Label-free fluorescent strategy for sensitive detection of tetracycline based on triple-helix molecular switch and G-quadruplex

Novel electrochemical sensing strategy for ultrasensitive detection of tetracycline based on porphyrin/metal phthalocyanine-covalent organic framework

In this work, a novel two-dimensional semiconducting metal covalent organic framework (CuTAPc-TFPP-COF) was synthesized and used as biosensing platform to construct aptasensor for trace detection of tetracycline (TC). The CuTAPc-TFPP-COF integrates the highly conjugated structure, large specific surface area, high porosity, abundant nitrogen functional groups, excellent electrochemical activity, and strong bioaffinity for aptamers, providing abundant active sites to effectively anchor aptamer strands. As a result, the CuTAPc-TFPP-COF-based aptasensor shows high sensitivity for detecting TC via specific recognition between aptamer and TC to form Apt-TC complex. An ultralow detection limit of 59.6 fM is deduced from the electrochemical impedance spectroscopy within a wide linear range of 0.1-100000 pM for TC. The CuTAPc-TFPP-COF-based aptasensor also exhibits good selectivity, reproducibility, stability, regenerability, and excellent applicability for real river water, milk, and pork samples. Therefore, the CuTAPc-TFPP-COF-based aptasensor will be promising for detecting trace harmful antibiotics residues in environmental water and food samples.

Aptamer-Based fluorescent DNA biosensor in antibiotics detection

The inappropriate employment of antibiotics across diverse industries has engendered profound apprehensions concerning their cumulative presence within human bodies and food commodities. Consequently, many nations have instituted stringent measures limiting the admissible quantities of antibiotics in food items. Nonetheless, conventional techniques employed for antibiotic detection prove protracted and laborious, prompting a dire necessity for facile, expeditious, and uncomplicated detection methodologies. In this regard, aptamer-based fluorescent DNA biosensors (AFBs) have emerged as a sanguine panacea to surmount the limitations of traditional detection modalities. These ingenious biosensors harness the binding prowess of aptamers, singular strands of DNA/RNA, to selectively adhere to specific target antibiotics. Notably, the AFBs demonstrate unparalleled selectivity, affinity, and sensitivity in detecting antibiotics. This comprehensive review meticulously expounds upon the strides achieved in AFBs for antibiotic detection, particularly emphasizing the labeling modality and the innovative free-label approach. It also elucidates the design principles behind a diverse array of AFBs. Additionally, a succinct survey of signal amplification strategies deployed within these biosensors is provided. The central objective of this review is to apprise researchers from diverse disciplines of the contemporary trends in AFBs for antibiotic detection. By doing so, it aspires to instigate a concerted endeavor toward the development of heightened sensitivity and pioneering AFBs, thereby contributing to the perpetual advancement of antibiotic detection methodologies.

Aptamer Sensors for the Detection of Antibiotic Residues- A Mini-Review

Food security is a global issue, since it is closely related to human health. Antibiotics play a significant role in animal husbandry owing to their desirable broad-spectrum antibacterial activity. However, irrational use of antibiotics has caused serious environmental pollution and food safety problems; thus, the on-site detection of antibiotics is in high demand in environmental analysis and food safety assessment. Aptamer-based sensors are simple to use, accurate, inexpensive, selective, and are suitable for detecting antibiotics for environmental and food safety analysis. This review summarizes the recent advances in aptamer-based electrochemical, fluorescent, and colorimetric sensors for antibiotics detection. The review focuses on the detection principles of different aptamer sensors and recent achievements in developing electrochemical, fluorescent, and colorimetric aptamer sensors. The advantages and disadvantages of different sensors, current challenges, and future trends of aptamer-based sensors are also discussed.

Potential Universal Engineering Component: Tetracycline Response Nanoswitch Based on Triple Helix-Graphene Oxide

The overuse of antibiotics can lead to the emergence of drug resistance, preventing many common diseases from being effectively treated. Therefore, based on the special composite platform of P1/graphene oxide (GO) and DNA triple helix, a programmable DNA nanoswitch for the quantitative detection of tetracycline (TC) was designed. The introduction of GO as a quenching agent can effectively reduce the background fluorescence; stabilizing the trigger strand with a triplex structure minimizes errors. It is worth mentioning that the designed model has been verified and analyzed by both computer simulation and biological experiments. NUPACK predicts the combined mode and yield of each strand, while visual DSD flexibly predicts the changes in components over time during the reaction. The feasibility analysis preliminarily confirmed the realizability of the designed model, and the optimal reaction conditions were obtained through optimization, which laid the foundation for the subsequent quantitative detection of TC, while the selective experiments in different systems fully demonstrated that the model had excellent specificity.

Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes

The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na⁺, K⁺, Ag⁺, Tl⁺, Cu⁺/Cu²⁺, Hg²⁺, and Pb²⁺) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.

Synthesis and Characterization of Fluorescence Active G4-Quartet and Direct Evaluation of Self-Assembly Impact on Emission

Fluorescence (FL) active 8-aryl guanosine derivatives were prepared and applied for cation mediated self-assembly to form the H-bonded G8-quadruplexes. The p-cyano (p-CN) and 8-anthracene (8-An) substituted guanosines were identified to give the strongest fluorescence with the formation of G8-octamers (G8) both in solution (NMR) and solid state (X-ray). This well-defined G8-octamer system has provided the first direct evidence on the self-assembled G-quadruplex fluorescence emission with aggregation-induced emission (AIE), which could be applied as the foundation for FL molecular probe design toward G-quadruplex recognition.

Novel DNA Aptameric Sensors to Detect the Toxic Insecticide Fenitrothion

Fenitrothion is an insecticide belonging to the organophosphate family of pesticides that is widely used around the world in agriculture and living environments. Today, it is one of the most hazardous chemicals that causes severe environmental pollution. However, detection of fenitrothion residues in the environment is considered a significant challenge due to the small molecule nature of the insecticide and lack of molecular recognition elements that can detect it with high specificity. We performed in vitro selection experiments using the SELEX process to isolate the DNA aptamers that can bind to fenitrothion. We found that newly discovered DNA aptamers have a strong ability to distinguish fenitrothion from other organophosphate insecticides (non-specific targets). Furthermore, we identified a fenitrothion-specific aptamer; FenA2, that can interact with Thioflavin T (ThT) to produce a label-free detection mode with a K_d of 33.57 nM (9.30 ppb) and LOD of 14 nM (3.88 ppb). Additionally, the FenA2 aptamer exhibited very low cross-reactivity with non-specific targets. This is the first report showing an aptamer sensor with a G4-quadruplex-like structure to detect fenitrothion. Moreover, these aptamers have the potential to be further developed into analytical tools for real-time detection of fenitrothion from a wide range of samples.

Sensitive and selective determination of tetracycline in milk based on sulfur quantum dot probes

A novel fluorescent probe based on sulfur quantum dots (SQDs) was fabricated for sensitive and selective detection of tetracycline (TC) in milk samples. The blue emitting SQDs were synthesized via a top–down method with assistance of H₂O₂. The synthesized SQDs showed excellent monodispersity, water solubility and fluorescence stability, with a quantum yield (QY) of 6.30%. Furthermore, the blue fluorescence of the obtained SQDs could be effectively quenched in the presence of TC through the static quenching effect (SQE) and inner filter effect (IFE) between TC and SQDs. Under the optimum conditions, a rapid detection of TC could be accomplished within 1 min and a wide linear range could be obtained from 0.1 to 50.0 μM with a limit of detection (LOD) of 28.0 nM at a signal-to-noise ratio of 3. Finally, the SQD-based fluorescent probe was successfully applied for TC determination in milk samples with satisfactory recovery and good relative standard deviation (RSD). These results indicate that the SQD-based fluorescent probe shows great potential in practical analysis of TC in real samples with high rapidity, selectivity, and sensitivity.

A SQD-based fluorescent probe was applied to detect TC based on the inner filter effect (IFE) and static quenching effect (SQE) without any extra surface modification for the first time.

Advances and perspectives of aptasensors for the detection of tetracyclines: A class of model compounds of food analysis

The residual tetracyclines in food are frequently applied as the model compounds to develop aptasensors. Until now, more than 100 advanced aptasensors towards tetracyclines have been developed and published in English. This review summarizes and discusses comprehensively these advanced aptasensors, in terms of the principle designs, applied frontier transducers/materials, working performance, and advantages/disadvantages. The aptasensors are classified according to the inherent transduction techniques, i.e., optics, optics-electricity, optics-mass, and electricity-mass. Moreover, the present challenges such as the limited specificity and limited affinity of the aptamers, the future prospects and trends such as further combination with other advanced materials and technologies, and the urgent need of expanding the practical application were discussed and prospected. We hope this review can serve as a powerful tool for both tracing the development progresses of aptasensors and providing adequate references for further development of aptasensing methods for food-related analytes.

New insight into G-quadruplexes; diagnosis application in cancer

Biochemical properties and flexibility of nitrogenous bases allow DNA to fold into higher-order structures. Among different DNA secondary structure, G-quadruplexes (tetrapelexes-G4) - which are formed in guanine rich sequences - have gained more attention because of their biological significance, therapeutic intervention, and application in molecular device and biosensor. G4-quadruplex studies categorize into three main fields, in vivo, in vitro, and in silico. The in vitro field includes G4 synthetic oligonucleotides. This review focuses on the G-quadruplex synthetic aptamers structure features and considers the applicability of G4-aptamers for cancer biomarkers detection. Various biosensing methods will be reviewed based on G-quadruplex aptamers for cancer detection.

G-quadruplex specific thioflavin T-based label-free fluorescence aptasensor for rapid detection of tetracycline

A label-free fluorescence aptasensor was developed for the rapid detection of tetracycline (TET) based on G-quadruplex structure of TET aptamers and G-quadruplex specific dye Thioflavin T (ThT). The fluorescence of free ThT is essentially weak in aqueous solution, whereas it selectively identifies the G-quadruplex of aptamers to form the G-quadruplex/ThT conjugates, resulting in an enormous increase of the fluorescence intensity. However, the fluorescence intensity of G-quadruplex/ThT conjugates was drastically suppressed due to the release of free ThT from G-quadruplex/ThT conjugates after the addition of TET via specific binding with TET aptamers. The key factors affecting sensitivity and selectivity including the reaction medium, binding time of ThT to TET aptamers, incubation time between TET aptamers and TET, concentration of ThT and TET aptamers were investigated in detail. The optimal conditions were as follows: ultrapure water as reaction medium, binding time of 5 min, incubation time of 1 min, 9.0 μmol/L ThT and 0.03 μmol/L aptamers. A good linear relationship (correlation coefficient of 0.9973) was obtained between the fluorescence quenching efficiency (F₀ - F) / F₀ and the logarithm of TET concentration in the range of 0.01-1.0 μmol/L. The limit of detection was 0.001 μmol/L (S/N = 3). The proposed assay was applied for the detection of TET in the spiked honey and milk samples with recoveries ranging from 93.5% to 106.9%. The developed label-free fluorescence aptasensor showed advantages of high specificity, low cost and short time-consuming, illustrating potential application for on-site detection of TET in foodstuffs.

A system composed of vanadium(IV) disulfide quantum dots and molybdenum(IV) disulfide nanosheets for use in an aptamer-based fluorometric tetracycline assay

A system composed of vanadium(IV) disulfide quantum dots (VS₂ QDs) and molybdenum(IV) disulfide (MoS₂) nanosheets for use in an aptamer-based fluorometric tetracycline assay was developed. The tetracycline (TET) aptamer was first immobilzed on the VS₂ QDs with a typical size of 3 nm. The blue fluorescence of the VS₂ QDs (labeled with aptamer) with emission maxima at 448 nm (under excitation at 360 nm) was subsequently quenched by MoS₂ nanosheets. If TET is recognized by the aptamer, the VS₂ QDs drift away from the basal plane of the MoS₂ nanosheets. This generated "turn-on" fluorescence of the VS₂ QDs. A VS₂ QD/MoS₂ nanosheet-based fluorometric TET aptasensor was thus constructed. Selective and sensitive TET bioanalysis was realized in a linear range of 1 to 250 ng mL^-1. The detection limit was 0.06 ng mL^-1. Its applicability of determination of TET in milk samples has been demonstrated. Graphical abstractSchematic representation of the aptamer-based fluorometric tetracycline assay.

Methods for field measurement of antibiotic concentrations: limitations and outlook

The growing prevalence of antibiotic resistance poses an increasingly serious threat to human health. Although an important driver of antibiotic resistance is the continuous exposure of bacteria to sublethal concentrations of antibiotics in natural environments, antibiotic pollutants are not currently tracked globally or systematically. This limits the international capacity to address the rise of antibiotic resistance at its source. To address this lack of data, the development of methods to measure antibiotic concentrations on-site is essential. These methods, ideally, must be sensitive to sublethal concentrations of antibiotics and require minimal technical expertise. Furthermore, factors such as cost, selectivity, biosafety and the ability to multiplex must be evaluated in the context of field use. Based on these criteria, we provide a critical review of current methods in antibiotic detection and evaluate their adaptability for use on-site. We categorize these methods into microbiological assays, physical and chemical assays, immunoassays, aptasensors and whole-cell biosensors. We recommend continued development of a dipstick or microfluidics approach with a bacterial promoter-based mechanism and colorimetric output. This technique would incorporate the advantageous aspects of existing methods, maximize shelf-life and ease-of-use, and require minimal resources to implement in the field.

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

Recent progress in DNA-based nanomaterials is summarized, ranging from applications in biosensors, biomedicine/imaging, and molecular logic gates to emerging nanomachines, as well as future perspective discussions.

Aptamer-Based Biosensors for Antibiotic Detection: A Review

Antibiotic resistance and, accordingly, their pollution because of uncontrolled usage has emerged as a serious problem in recent years. Hence, there is an increased demand to develop robust, easy, and sensitive methods for rapid evaluation of antibiotics and their residues. Among different analytical methods, the aptamer-based biosensors (aptasensors) have attracted considerable attention because of good selectivity, specificity, and sensitivity. This review gives an overview about recently-developed aptasensors for antibiotic detection. The use of various aptamer assays to determine different groups of antibiotics, like β-lactams, aminoglycosides, anthracyclines, chloramphenicol, (fluoro)quinolones, lincosamide, tetracyclines, and sulfonamides are presented in this paper.

Tetrazolylpyrene unnatural nucleoside as a human telomeric multimeric G-quadruplex selective switch-on fluorescent sensor

Specific sensing of dimeric H45 G-quadruplex DNA using a fluorescence light-up probe, tetrazolylpyrene nucleoside (^TzPyB_Do), is reported.