Organophosphorus pesticides detection using broad-specific single-stranded DNA based fluorescence polarization aptamer assay

A photoelectrochemical aptasensor for omethoate determination based on a photocatalysis of CeO2@MnO2 heterojunction for glucose oxidation

In the present work, we developed a photoelectrochemical aptasensor to determine omethoate (OMT) based on the dual signal amplification of CeO2@MnO2 photocatalysis for glucose oxidation and exonuclease I-assisted cyclic catalytic hydrolysis. CeO2@MnO2 heterojunction material prepared by hydrothermal method was linked with captured DNA (cDNA) and then assembled on the ITO conductive glass to form ITO/CeO2@MnO2-cDNA, which exhibited significant photocurrent response and good photocatalytic performance for glucose oxidation under visible light irradiation, providing the feasibility for sensitive determining OMT. After binding with the aptamer of OMT (apt), the formation of rigid double stranded cDNA/apt kept CeO2@MnO2 away from ITO surface, which ensured a low photocurrent background for the constructed ITO/CeO2@MnO2-cDNA/apt aptasensor. In the presence of target OMT, the restoration of the cDNA hairpin structure and the exonuclease I-assisted cyclic catalytic hydrolysis led to the generation and amplification of measurement photocurrent signals, and allowed the aptasensor to have an ideal quantitative range of 0.01-10.0 nM and low detection limit of 0.0027 nM. Moreover, the aptasensor has been applied for selective determination of OMT in real samples with good precision of the relative standard deviation less than 6.2 % and good accuracy of the recoveries from 93 % to 108 %. What's more, the aptasensor can be used for other target determination only by replacing the captured DNA and corresponding aptamer.

Ti3C2Tx MXene-Based Fluorescent Aptasensor for Detection of Dimethoate Pesticide

Dimethoate contaminants in food pose a threat to human health. Rapid and sensitive trace detection methods are required to keep food safe. In this study, a novel fluorescent aptasensor was developed for the sensitive detection of dimethoate based on carbon quantum dots labeled with double-stranded DNA (CQDs-apt-cDNA) and Ti3C2Tx flakes. Under optimal conditions, the aptasensor showed a good linear range of 1 × 10-9 to 5 × 10-5 M for dimethoate with a coefficient of determination (R2) of 0.996. Besides, a low detection limit of 2.18 × 10-10 M was obtained. The aptasensor showed high selectivity in interference samples and good reproducibility with an RSD of 3.06% (<5%) for dimethoate detection. Furthermore, the proposed aptasensor was applied to the detection of dimethoate in apple juice and tap water with satisfactory recoveries from 96.2 to 104.4%. Because of these benefits, this aptasensor has the potential and promise for detecting food contaminants in the food industry.

Organophosphorus and carbamate pesticides: Molecular toxicology and laboratory testing

Population and food requirements are increasing daily throughout the world. To fulfil these requirements application of pesticides is also increasing. Organophosphorous (OP) and Organocarbamate (OC) compounds are widely used pesticides. These pesticides are used for suicidal purposes too. Both inhibit Acetylcholinesterase (AChE) and cholinergic symptoms are mainly used for the diagnosis of pesticide poisoning. Although the symptoms of the intoxication of OP and OC are similar, recent research has described different targets for OP and OC pesticides. Researchers believe the distinction of OP/OC poisoning will be beneficial for the management of pesticide exposure. OP compounds produce adducts with several proteins. There is a new generation of OP compounds like glyphosate that do not inhibit AChE. Therefore, it's high time to develop biomarkers that can distinguish OP poisoning from OC poisoning.

Recent Advances in Aptasensors for Rapid Pesticide Residues Detection

Pesticides are applied widely to increase agricultural output and quality, however, this practice results in residual issues that not only harm the environment but also put people and animals' lives and health at risk. As a result, it is critical to find pesticide residues in a variety of sources, including crops, water supplies, and soil. Aptamers are more flexible in their synthesis and modification, have a high level of specificity, are inexpensive, and have good stability compared to conventional detection methods. They have therefore attracted a lot of interest in the industry. This study reviews the most recent aptasensor advancements in the detection of pesticide residues. Firstly, aptamers specifically binding to many pesticides are summarized. Secondly, the combination of aptasensors with colorimetric, fluorescent, surface enhanced Raman spectroscopy (SERS), resonance Light Scattering (RLS), chemiluminescence (CL), electrochemical, and electrochemiluminescence (ECL) technologies are systematically introduced, and their advantages and disadvantages are expounded. Importantly, the aptasensors for the detection of various pesticides (organochlorine, organophosphorus, neonicotinoids, carbamates, and pyrethroids) that have been developed so far are systematically analyzed and discussed. Finally, the furture prospects and challenges of the aptasensors are highlighted. It is expected to offer suggestions for the later creation of novel, highly effective and sensitive aptasensors for the detection of pesticide residues.

Advances in Microfluidics Techniques for Rapid Detection of Pesticide Residues in Food

Food safety is a significant issue that affects people worldwide and is tied to their lives and health. The issue of pesticide residues in food is just one of many issues related to food safety, which leave residues in crops and are transferred through the food chain to human consumption. Foods contaminated with pesticide residues pose a serious risk to human health, including carcinogenicity, neurotoxicity, and endocrine disruption. Although traditional methods, including gas chromatography, high-performance liquid chromatography, chromatography, and mass spectrometry, can be used to achieve a quantitative analysis of pesticide residues, the disadvantages of these techniques, such as being time-consuming and costly and requiring specialist staff, limit their application. Therefore, there is a need to develop rapid, effective, and sensitive equipment for the quantitative analysis of pesticide residues in food. Microfluidics is rapidly emerging in a number of fields due to its outstanding strengths. This paper summarizes the application of microfluidic techniques to pyrethroid, carbamate, organochlorine, and organophosphate pesticides, as well as to commercial products. Meanwhile, the study also outlines the development of microfluidics in combination with 3D printing technology and nanomaterials for detecting pesticide residues in food.

A novel electrochemical aptasensor for ultrasensitive detection of herbicide prometryn based on its highly specific aptamer and Ag@Au nanoflowers

Herbicide prometryn has become a common pollutant in aquatic environments and caused adverse impacts on ecosystems. This study developed an ultrasensitive electrochemical aptasensor for prometryn based on its highly affinitive and specific aptamer and Ag@Au nanoflowers (Ag@AuNFs) for signal amplification. Firstly, this study improved the Capture-SELEX strategy to screen aptamers and obtained aptamer P60-1, which had a high affinity (Kd: 23 nM) and could distinguish prometryn from its structural analogues. Moreover, the typical stem-loop structure in aptamer P60-1 was found to be the binding pocket for prometryn. Subsequently, an electrochemical aptasensor for prometryn was established using multiwalled carbon nanotubes and reduced graphene oxide as electrode substrate, Ag@Au NFs as signal amplification element, and aptamer P60-1 as recognition element. The aptasensor had a detection range of 0.16-500 ng/mL and a detection limit of 60 pg/mL, which was much lower than those of existing detection methods. The aptasensor had high stability and good repeatability, and could specifically detecting prometryn. Furthermore, the utility of the aptasensor was validated by measuring prometryn in environmental and biological components. Therefore, this study provides a robust and ultrasensitive aptasensor for accurate detection for prometryn pollution.

An enzyme-free, ultrasensitive strategy for simultaneous screening of the p-nitrophenyl substituent organophosphorus pesticides

An enzyme-free, sensitive, and convenient approach was reported for the P-nitrophenyl substituent organophosphorus pesticides (NSOPs) of paraoxon-methyl (PM), paraoxon-ethyl (PE), parathion-methyl (PTM) and parathion-ethyl (PTE)) by indirectly quantification of the 4-nitrophenol (4-NP, hydrolysis product of the NSOPs). NaOH instead of hydrolase/nanozyme was applied, and temperature, pH, ultrasound was investigated to improve the NSOPs hydrolysis. Under the optimized conditions, the hydrolysis efficiencies were up to 99.9 %, 99.9 %, 99.6 %, 96.0 % for PM (10 min), PE (30 min), PTM (90 min) and PTE (120 min), based on which a low detection limits of 0.06 (PM), 0.07 (PE), 0.06 (PTM) and 0.07 (PTE) ppb were calculated with the 4-NP detection limit (0.03 ppb). Furthermore, the method exhibited good performance for the NSOPs with recoveries from 88.87 % to 100.33 % in real samples. This indirect approach offered an ultrasensitive alternative for the NSOPs detection, which holds great potential in practical application for the assessment of food safety and environmental risks.

Multiplex strategy electrochemical platform based on self-assembly dual-site DNA tetrahedral scaffold for one-step detection of diazinon and profenofos

In the work, based on self-assembly dual-site DNA tetrahedral scaffold (DTS), thionine (Thi), and 6-(Ferrocenyl)hexanethiol (Fc6S), a multiplex strategy electrochemical platform was fabricated for the simultaneous detection of profenofos (PFF) and diazinon (DZN). Thi and Fc6S were used to label aptamers for the synthesis of probes respectively. Notably, Thi and Fc6S engendered recognizable DPV peaks at different potentials to achieve simultaneous detection of PFF and DZN. In addition to increasing the conductivity of the electrode, the combination of carboxylic acid functionalized multi-walled carbon nanotubes and ferroferric oxide nanoparticles could also increase its higher specific surface area of the electrode interface to adsorb more DTS. Because of the mechanical rigidity of the DTS, the DTS could keep a complementary chain upright and provide more binding sites for aptamers, the binding efficiency between the complementary chain and 2 binding aptamers could be improved. Comparing the aptasensors performance of single-strand DNA with that of the DTS with complementary strands, the benefits of the DTS were highlighted in this system. Under optimal conditions, the detection limits of PFF and DZN were both 3.33 pg/mL and the detection ranges were both 1.00 × 10¹-1.00 × 10⁷ pg/mL. Meanwhile, the recoveries of PFF and DZN were 87.15%-117.34% and 91.20%-114.19%, respectively. The aptasensor could realize the simultaneous detection of PFF and DZN in vegetables. Furthermore, the aptasensor also had good stability and selectivity. This strategy could provide a good reference for developing effective aptasensors for the simultaneous detection of other small molecules and toxins.

Detection of Emerging Pollutants Using Aptamer-Based Biosensors: Recent Advances, Challenges, and Outlook

The synergistic potentialities of innovative materials that include aptamers have opened new paradigms in biosensing platforms for high-throughput monitoring systems. The available nucleobase functional moieties in aptamers offer exclusive features for bioanalytical sensing applications. In this context, compared to various in-practice biological recognition elements, the utilization of aptamers in detection platforms results in an extensive range of advantages in terms of design flexibility, stability, and sensitivity, among other attributes. Thus, the utilization of aptamers-based biosensing platforms is extensively anticipated to meet unaddressed challenges of various in-practice and standard analytical and sensing techniques. Furthermore, the superior characteristics of aptasensors have led to their applicability in the detection of harmful pollutants present in ever-increasing concentrations in different environmental matrices and water bodies, seeking to achieve simple and real-time monitoring. Considering the above-mentioned critiques and notable functional attributes of aptamers, herein, we reviewed aptamers as a fascinating interface to design, develop, and deploy a new generation of monitoring systems to aid modern bioanalytical sensing applications. Moreover, this review aims to summarize the most recent advances in the development and application of aptasensors for the detection of various emerging pollutants (EPs), e.g., pharmaceutical, and personal care products (PPCPs), endocrine-disrupting chemicals (EDCs), pesticides and other agricultural-related compounds, and toxic heavy elements. In addition, the limitations and current challenges are also reviewed, considering the technical constraints and complexity of the environmental samples.

Nucleic Acid Aptamers for Pesticides, Toxins, and Biomarkers in Agriculture

Nucleic acid aptamers are short single-stranded DNA/RNA (ssDNA/RNA) oligonucleotides that can selectively bind to the targets. They are widely used in medicine, biosensing, and diagnostic assay. They have also been identified and extensively used for various targets in agriculture. In this review we summarize the progress of nucleic acid aptamers on pesticides (herbicides, insecticides, and fungicides), toxins, specific biomarkers of crops, and plant growth regulators in agricultural field in recent years. The basic process of aptamer selection, the already identified DNA/RNA aptamers and the aptasensors are discussed. We also discuss the future perspectives and the challenges for aptamer development in agriculture.

Novel colorimetric aptasensor based on MOF-derived materials and its applications for organophosphorus pesticides determination

For the visual detection of four organophosphorus pesticides (OPs), a colorimetric aptasensor was developed based on aptamer-mediated bimetallic metal-organic frameworks (MOFs) nano-polymers. Fe-Co magnetic nanoparticles (MNPs) and Fe-N-C nanozymes were prepared based on pyrolytic reaction, and were labeled with broad spectrum aptamers and complementary chains of organophosphorus pesticides respectively. The hybridization of aptamers and complementary chains led to the formation of nano-polymers. In the presence of target pesticides, they competed with complementary chains for aptamers on Fe-Co MNPs, resulting in a large number of Fe-N-C nanozymes signal labels being released into the supernatant. Fe-N-C nanozymes showed similar activity to peroxidase and catalyzed the 3,3',5,5'-tetramethylbenzidine-hydrogen peroxide (TMB-H₂O₂) color system to turn the solution blue-green under mild conditions. The magnetic probes had good selectivity and sensitivity, and were easily separated by magnetic absorption. The sensor functioned well under optimal conditions, demonstrating good stability and specificity for four pesticides: phorate, profenofos, isocarbophos and omethoate, and the detection limits of four pesticides were as low as 0.16 ng/mL, 0.16 ng/mL, 0.03 ng/mL and 1.6 ng/mL respectively, and the recovery rate of OPs residue in vegetable samples was satisfactory. The work described here provided a simple, rapid and sensitive way to construct a biosensor.

Fluorescence Assay for Detecting Four Organophosphorus Pesticides Using Fluorescently Labeled Aptamer

In this work, we reported a rapid and sensitive fluorescence assay in homogenous solution for detecting organophosphorus pesticides by using tetramethylrhodamine (TAMRA)-labeled aptamer and its complementary DNA (cDNA) with extended guanine (G) bases. The hybridization of cDNA and aptamer drew TAMRA close to repeated G bases, then the fluorescence of TAMRA was quenched by G bases due to the photoinduced electron transfer (PET). Upon introducing the pesticide target, the aptamer bound to pesticide instead of cDNA because of the competition between pesticide and cDNA. Thus, the TAMRA departed from G bases, resulting in fluorescence recovery of TAMRA. Under optimal conditions, the limits of detection for phorate, profenofos, isocarbophos, and omethoate were 0.333, 0.167, 0.267, and 0.333 µg/L, respectively. The method was also used in the analysis of profenofos in vegetables. Our fluorescence design was simple, rapid, and highly sensitive, which provided a means for monitoring the safety of agricultural products.

Advanced screening and tailoring strategies of pesticide aptamer for constructing biosensor

The rapid development of aptamers has helped address the challenges presented by the wide existed pesticides contaminations. Screening of aptamers with excellent performance is a prerequisite for successfully constructing biosensors, while further tailoring of aptamers with enhanced activity greatly improved the assay performance. Firstly, this paper reviewed the advanced screening strategies for pesticides aptamers, including immobilization screening that preserves the native structures of targets, non-immobilized screening based on nanomaterials, capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX), virtual screening in silico, high-throughput selection, and rational secondary library generation methods, which contributed significantly to improve the success rate of screening, reduce the screening time, and ensure aptamer binding affinity. Secondly, the precise tailoring strategies for pesticides aptamers were modularly elaborated, containing deletion, splitting, elongation, and fusion, which provided various advantages like cost-efficiency, enhanced binding affinity, and new derived functional motifs. Thirdly, the developed aptamer-based biosensors (aptasensors) for pesticide detection were systematically reviewed according to the different signal output modes. Finally, the challenges and future perspectives of pesticide detection are discussed comprehensively.

Green route for recycling of low-cost waste resources for the biosynthesis of nanoparticles (NPs) and nanomaterials (NMs)-A review

Nowadays, nanoparticles (NPs) and nanomaterials (NMs) are used extensively in various streams such as medical science, solar energy, drug delivery, water treatment, and detection of persistent pollutants. Intensive synthesis of NPs/NMs carried out via physico-chemical technologies is deteriorating the environment globally. Therefore, an urgent need to adopt cost-effective and green technologies to synthesize NPs/NMs by recycling of secondary waste resources is highly required. Environmental wastes such as metallurgical slag, electronics (e-waste), and acid mine drainage (AMD) are rich sources of metals to produce NPs. This concept can remediate the environment on the one hand and the other hand, it can provide a future roadmap for economic benefits at industrial scale operations. The waste-derived NPs will reduce the industrial consumption of limited primary resources. In this review article, green emerging technologies involving lignocellulosic waste to synthesize the NPs from the waste streams and the role of potential microorganisms such as microalgae, fungi, yeast, bacteria for the synthesis of NPs have been discussed. A critical insight is also given on use of recycling technologies and the incorporation of NMs in the membrane bioreactors (MBRs) to improve membrane functioning and process performance. Finally, this study aims to mitigate various persisting scientific and technological challenges for the safe disposal and recycling of organic and inorganic waste for future use in the circular economy.

β-Cyclodextrin Polymer-Based Host-Guest Interaction and Fluorescence Enhancement of Pyrene for Sensitive Isocarbophos Detection

The extensive use of organophosphorus pesticides in agriculture poses a high risk to human health and has boosted the demands for developing sensitive monitoring methods. Herein, we developed a facile and sensitive method for isocarbophos detection based on the remarkable fluorescence enhancement of pyrene during host-guest interaction of β-cyclodextrin polymer (β-CDP) and pyrene. The 3'-pyrene-labeled isocarbophos aptamer could be cleaved by exonuclease I to obtain free pyrene that was tagged on mononucleotides, which could enter the hydrophobic cavity of β-CDP, resulting in a prominent fluorescence enhancement. While the target isocarbophos was added, aptamer could undergo a conformational change into a hairpin complex, which prevented the cleavage and host-guest interaction because of the steric hindrance, leading to a weak fluorescence. The isocarbophos has been sensitively and selectively analyzed by detecting the system fluorescence intensity with a detection limit as low as 1.2 μg/L. In addition, we have verified the ability of our proposed method in real sample detection from fruit extract.

Aptamer-binding zirconium-based metal-organic framework composites prepared by two conjunction approaches with enhanced bio-sensing for detecting isocarbophos

A novel label-free and enzyme-free detection strategy has been developed for the electrochemical biosensor detection of isocarbophos (ICP) using UiO-66-NH₂ and aptamer as the signal transducers. In this work, the ICP aptamers were attached to UiO-66-NH₂ through physical mixing and chemical combination methods. In the presence of ICP, the aptamers could undergo conformational change and bind to them, which prevent the electron transfer to the surface of electrode. By comparing the two conjunction approaches of aptasensors, these proposed strategies could selectively and sensitively detect ICP with a detection limit of 6 ng mL^-1 (20.74 nM) and 0.9 ng mL^-1 (3.11 nM). Furthermore, we have also demonstrated the capability of this strategy in the detection of ICP in real samples from vegetable and fruit extract, indicating the potential application of this strategy in food safety issues.

Target-receptive structural switching of ssDNA as selective and sensitive biosensor for subsequent detection of toxic Pb2+ and organophosphorus pesticide

A structural switching in Single-stranded DNA (ssDNA) fluorescence biosensor for quick turn-on/off detection of Pb²⁺ ions and pesticide was reported. The design strategy of Hex-labelled ssDNA consists of two types of aptamer probe, G-rich base pair sequence forms G-quadruplex confirmation with Pb²⁺ ions. While other part of base pair sequence exhibits affinity to fold isocarbophos pesticide. MoS₂ nanosheets were identified as quick quencher of Hex fluorescence intensity via Vander-Waals interaction and its significance was compared with other nanomaterials. This sensing mechanism proposes a specific affinity of GA-rich ssDNA with Pb²⁺ to form G-quadruplex via G-Pb²⁺-G sequences. Consequently, ssDNA relived from MoS₂ nanosheets to restore the fluorescence intensity (turn-on). Subsequent addition of pesticide shows stronger affinity towards unfolded aptamer probe to form a random coil like structure. This causes Hex-labelled 5' end closer to the G-quadruplex connected at the 3' end of ssDNA resulting in a remarkable fluorescence quenching (turn-off) owing to PET process. Moreover, the sensing probe (Hex-labelled GA-rich ssDNA) was recycled by introducing acetylcholinesterase enzyme and thiocoline into the reaction mixture. The detection limits of Pb²⁺ and isocarbophos pesticide was estimated to be 0.6 nM and 0.018 μg/L respectively. Moreover, this study reveals a high sensitivity and selectivity towards target molecules in environmental samples.

A novel electrochemiluminescence aptasensor based on copper-gold bimetallic nanoparticles and its applications

In this work, a novel electrochemiluminescence (ECL) aptasensor was structured for the detection of four organophosphorus pesticides (OPs). Firstly, multi-walled carbon nanotubes (MWCNTs) were used to create a favorable loading interface for the fixation of tris (2, 2'-bipyridyl) ruthenium (II) (Ru (bpy)₃²⁺). At the same time, copper (core)-gold (shell) bimetallic nanoparticles (Cu@Au NPs) were synthesized in the aqueous phase for the sensor construction. Gold nanoparticles (Au NPs) could promote the electrochemiluminescence intensity of Ru (bpy)₃²⁺ with high efficiency by catalyzing the oxidation process of tri-n-propylamine (TPrA). Compared with the Au NPs, Cu@Au NPs increased the solid loading of Au NPs by virtue of the large specific surface area of copper nanoparticles (Cu NPs), which could further improve the sensitivity of aptasensor. When OPs were added, the ECL intensity was significantly reduced, and the concentration of OPs could be detected through the ECL intensity. Under the optimum conditions, the aptasensor had a wider dynamic range and ultra-low detection limit for the detection of four pesticides: profenofos, isocarbophos, phorate, and omethoate, and their detection limits were 3 × 10^-4 ng/mL, 3 × 10^-4 ng/mL, 3 × 10^-3 ng/mL, and 3 × 10^-2 ng/mL respectively (S/N = 3). The aptasensor had the merits of good stability, reproducibility, and specificity, and had a favorable recovery rate in detecting OPs residues in vegetables. This work provided an effective method for the construction of a simple, rapid, and sensitive biosensor.

Recognition elements based on the molecular biological techniques for detecting pesticides in food: A review

Excessive use of pesticides can cause contamination of the environment and agricultural products that are directly threatening human life and health. Therefore, in the process of food safety supervision, it is crucial to conduct sensitive and rapid detection of pesticide residues. The recognition element is the vital component of sensors and methods for fast testing pesticide residues in food. Improper recognition elements may lead to defects of testing methods, such as poor stability, low sensitivity, high economic costs, and waste of time. We can use the molecular biological technique to address these challenges as a good strategy for recognition element production and modification. Herein, we review the molecular biological methods of five specific recognition elements, including aptamers, genetic engineering antibodies, DNAzymes, genetically engineered enzymes, and whole-cell-based biosensors. In addition, the application of these identification elements combined with biosensor and immunoassay methods in actual detection was also discussed. The purpose of this review was to provide a valuable reference for further development of rapid detection methods for pesticide residues.

Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method

The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (Apt_EpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the Apt_EpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the Apt_EpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For Apt_EpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each Apt_EpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable Apt_EpA/EpCAM complex in water.

Anti-pesticide DNA aptamers fail to recognize their targets with asserted micromolar dissociation constants

Herein, we originally aimed at developing fluorescence anisotropy biosensor platforms devoted to the homogeneous-phase detection of isocarbophos and phorate pesticides by using previously isolated DNA aptamers. To achieve this, two reporting approaches displaying very high generalizability features were implemented, based on either the complementary strand or the SYBR green intercalator displacement strategies. Unfortunately, none of the transduction methods led to phorate-dependent signals. Only the SYBR green displacement method provided a small output in the presence of isocarbophos, but at an analyte concentration greater than 100 μM. In order to identify the origin of such data, isothermal titration calorimetry (ITC) experiments were subsequently performed. It was shown that aptamers bind neither isocarbophos nor phorate in free solution with the claimed micromolar dissociation constants. This work puts forward some doubts about the previously described aptasensors that rely on the use of these functional DNA molecules. It also highlights the need to carefully investigate the binding capabilities of aptamers after their isolation and to include appropriate control experiments with scrambled or mutated oligonucleotides.

Capture-SELEX for aptamer selection: A short review

The emerging aptamer, developed through the systematic evolution of ligands by exponential enrichment (SELEX) process, has revolutionized and facilitated the discoveries in basic research. Among all SELEX technology, Capture-SELEX is a variant of the in vitro selection process, which is suitable for isolating aptamers against small molecules. Capture-SELEX library was developed to enable the immobilization of the oligonucleotides instead of the target molecules during the aptamer selection process. The review provides an update on the recent-advances in this new screening method with particular emphasis on key points of capture protocol and its applications. The limitations and the prospects of the Capture-SELEX are also discussed. We hope that present review will inspire more researchers to understand the selection problems from the perspective of Capture-SELEX. Moreover, it will open new pave to improve the efficiency and success of screening to meet the growing demand for aptasensor discovery in small molecules.

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.

Pesticide Aptasensors-State of the Art and Perspectives

Contamination by pesticides in the food chain and the environment is a worldwide problem that needs to be actively monitored to ensure safety. Unfortunately, standard pesticide analysis based on mass spectrometry takes a lot of time, money and effort. Thus, simple, reliable, cost-effective and field applicable methods for pesticide detection have been actively developed. One of the most promising technologies is an aptamer-based biosensor or so-called aptasensor. It utilizes aptamers, short single-stranded DNAs or RNAs, as pesticide recognition elements to integrate with various innovative biosensing technologies for specific and sensitive detection of pesticide residues. Several platforms for aptasensors have been dynamically established, such as colorimetry, fluorometry, electrochemistry, electrochemiluminescence (ECL) and so forth. Each platform has both advantages and disadvantages depending on the purpose of use and readiness of technology. For example, colorimetric-based aptasensors are more affordable than others because of the simplicity of fabrication and resource requirements. Electrochemical-based aptasensors have mainly shown better sensitivity than others with exceedingly low detection limits. This paper critically reviews the progression of pesticide aptasensors throughout the development process, including the selection, characterization and modification of aptamers, the conceptual frameworks of integrating aptamers and biosensors, the ASSURED (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free and deliverable to end users) criteria of different platforms and the future outlook.

Recent advances in computational methods for biosensor design

Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.

Photoresponsive Surface Molecularly Imprinted Polymers for the Detection of Profenofos in Tomato and Mangosteen

As a moderately toxic organophosphorus pesticide, profenofos (PFF) is widely used in agricultural practice, resulting in the accumulation of a high amount of PFF in agricultural products and the environment. This will inevitably damage our health. Therefore, it is important to establish a convenient and sensitive method for the detection of PFF. This paper reports a photoresponsive surface-imprinted polymer based on poly(styrene-co-methyl acrylic acid) (PS-co-PMAA@PSMIPs) for the detection of PFF by using carboxyl-capped polystyrene microspheres (PS-co-PMAA), PFF, 4-((4-(methacryloyloxy)phenyl)diazenyl) benzoic acid, and triethanolamine trimethacrylate as the substrate, template, functional monomer, and cross-linker, respectively. PS-co-PMAA@PSMIP shows good photoresponsive properties in DMSO/H2O (3:1, v/v). Its photoisomerization rate constant exhibits a good linear relationship with PFF concentration in the range of 0~15 μmol/L. PS-co-PMAA@PSMIP was applied for the determination of PFF in spiked tomato and mangosteen with good recoveries ranging in 94.4-102.4%.

Fullerol Nanocatalysis and Trimodal Surface Plasmon Resonance for the Determination of Isocarbophos

Fullerol (C₆₀OH) has been shown to catalyze the trisodium citrate (TSC)-silver nitrate reaction to generate Ag nanoparticles (AgNPs). These AgNPs exhibit significant nanoplasmic surface-enhanced Raman scattering (SERS), resonance Rayleigh scattering (RRS), and absorption (Abs). When an aptamer (Apt) adsorbs on the C₆₀OH surface, catalysis is inhibited, and the intensities of SERS, RRS, and Abs decrease. In the presence of isocarbophos (IPS), Apt forms a stable complex (Apt-IPS) and releases C₆₀OH. As a result, SERS, RRS, and Abs intensities increase with increasing IPS concentration. Accordingly, a new SERS, RRS, and Abs trimodal method using Apt-labeled fullerol was established for the determination of IPS. Of the three spectral methods, SERS was the most sensitive, while the Abs method was the most cost-effective.

Fabrication of refreshable aptasensor based on hydrophobic screen-printed carbon electrode interface

In order to solve the problem that the sensor cannot be reused due to the passivation of the electrode surface, a refreshable electrochemical aptasensor based on a hydrophobic electrode and a magnetic nanocomposite had been developed. Therein, the hydrophobic electrode was formed by modifying a screen-printed carbon electrode (SPCE) with polydimethylsiloxane (PDMS), which could avoid adsorption of molecules on the electrode surface due to its hydrophobicity. Combined with aptamer (Apt), the synthesized graphene oxide-ferroferric oxide (GO-Fe₃O₄) was used as a magnetic catcher to capture specific organophosphorus pesticides (OPs), which could be removed to the working area of SPCE with a magnet for electrochemical detection. The performance analysis of hydrophobic electrode showed that the SPCE could be used twice. When the electrochemical signals of Apt/GO-Fe₃O₄ and OPs/Apt/GO-Fe₃O₄ were recorded using the same SPCE, the current differences between them were directly related to the concentrations of OPs. Through the contrast test between the spiked vegetable samples and the OPs standard solutions, it was found that the OPs concentrations could be qualitatively evaluated by comparing the current differences. At the same time, the characteristic of collecting target with magnetic catcher was helpful for detecting OPs with a low concentration. Therefore, the refreshable aptasensor provided a huge potential to small molecule target evaluation.

Fluorescence assay for three organophosphorus pesticides in agricultural products based on Magnetic-Assisted fluorescence labeling aptamer probe

There has been increasing recent concern about the agricultural use of organophosphorus pesticides. A rapid and sensitive fluorescence assay for the detection of three organophosphorus pesticides has therefore been developed using 6-carboxy-fluorescein labeling aptamer as the probe and functionalized magnetic nanoparticles as the separation carrier. The aptamer hybridized with complementary DNA conjugated on the surface of the magnetic nanoparticles to form a magnetic aptamer-complementary DNA complex. Upon introducing the target organophosphorus pesticide, the aptamer departed from the complementary DNA, resulting in the fluorescence signal. Under optimized conditions, the limits of detection (LODs, S/N = 3) for trichlorfon, glyphosate, and malathion were 72.20 ng L-1, 88.80 ng L-1, and 195.37 ng L-1, respectively. The method was applied for the detection of trichlorfon, glyphosate, and malathion in spiked lettuce and carrot samples. The recoveries were in the range of 79.4%-118.7%, which were in good agreement with those obtained by gas chromatography, and the relative standard deviations were also acceptable. The method therefore has high sensitivity, so provides a means for the detection of multiple organophosphorus pesticides.

Voltammetric determination of organophosphorus pesticides using a hairpin aptamer immobilized in a graphene oxide-chitosan composite

An aptasensor is described for electrochemical determination of organophosphorus pesticides (OPPs), specifically of profenofos, phorate, isocarbophos, and omethoate. The method uses a hairpin aptamer as signalling donor. Its 5' and 3' ends were modified with amino groups and the redox probe ferrocene (Fc), respectively. A nanocomposite consisting of graphene oxide and chitosan (GO-chit) was used to immobilize the aptamer via formation of an amide link. Its good conductivity facilitates monitoring of the electrochemical responses. Upon addition of an OPP, it will be bound by the aptamer. This results in an opening of the hairpin structure. Thus, Fc is shifted away from the surface of the electrode. As a result, the impedance increases and the redox signal of Fc decreases. The electrochemical performance, binding capacity and response of the aptasensor for profenofos, phorate, isocarbophos and omethoate were studied. The limits of detection are as low as 0.01, 0.1, 0.01 and 0.1 nM, respectively. Graphical abstract Schematic representation of an electrochemical aptasensor prepared by immobilizing ferrocene (Fc) labeled hairpin aptamer (HP) on the surface of graphene oxide-chitosan (GO-chit) modified electrode, and its application to the determination of organophosphorus pesticides (OPPs) by voltammetry.

Dual-modal aptasensor for the detection of isocarbophos in vegetables

An aptamer-based colorimetric-phosphorescent assay was developed for the detection of isocarbophos. The colorimetric assay relied on the aggregation of gold nanoparticles (AuNPs) caused by the competitive binding of aptamer between isocarbophos and AuNPs in the presence of a high salt concentration. The further addition of persistent luminescence nanorods (PLNRs) into the system showed the phosphorescence sensitively proportional to the concentration of isocarbophos, due to the inner filter effect between PLNRs and AuNPs. The assay showed good linearity within 50-500 μg/L and 5-160 μg/L, and limit of detection of 7.1 μg/L and 0.54 μg/L in colorimetry and phosphorescence mode, respectively. The feasibility of this approach for food analysis was demonstrated with the sensitive and selective determination of isocarbophos residues in vegetables.

Oligonucleotides and pesticide regulated peroxidase catalytic activity of hemin for colorimetric detection of isocarbophos in vegetables by naked eyes

A novel colorimetric sensing platform based on the peroxidase activity of hemin regulated by oligonucleotide and pesticide was reported for the ultrasensitive and selective detection of isocarbophos. Oligonucleotides can accumulate on the surface of hemin in acid condition and temporarily inhibit its catalytic activity, which results in the loss of one electron of TMB molecule and produce the blue products. With the addition of isocarbophos, the pesticide molecules can interact with oligonucleotides to form some complexes, which relieve the inhibition of ssDNA to hemin and further enhance its catalytic activity. Thus, the TMB molecules are further oxidized to lose another electron and produce the yellow product in a few minutes, which has the characteristic absorption peak at 450 nm. The color change of the sensing system is related to the amount of isocarbophos, so this method can quickly discriminate whether the target pesticide exceeds the maximal residue limit just by naked eyes. To improve the performance of sensing platform, some important parameters like buffer condition and ssDNA have been investigated, and the peroxidase activity of hemin was further studied to verify the catalytic mechanism. The proposed sensing platform has a detection limit as low as 0.6 μg/L and displays good selectivity against other competitive pesticides. Moreover, the developed sensing platform also exhibits favorable accuracy and stability, indicating that it has potential applications in the detection of pesticide residues in agricultural products. Graphical abstract A novel colorimetric sensing platform based on oligonucleotides and pesticide regulation; the peroxidase catalytic activity of hemin was firstly reported for the ultrasensitive and selective detection of isocarbophos pesticide.

Rational in silico design of aptamers for organophosphates based on the example of paraoxon

Poisoning by organophosphates (OPs) takes one of the leading places in the total number of exotoxicoses. Detoxication of OPs at the first stage of the poison entering the body could be achieved with the help of DNA- or RNA-aptamers, which are able to bind poisons in the bloodstream. The aim of the research was to develop an approach to rational in silico design of aptamers for OPs based on the example of paraoxon. From the published sequence of an aptamer binding organophosphorus pesticides, its three-dimensional model has been constructed. The most probable binding site for paraoxon was determined by molecular docking and molecular dynamics (MD) methods. Then the nucleotides of the binding site were mutated consequently and the values of free binding energy have been calculated using MD trajectories and MM-PBSA approach. On the basis of the energy values, two sequences that bind paraoxon most efficiently have been selected. The value of free binding energy of paraoxon with peripheral anionic site of acetylcholinesterase (AChE) has been calculated as well. It has been revealed that the aptamers found bind paraoxon more effectively than AChE. The peculiarities of paraoxon interaction with the aptamers nucleotides have been analyzed. The possibility of improving in silico approach for aptamer selection is discussed.