mL of methanol-water (80:20, v/v) and diluted by 4-fold running buffer to eliminate the matrix and methanol interferences. Under optimized conditions, the aptamer-based assay showed a visual limit of detection (LOD) of 1ngmL(-1), and with no significant cross-reactivity with several homologous toxins. The whole detection could be completed within 15min without special equipment because of available visual results. One out of nine A. membranaceus samples was found to be positive of OTA, which was in a good agreement with those obtained from LC-MS/MS analysis. The results demonstrated that the aptamer-based lateral flow assay could be used as a rapid, reliable, cost-effective and robust on-site screening technique for mycotoxins at trace level in complex matrices without special instrumentation.

Direct detection of OTA by impedimetric aptasensor based on modified polypyrrole-dendrimers

Ochratoxin A (OTA) is a carcinogenic mycotoxin that contaminates food such as cereals, wine and beer; therefore it represents a risk for human health. Consequently, the allowed concentration of OTA in food is regulated by governmental organizations and its detection is of major agronomical interest. In the current study we report the development of an electrochemical aptasensor able to directly detect trace OTA without any amplification procedure. This aptasensor was constructed by coating the surface of a gold electrode with a film layer of modified polypyrrole (PPy), which was thereafter covalently bound to polyamidoamine dendrimers of the fourth generation (PAMAM G4). Finally, DNA aptamers that specifically binds OTA were covalently bound to the PAMAM G4 providing the aptasensor, which was characterized by using both Atomic Force Microscopy (AFM) and Surface Plasmon Resonance (SPR) techniques. The study of OTA detection by the constructed electrochemical aptasensor was performed using Electrochemical Impedance Spectroscopy (EIS) and revealed that the presence of OTA led to the modification of the electrical properties of the PPy layer. These modifications could be assigned to conformational changes in the folding of the aptamers upon specific binding of OTA. The aptasensor had a dynamic range of up to 5 μg L(-1) of OTA and a detection limit of 2 ng L(-1) of OTA, which is below the OTA concentration allowed in food by the European regulations. The efficient detection of OTA by this electrochemical aptasensor provides an unforeseen platform that could be used for the detection of various small molecules through specific aptamer association.