Colorimetric aptasensor targeting zearalenone developed based on the hyaluronic Acid-DNA hydrogel and bimetallic MOFzyme

Magnetic aptamer copper nanoclusters fluorescent biosensor for the visual detection of zearalenone based on docking-aided rational tailoring

To address the food safety issues caused by toxins, we established a fluorescent copper nanocluster biosensor based on magnetic aptamer for the visual and quantitative detection of ZEN. Specifically, we utilized the docking-aided rational tailoring (DART) strategy to analyze intermolecular force and interaction sites between zearalenone (ZEN) and the aptamer, and optimize the long-chain aptamer step by step to enhance the binding affinity by 3.4 times. The magnetic bead-modified aptamer underwent conformational changes when competing with complementary sequences to bind with ZEN. Then, the released complementary sequences will be amplified in template-free mode with the presence of the terminal deoxynucleotidyl transferase (TdT), and generating T-rich sequences as the core sequences for the luminescence of copper nanoclusters. The luminescence could be visualized and quantitatively detected through ultraviolet irradiation. The proposed label-free aptasensor exhibited high sensitivity and specificity, with a low limit of detection (LOD) of 0.1 ng/mL.

Hydrogel-integrated sensors for food safety and quality monitoring: Fabrication strategies and emerging applications

Food safety is a global issue in public hygiene. The accurate, sensitive, and on-site detection of various food contaminants performs significant implications. However, traditional methods suffer from the time-consuming and professional operation, restricting their on-site application. Hydrogels with the merits of highly porous structure, high biocompatibility, good shape-adaptability, and stimuli-responsiveness offer a promising biomaterial to design sensors for ensuring food safety. This review describes the emerging applications of hydrogel-based sensors in food safety inspection in recent years. In particular, this study elaborates on their fabrication strategies and unique sensing mechanisms depending on whether the hydrogel is stimuli-responsive or not. Stimuli-responsive hydrogels can be integrated with various functional ligands for sensitive and convenient detection via signal amplification and transduction; while non-stimuli-responsive hydrogels are mainly used as solid-state encapsulating carriers for signal probe, nanomaterial, or cell and as conductive media. In addition, their existing challenges, future perspectives, and application prospects are discussed. These practices greatly enrich the application scenarios and improve the detection performance of hydrogel-based sensors in food safety detection.

A G-quadruplex-assisted target-responsive dual-mode aptasensor based on copper nanoclusters synthesized in situ in a DNA hydrogel for ultrasensitive detection of ochratoxin A

Developing ultrasensitive sensing platforms for trace ochratoxin A (OTA) in food safety is still challenging. Herein, we presented a novel dual-mode sensing strategy for fluorescence and colorimetric detection of OTA by combining the target-responsive hemin-encapsulated and copper nanoclusters (CuNCs) functionalized DNA hydrogel. Through simple assembly and in situ synthesis methods, fluorescence CuNCs are synthesized and modified on the 3D hydrophilic network structure of DNA cross-linked. OTA specifically recognized by Apt-linker can control the collapse of hydrogel, resulting in the fluorescence quenching of CuNCs and release of coated hemin. Interestingly, OTA could trigger Apt-linker conformational changes to form G-quadruplex structures, allowing the released hemin to form G-quadruplex/hemin DNAzyme via self-assembly. Fluorescence signal amplification could be achieved through further fluorescence quenching of CuNCs caused by DNAzyme-catalyzed hydrogen peroxide (H2O2) because of the peroxidase activity of DNAzyme. Simultaneously, DNAzyme could catalyze the H2O2-mediated oxidation of TMB to provide colorimetric signal. Thereafter, the DNA-CuNCs hydrogel exhibited low detection limits of 3.49 pg/mL in fluorescence mode and 0.25 ng/mL in colorimetric modality. Real sample analyses of foodstuffs showed satisfactory results, providing prospective potential for monitoring mycotoxin contaminant.

Preparation Strategies, Functional Regulation, and Applications of Multifunctional Nanomaterials-Based DNA Hydrogels

With the extensive attention of DNA hydrogels in biomedicine, biomaterial, and other research fields, more and more functional DNA hydrogels have emerged to match the various needs. Incorporating nanomaterials into the hydrogel network is an emerging strategy for functional DNA hydrogel construction. Surprisingly, nanomaterials-based DNA hydrogels can be engineered to possess favorable properties, such as dynamic mechanical properties, excellent optical properties, particular electrical properties, perfect encapsulation properties, improved magnetic properties, and enhanced antibacterial properties. Herein, the preparation strategies of nanomaterials-based DNA hydrogels are first highlighted and then different nanomaterial designs are used to demonstrate the functional regulation of DNA hydrogels to achieve specific properties. Subsequently, representative applications in biosensing, drug delivery, cell culture, and environmental protection are introduced with some selected examples. Finally, the current challenges and prospects are elaborated. The study envisions that this review will provide an insightful perspective for the further development of functional DNA hydrogels.

A bimetallic organic framework based fluorescent aptamer probe for the detection of zearalenone in cereals

In this work, a bimetallic organic framework (Cu/UiO-66) based "turn on" fluorescent aptamer probe was designed for the high-efficiency detection of zearalenone (ZEN). In the probe, the 6-carboxyfluorescein-labeled aptamer (FAM-Apt) was used as the recognition element, and the electrostatic interaction, coordination effect, and photoinduced electron transfer effect between FAM-Apt and Cu/UiO-66 caused fluorescence quenching. When ZEN existed, FAM-Apt recognized ZEN specifically, causing FAM-Apt to separate from the surface of Cu/UiO-66 and recovery of fluorescence. Under the optimal conditions, the probe had a linear detection range of 0.5 ng/mL-60 ng/mL, and the detection limit was 0.048 ng/mL. The application potential of the probe was verified by real detection of various cereals and their products, with a standard recovery from 83.67 %-106.8 %. The development of this efficient, rapid, and sensitive ZEN detection method provides a new platform for the quality control of cereals and their products.

A colorimetric sensor array based on nanoceria crosslinked and heteroatom-doped graphene oxide nanoribbons for the detection and discrimination of multiple pesticides

Nanozymes have demonstrated high potential in constructing colorimetric sensor array for pesticides. However, rarely array for pesticides constructed without bio-enzyme were reported. Herein, nanoceria crosslinked graphene oxide nanoribbons (Ce-GONRs) and heteroatom-doped graphene oxide nanoribbons (Ce-BGONRs and Ce-NGONRs) were prepared, demonstrating excellent peroxidase-like activities. A colorimetric sensor array was developed based on directly inhibiting the peroxidase-like activities of the above three nanozymes, which realized the discrimination and quantitative analysis of six pesticides. In the presence of pesticides including carbaryl (Car), fluroxypyr-mepthyl (Flu), thiophanate-methyl (Thio), thiram (Thir), diafenthiuron (Dia) and fomesafen (Fom), the peroxidase-like activities of three nanozymes were inhibited to different degrees, resulting in different fingerprint responses. The six pesticides in the concentration range of 0.1-50 μg/mL and two pesticides mixtures at varied ratios could be detected and discriminated, and minimum detection limit for pesticides was 0.022 μg/mL. In addition, this sensor array has been successfully applied for pesticides discrimination in lake water and apple samples. This work provided a new strategy of constructing simple and sensitive colorimetric sensor array for pesticides based on directly inhibiting the catalytic activities of nanozymes.

Colorimetric and photothermal dual-mode immunosensor based on Ti3C2Tx/AuNPs nanocomposite with enhanced peroxidase-like activity for ultrasensitive detection of zearalenone in cereals

A novel peroxidase-like nanozyme has been constructed by decorating two-dimensional Ti3C2Tx nanosheets (Ti3C2Tx NSs) with gold nanoparticles (AuNPs) to develop a colorimetric and photothermal dual-mode immunosensor. The Ti3C2Tx/AuNPs nanocomposite-catalyzed 3,3',5,5'-tetramethylbenzidine (TMB)-H2O2 reaction system produces the one-electron oxidation product of TMB (oxTMB), which exhibits color change and strong near-infrared (NIR) laser-driven photothermal effect at 808 nm laser irradiation. Given these characteristics, the developed immunosensor achieves ultrasensitive dual-mode detection of zearalenone (ZEN) by measuring colorimetric and photothermal signals with a microplate reader and a portable infrared thermometer, respectively. Under optimal working conditions, the limit of detection (LOD) of ZEN is 0.15 pg mL-1 for the colorimetric mode and 0.48 pg mL-1 for the photothermal mode. In the analysis of actual contaminated cereals samples, the test result of this method was consistent with that of UPLC-MS/MS. The proposed colorimetric and photothermal dual-mode immunosensor offers a new strategy for the low-cost detection of hazardous substances. The application of a widely used household infrared thermometer makes the signal readout more convenient, which provides great prospects in food safety and environment inspection applications.

The Establishment of a Tobramycin-Responsive Whole-Cell Micro-Biosensor Based on an Artificial Ribozyme Switch

In this study, a tobramycin concentration-dependent whole-cell micro-biosensor (tob-HHAz) was constructed by fusing a tobramycin aptamer with a hammerhead ribozyme (HHR) from Schistosoma mansoni. The biosensor was obtained by integrating all the modules into one complete RNA sequence, which was easily introduced into E. coli without suffering from harsh external environments. Three independent tobramycin-sensitive RNA structures were identified via high-throughput screening in vivo and were further verified in vitro to undergo the desired self-cleavage reaction. The computation prediction of the RNA structure was performed to help analyze the mechanisms of various conformations by performing a qualitative and rapid detection of tobramycin in practical samples; two sensors exhibited high responsiveness to spiked milk, with a detection limit of around 40 nM, which is below the EU's antibiotic maximum residual level. One of the structures provides a linear range from 30 to 650 nM with a minimum detection limit of 30 nM and showed relatively good selectivity in spiked urine. This study is the first in which in vivo screening was combined with computation analysis to optimize the pivotal structure of sensors. This strategy enables researchers to use artificial ribozyme-based biosensors not only for antibiotic detection but also as a generally applicable method for the further detection of substances in living cells.

Novel insights into versatile nanomaterials integrated bioreceptors toward zearalenone ultrasensitive discrimination

Detrimental contamination of zearalenone (ZEN) in crops and foodstuffs has drawn intensive public attention since it poses an ongoing threat to global food security and human health. Highly sensitive and rapid response ZEN trace analysis suitable for complex matrices at different processing stages is an indispensable part of food production. Conventional detection methods for ZEN encounter many deficiencies and demerits such as sophisticated equipment and heavy labor intensity. Alternatively, the nanomaterial-based biosensors featured with high sensitivity, portability, and miniaturization are springing up and emerging as superb substitutes to monitor ZEN in recent years. Herein, we predominantly devoted to overview the progress in the fabrication strategies and applications of various nanomaterial-based biosensors, highlighting rationales on sensing mechanisms, response types, and practical analytical performance. Synchronously, the versatile nanomaterials integrating with diverse recognition elements for augmenting sensing capabilities are emphasized. Finally, critical challenges and perspectives to expedite ZEN detection are outlooked.

Study of binding mechanism of aptamer to kanamycin and the development of fluorescent aptasensor in milk detection

Aptasensors being versatile sensing platforms presented higher sensitivity toward target detection. However, lacking theoretical basis of recognition between most targets and their corresponding aptamers has impeded their applications. Herein, we conducted a study to explore the binding mechanism of aptamer to kanamycin (Kana) and developed rapid fluorescent aptasensing methods. Based on the fluorescence polarization results, base mutations were performed at different sites of the aptamer. The key binding nucleotides of Kana was identified as T7, T8, C13 and A15 by using isothermal titration calorimetry (ITC). The Kmut3 (2.18 μM) with lower dissociation constants (Kd), one-third of the native aptamer (6.91 μM), was also obtained. In addition, the lower K⁺ concentration and temperature were found to be conducive to Kana binding. Circular dichroism (CD) results revealed that the binding of Kana can trigger the change of base stacking force and helix force. On the aforementioned basis, a fluorescent sensor was designed with the native aptamer and Kmut3 as recognition elements. The comparison results proved that the Kmut3 presented a 3 times lower limit of detection of 59 nM compared to the native aptamer (148 nM). Notably, this developed aptasensor can be finished in 45 min and was convenient to operate.

Stimulus-Responsive DNA Hydrogel Biosensors for Food Safety Detection

Food safety has always been a major global challenge to human health and the effective detection of harmful substances in food can reduce the risk to human health. However, the food industry has been plagued by a lack of effective and sensitive safety monitoring methods due to the tension between the cost and effectiveness of monitoring. DNA-based hydrogels combine the advantages of biocompatibility, programmability, the molecular recognition of DNA molecules, and the hydrophilicity of hydrogels, making them a hotspot in the research field of new nanomaterials. The stimulus response property greatly broadens the function and application range of DNA hydrogel. In recent years, DNA hydrogels based on stimulus-responsive mechanisms have been widely applied in the field of biosensing for the detection of a variety of target substances, including various food contaminants. In this review, we describe the recent advances in the preparation of stimuli-responsive DNA hydrogels, highlighting the progress of its application in food safety detection. Finally, we also discuss the challenges and future application of stimulus-responsive DNA hydrogels.

Colorimetric aptasensor for fumonisin B1 detection based on the DNA tetrahedra-functionalized magnetic beads and DNA hydrogel-coated bimetallic MOFzyme

The toxicity and incidence of fumonisin B₁ (FB₁) pose a major challenge to public health and the environment, prompting the development of alternative quantitative strategies for FB₁. Herein, a colorimetric aptasensor was constructed based on DNA tetrahedra-functionalized magnetic beads (MBs) and DNA hydrogel-coated Mn-Zr bimetallic metal-organic frameworks-based nanozyme (MOFzyme). Initially, MBs functionalized by DNA tetrahedra demonstrated excellent capturing capability for FB₁. Along with the capture of FB₁, catalyst DNA (C) was released into the supernatant. Aided by fuel DNA (F), C can trigger continuous cleavage of the main chains and cross-linking points of the DNA hydrogel through an entropy-driven DNA circuit integrated into the hydrogel coating. Subsequently, the bimetallic MOFzyme encapsulated inside the DNA hydrogel was exposed and exerted its superb peroxidase-like activity, producing a colorimetric signal whose intensity was positively dependent on the amount of FB₁. The developed aptasensor exhibited good linearity in the range of 5 × 10^-4 to 50 ng mL^-1 with a limit of detection (LOD) of 0.38 pg mL^-1, and reasonable specificity in different matrices. Furthermore, the aptasensor was successfully applied to quantify FB₁ in actual samples with recoveries fell within 92.25 %- 108.00 %, showing its great potential in environmental monitoring and food safety.

Advances in riboswitch-based biosensor as food samples detection tool

Food safety has always been a hot issue of social concern, and biosensing has been widely used in the field of food safety detection. Compared with traditional aptamer-based biosensors, aptamer-based riboswitch biosensing represents higher precision and programmability. A riboswitch is an elegant example of controlling gene expression, where the target is coupled to the aptamer domain, resulting in a conformational change in the downstream expression domain and determining the signal output. Riboswitch-based biosensing can be extensively applied to the portable real-time detection of food samples. The numerous key features of riboswitch-based biosensing emphasize their sustainability, renewable, and testing, which promises to transform engineering applications in the field of food safety. This review covers recent developments in riboswitch-based biosensors. The brief history, definition, and modular design (regulatory mode, reporter, and expression platform) of riboswitch-based biosensors are explained for better insight into the design and construction. We summarize recent advances in various riboswitch-based biosensors involving theophylline, malachite green, tetracycline, neomycin, fluoride, thrombin, naringenin, ciprofloxacin, and paromomycin, aiming to provide general guidance for the design of riboswitch-based biosensors. Finally, the challenges and prospects are also summarized as a way forward stratagem and signs of progress.

Design and application of stimuli-responsive DNA hydrogels: A review

Deoxyribonucleic acid (DNA) hydrogels combine the properties of DNAs and hydrogels, and adding functionalized DNAs is key to the wide application of DNA hydrogels. In stimuli-responsive DNA hydrogels, the DNA transcends its application in genetics and bridges the gap between different fields. Specifically, the DNA acts as both an information carrier and a bridge in constructing DNA hydrogels. The programmability and biocompatibility of DNA hydrogel make it change macroscopically in response to a variety of stimuli. In order to meet the needs of different scenarios, DNA hydrogels were also designed into microcapsules, beads, membranes, microneedle patches, and other forms. In this study, the stimuli were classified into single biological and non-biological stimuli and composite stimuli. Stimuli-responsive DNA hydrogels from the past five years were summarized, including but not limited to their design and application, in particular logic gate pathways and signal amplification mechanisms. Stimuli-responsive DNA hydrogels have been applied to fields such as sensing, nanorobots, information carriers, controlled drug release, and disease treatment. Different potential applications and the developmental pro-spects of stimuli-responsive DNA hydrogels were discussed.

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DNA hydrogel, favored by researchers, combines properties of DNA and hydrogels.

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Both DNA and skeleton, having many response characteristics, can respond to stimuli.

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Sensing, nano robots, information carriers, drug delivery, and disease treatment uses.

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Three stimulus response types: single biological, single abiotic and compound.

Recent Progress in Aptamer-Functionalized Metal-Organic Frameworks-Based Optical and Electrochemical Sensors for Detection of Mycotoxins

Mycotoxin contamination in foodstuffs and agricultural products has posed a serious hazard to human health and raised international concern. The progress of cost-effective, facile, rapid and reliable analytical tools for mycotoxin determination is in urgent need. In this regard, the potential utility of metal-organic frameworks (MOFs) as a class of crystalline porous materials has sparked immense attention due to their large specific surface area, adjustable pore size, nanoscale framework structure and good chemical stability. The amalgamation of MOFs with high-affinity aptamers has resulted in the progress of advanced aptasensing methods for clinical and food/water safety diagnosis. Aptamers have many advantages over classical approaches as exceptional molecular recognition constituents for versatile bioassays tools. The excellent sensitivity and selectivity of the MOF-aptamer biocomposite nominate them as efficient lab-on-chip tools for portable, label-free, cost-effective and real-time screening of mycotoxins. Current breakthroughs in the concept, progress and biosensing applications of aptamer functionalized MOFs-derived electrochemical and optical sensors for mycotoxins have been discussed in this study. We first highlighted an overview part, which provides some insights into the functionalization mechanisms of MOFs with aptamers, offering a foundation to create MOFs-based aptasensors. Then, we discuss various strategies to design high-performance MOFs-based aptamer scaffolds, which serve as either signal nanoprobe carriers or signal nanoprobes and their applications. We perceived that applications of optical aptamers are in their infancy in comparison with electrochemical MOFs-derived aptasensors. Finally, current challenges and prospective trends of MOFs-aptamer sensors are discussed.