DNAzyme-powered DNA walking machine for ultrasensitive fluorescence aptasensing of kanamycin

Application and development of signal amplification strategy in detection of antibiotic residues in food

Food is essential for the proper functioning of the human body, and small molecule contaminants, such as antibiotics, have become a growing concern due to their harmful effects on both biological systems and the environment. These contaminants can enter the food supply through the use of antibiotics in animals, potentially causing significant health and ecological damage. As a result, detecting these pollutants, especially at trace levels, has become increasingly important. Aptamer sensors have gained popularity for this purpose because of their high stability, specificity, ease of modification, and low cost. To improve the sensitivity of these sensors, various signal enhancement strategies are used. These strategies aim to better detect small molecule contaminants, with many relying on nanomaterials and nucleic acid amplification techniques to amplify signals. Nanomaterials, which come in different forms such as zero-dimensional, one-dimensional, two-dimensional, and three-dimensional, play a crucial role in improving the performance of these sensors. This article provides an overview of these signal enhancement approaches, discussing the challenges and potential future directions for the development of aptamers in food contamination detection.

Recent Advances of Fluorescent Aptasensors for the Detection of Antibiotics in Food

Antibiotics can accumulate in the body via ingestion, presenting serious health and safety risks to humans, and have garnered extensive international attention in recent years. Meanwhile, aptamers have been applied in the detection of antibiotics, mainly because of their good stability, high specificity, easy synthesis, and low cost. Among various kinds of aptasensors, fluorescent dye-based or nanomaterial-based fluorescent aptasensors serve as highly efficient tools for the rapid quantification of antibiotics owing to their remarkable sensitivity, specificity, and selectivity. In addition, some novel techniques such as aptamer tailoring, signal amplification, and artificial intelligence for aptasensors are also presented. This paper provides a detailed and comprehensive review of fluorescent aptasensors for antibiotic detection. Moreover, it pinpoints the challenges encountered during the development of the aforesaid fluorescent aptasensors and puts forward future research directions.

A novel photoelectrochemical aptasensor based on 3D flower-like g-C3N4/BiOI p-n heterojunction for the sensitive detection of kanamycin

BACKGROUND

Kanamycin (KAN) residues in animal-derived foods continuously enter the human body, which will pose serious threats to human health such as hearing loss, nephrotoxicity and other complications. Therefore, to sensitively detect KAN residues by a reliable technology is extremely urgent in food quality and safety. Compared with traditional methods being limited by cost and complexity, photoelectrochemical (PEC) biosensors benefit from some merits such as rapid response, excellent sensitivity and good stability. In this study, the construction of a highly efficient PEC platform to realize KAN residues detection is discussed.

RESULTS

Herein, a novel p-n heterojunction consisting of flower-like BiOI microspheres and graphite carbon nitride (g-C3N4) nanoflakes was developed to establish a PEC aptasensor for KAN detection at 0 V. The prepared g-C3N4/BiOI heterostructure showed not only significantly enhanced PEC activity due to the larger specific surface area but also greatly increased charge separation efficiency owing to the strong internal electric field. Meanwhile, using g-C3N4/BiOI as a highly efficient photoactive material for binding amine-functionalized aptamers to capture KAN, the photocurrent signals showed a 'turn off' mode to achieve the sensitive detection of KAN. The proposed PEC aptasensor exhibited linear response for KAN from 5 × 10-9 to 3 × 10-7 mol L-1 with a low detection limit of 1.31 × 10-9 mol L-1, and satisfactory recoveries (97.44-107.38 %) were obtained in real food samples analysis.

SIGNIFICANCE

This work presented a novel p-n heterojunction-based PEC aptasensor with strong selectivity and stability, rendering it allowed to detect KAN in animal-derived foods including milk, honey and pork. Additionally, the detection range satisfied the MRLs for KAN specified by the national standards, demonstrating the potential application for food analysis. The study provides a new insight into the development of efficient and practical biosensors for antibiotic residues detection.

Antibody-Bridged DNAzyme Walker for Sensitive Detection of Small Molecules

Sensitive detection of small molecules with biological and environmental interests is important for many applications, such as food safety, disease diagnosis, and environmental monitoring. Herein, we propose a highly selective antibody-bridged DNAzyme walker to sensitively detect small molecules. The antibody-bridged DNAzyme walker consists of a track, small-molecule-labeled DNAzyme walking strand, and antibody against small molecules. The track is built by co-modifying fluorophore-labeled substrates and small-molecule-labeled DNA linkers onto a gold nanoparticle (AuNP). In the absence of the target molecule, the antibody binds small molecule labels at the DNAzyme walking strand and the DNA linker, driving the DNAzyme walking strand on the surface of the AuNP. The attached DNAzyme walking strand moves along the track and cleaves substrates to generate high fluorescence signals to achieve signal amplification. As target molecules exist, they competitively bind with antibody to displace the small-molecule-labeled linker and DNAzyme walking strand, rendering the DNAzyme walker inactive in substrate cleavage and causing weak fluorescence. By using this antibody-bridged DNAzyme walker, we achieved sensitive detection of two biologically important small molecules, digoxin and folic acid. This work provides a new paradigm by combining the signal amplification strategy of a DNA walker and immunorecognition for sensitive and selective detection of small molecules.

A multiple signal amplification photoelectrochemical biosensor based on biotin-avidin system for kanamycin sensing in fish and milk via synergism of g-C3N4 and Ru@SiO2

BACKGROUND

The residues of kanamycin can accumulate in the human body for a long time and pose serious health risks, including hearing loss, kidney poisoning, and drug allergic reactions. Therefore, it is crucial to develop a rapid, highly sensitive, and low-cost method for detecting kanamycin residues in foods. However, the current methods have limitations such as low sensitivity, expensive instruments, and multiple steps, which make them impractical for use in resource-limited environments and emergencies. In this study, the creation of a multiple-signal amplification photoelectrochemical biosensor to address these aforementioned issues is discussed.

RESULTS

Herein, we proposed a multiple signal amplification photoelectrochemical (PEC) biosensor based on carboxylated g-C3N4 and avidin functionalized Ru@SiO2 for the ultrasensitive detection of kanamycin. The carboxylated g-C3N4 was a highly efficient photoactive substance for amplifying photoelectric signals and a substrate for aptamer immobilization. The DOS and PDOS of g-C3N4 were studied by simulation, and the sensing mechanism of the probe at the molecular level was revealed. Meanwhile, using Ru@SiO2 as a signal amplifying unit, through the cooperative work between Ru@SiO2 and g-C3N4, the photoelectric signal could be double amplified to produce an excellent photocurrent response. Under optimized conditions, the photocurrent response of the PEC biosensor to kanamycin was obtained at concentrations from 0.1 nM to 1000 nM with a lower detection limit of 4.1052 × 10-11 mol L-1. This protocol demonstrates high sensitivity, brilliant specific recognition ability, excellent reproducibility, and acceptable stability.

SIGNIFICANCE

The first combination of g-C3N4 and avidin-Ru@SiO2 as photocurrent materials greatly enhanced the sensitivity of the PEC biosensors. Moreover, the specificity and sensitivity of the PEC biosensor were further improved through the specific interaction between kanamycin and aptamer. The photoelectric conversion mechanism based on g-C3N4 and two pathways for enhancing the photocurrent by Ru(byp)32+ were proposed. Through simulations of the DOS and PDOS of g-C3N4, the sensing mechanism of the probe at the molecular level was revealed. Under the optimum conditions, the PEC biosensor exhibited a wide linear concentration range and a low detection limit.

Recent Advances in Biological Applications of Aptamer-Based Fluorescent Biosensors

Aptamers have been spotlighted as promising bio-recognition elements because they can be tailored to specific target molecules, bind to targets with a high affinity and specificity, and are easy to chemically synthesize and introduce functional groups to. In particular, fluorescent aptasensors are widely used in biological applications to diagnose diseases as well as prevent diseases by detecting cancer cells, viruses, and various biomarkers including nucleic acids and proteins as well as biotoxins and bacteria from food because they have the advantages of a high sensitivity, selectivity, rapidity, a simple detection process, and a low price. We introduce screening methods for isolating aptamers with q high specificity and summarize the sequences and affinities of the aptamers in a table. This review focuses on aptamer-based fluorescence detection sensors for biological applications, from fluorescent probes to mechanisms of action and signal amplification strategies.

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.

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.

A graphene-oxide-based aptasensor for fluorometric determination of chloramphenicol in milk and honey samples utilizing exonuclease III-assisted target recycling and Nb.BbvCI-powered DNA walker cascade amplification

Herein, a graphene oxide (GO)-based fluorescence aptasensor was developed for the sensitive and selective detection of chloramphenicol (CAP), based on exonuclease III (Exo III)-assisted target recycling and Nb.BbvCI-driven DNA walker cascade amplification. Interactions between CAP, hairpin1(HP1), hairpin2 (HP2), and 3'-amino modified hairpin3 (HP3) labeled with carboxyfluorescein (FAM) and covalently coupled to GO enabled efficient CAP detection. CAP was quantitatively assayed by measuring fluorescence at excitation/emission wavelengths of 480/514 nm, resulting from the accumulation of released FAM. A good linear range of 1 fM to 1 nM and a limit of detection (LOD) of 0.875 fM (signal-to-noise (S/N)= 3) were achieved. This aptasensor can distinguish the CAP from interference antibiotics with good specificity and selectivity, even if the concentration of the interfering substance is ten-fold higher than the target concentration. Moreover, the developed fluorescence aptasensor was successfully applied for the detection of CAP in spiked milk and honey samples. Thus, this method is potentially applicable for assaying CAP in foods and provides a promising strategy for the development of fluorescence aptasensors for environmental sample analysis.

Construction of a fluorescence biosensor for ochratoxin A based on magnetic beads and exonuclease III-assisted DNA cycling signal amplification

Specific and sensitive detection of hazardous mycotoxins in agricultural crops is one of the most important goals of food safety. A fluorescence biosensor for sensitive detection of ochratoxin A (OTA) was constructed via magnetic beads and the exonuclease III (Exo III)-assisted trigger DNA circle amplification approach. Exo III-assisted trigger DNA circle amplification can be utilized as an effective strategy for the sensitive detection of OTA. The employment of streptavidin labeled magnetic beads offers a manner for the accumulation and separation of the hairpin signal probe sDNA-FAM in solution. After target specific recognition, the aptamers combined with OTA were released and the remaining block DNA (bDNA) probes captured the signal probes on magnetic bead modified fluorophores. Subsequently, the enzyme digestion reaction leads to the fluorophore free solution. Exo III-assisted DNA circle amplification contributed to the high sensitivity of the presented OTA fluorescence aptasensor. The experimental results demonstrate that the aptasensor is sensitive with the limit of detection as low as 0.28 ng mL^-1 for OTA, which was lower than that of the proposed aptasensors reported by the other literature on fluorescence methods. Additionally, the developed aptasensor with the diverse aptamer sequence shows promising potential applications in food monitoring.

A highly sensitive electrochemical aptasensor for cocaine detection based on CRISPR-Cas12a and terminal deoxynucleotidyl transferase as signal amplifiers

Cocaine is one of the mainly used illegal drugs in the world. Using the signal amplification elements of terminal deoxynucleotidyl transferase (TdT) and CRISPR-Cas12a, a highly sensitive and simple electrochemical aptasensor was introduced for cocaine quantification. When, no cocaine existed in the sample, the 3'-end of complementary strand of aptamer (CS) was extended by TdT, leading to the activation of CRISPR-Cas12a and remaining of very short oligonucleotides on the working electrode. So, the current signal was remarkably promoted. With the presence of cocaine, CS left the electrode surface. Thus, nothing changed following the incubation of TdT and CRISPR-Cas12a and the Aptamer/Cocaine complex presented on the electrode. Consequently, the [Fe(CN)₆]^3-/4- could not freely reach the electrode surface and the signal response was weak. Under optimal situations, the biosensor revealed a wide linear relation from 40 pM to 150 nM with detection limit of 15 pM for cocaine. The sensitivity of the analytical system was comparable and even better than other reported methods for cocaine detection. The designed method displayed excellent cocaine selectivity. The aptasensor could work well for cocaine assay in serum samples. So, the aptasensor is expected to be an efficient analytical method with broad applications in the determination of diverse analytes.

Preparation of Bi/BiOBr sensitized titania nanorod array via one-pot solvothermal method and construction of kanamycin photoelectrochemical aptasensor

In this work, a photoelectrochemical (PEC) aptasensor for detecting kanamycin (KAN) was designed based on aptamer modified Bi/BiOBr/ titania nanorod array (TiO2 NRA). Bi/BiOBr was loaded onto TiO2 NRA via...

A novel electrochemical sensor based on process-formed laccase-like catalyst to degrade polyhydroquinone for tumor marker

Methods to improve the sensitivity of electrochemical sensors based on catalytic reactions generally require adscititious or pre-modified catalysts, which make the sensitive detection of sensors extremely challenging. This is because the activity of the catalyst is susceptible to the storage and modification process, such as aggregation during storage or loss of active sites during multi-step modification, which impairs the performance of the sensor. To solve this thorny issue, a novel electrochemical sensor based on a process-formed laccase-like catalyst was constructed for sensitive detection of tumor markers. Cu²⁺-polydopamine (CuPDA) combined with antibody (Ab₂) were employed as copper-containing immunoprobe, which released Cu(Ⅱ) ions under acidic stimulation. Cu(Ⅱ) ions coordinate with the self-assembly cationic diphenylalanine-glutaraldehyde nanospheres (CDPGA) to form a laccase-like catalyst, which had stronger catalytic activity than laccase. The freshly formed catalyst was immediately used to degrade the polyhydroquinone-reduced graphene oxide (PHQ-rGO) composite, resulting in a significant reduction in the current signal. The PHQ-rGO composite plays dual roles of signal substance and substrate on the sensing interface. The proposed electrochemical sensor demonstrated wide linearity for the determination of a model analyte, human epididymis protein 4 (HE4), from 1 pg mL^-1 to 100 ng mL^-1, and the detection limit was as low as 0.302 pg mL^-1 (S/N = 3), which had good consistency with that of electrochemiluminescence method. This process-formed catalyst approach will have potential reference significance for the construction of other sensors.

DNA cyclic assembling control in an electrochemical strategy with MoS2@AuNPs for determination of kanamycin

A sensitive electrochemical strategy was established for kanamycin determination. A specific aptamer was modified on the electrode as the probe, followed by a cyclic hybridization chain reaction (HCR) with methylene blue, causing an increasing signal response. In the presence of kanamycin, it can initiatively convolve the aptamer and prevent further DNA assembling, resulting in a signal distinction sensitive to the target amount. However, the signal reproducibility is low. To improve the precision, the HCR procedure was investigated. The results demonstrated that the optimal amount of assembled DNA is 12-fold to that of aptamer. This amount was then controlled in further assays. Admittedly, controlled DNA assembling commonly indicates a limited signal amplification. To further enhance the sensitivity, a nanocomposite based on MoS₂ and AuNPs was modified on the electrode. The results of the assay proved that the signal distinction sensitive to target amount increased by 50%. A linearity range is obtained from 0.01 nM to 1.0 μM of kanamycin, and the LOD is 8.4 pM. Subsequently, this strategy was employed to detect kanamycin in chicken liver and milk sample; the recovery results suggest that it possess a satisfactory application prospect in analysis of agricultural products.