Metal and pH-Dependent Aptamer Binding of Tetracyclines Enabling Highly Sensitive Fluorescence Sensing

Characterization of the Binding Properties of Ten Aptamers Using the Intrinsic Fluorescence of Oxytetracycline

Tetracyclines are a class of commonly used four-ringed antibiotics. A series of DNA aptamers were recently obtained using the capture-SELEX (systematic evolution of ligands by exponential enrichment) method to bind to oxytetracycline, and one of the aptamers can bind to a few other tetracycline antibiotics as well. Upon binding to the aptamers, the intrinsic fluorescence of tetracycline antibiotics can be enhanced. At least 10 different DNA aptamers were isolated from the previous selection experiment. In this work, a systematic characterization of these ten aptamers was performed. Each of these aptamers shows a different degree of fluorescence enhancement ranging from around 1-fold to over 20-fold. Fluorescence enhancement was boosted in the presence of Mg2+. Isothermal titration calorimetry (ITC) studies were done and showed a great variety in dissociation constant (Kd) from 62 nM to 1.6 μM. Steady-state fluorescence spectroscopy and fluorescence lifetime studies showed a correlation between fluorescence lifetime and degree of fluorescence enhancement. A few aptamers showed slow binding kinetics, although no correlation was found between the kinetics of fluorescence change and degree of fluorescence enhancement. This is the first study of ten different aptamers for the same target, providing fundamental insights into aptamer binding and bioanalytical applications.

Intramolecular aptamer switches

Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer switches. Recently, many new aptamers with an overall hairpin structure have been reported. In this study, intramolecular aptamer switches were developed by adding new base pairs to the end of aptamers. The additional nucleotides can pair with the internal domains of the aptamer, causing a change in its conformation from the original secondary structure without a target. When a target binds to an aptamer, a marked change in the structure of the aptamer is expected. As models for testing this intramolecular aptamer switch idea, aptamers of oxytetracycline (OTC), 17β-estradiol (E2), and adenosine were employed. When the additional base pairs are too long, binding the target to the aptamer becomes more challenging. This research offers valuable insights into the development of intramolecular aptamer switches and their potential applications in biosensor design.

Light-up split aptamers: binding thermodynamics and kinetics for sensing

Due to their programmable structures, many aptamers can be readily split into two halves while still retaining their target binding function. While split aptamers are prevalent in the biosensor field, fundamental studies of their binding are still lacking. In this work, we took advantage of the fluorescence enhancement property of a new aptamer named OTC5 that can bind to tetracycline antibiotics to compare various split aptamers with the full-length aptamer. The split aptamers were designed to have different stem lengths. Longer stem length aptamers showed similar dissociation constants (Kd) to the full-length aptamer, while a shorter stem construct showed an 85-fold increase in Kd. Temperature-dependent fluorescence measurements confirmed the lower thermostability of split aptamers. Isothermal titration calorimetry indicated that split aptamer binding can release more heat but have an even larger entropy loss. Finally, a colorimetric biosensor using gold nanoparticles was designed by pre-assembling two thiolated aptamer halves, which can then link gold nanoparticles to give a red-to-blue color change.

Development and Evaluation of EDTA-Treated Rabbits for Bioavailability Study of Chelating Drugs Using Levofloxacin, Ciprofloxacin, Hemiacetal Ester Prodrugs, and Tetracycline

Laboratory rabbits are fed foods rich with cationic metals, and while fasting cannot empty gastric contents because of their coprophagic habits. This implies that, in rabbits, the oral bioavailability of chelating drugs could be modulated by the slow gastric emptying rates and the interaction (chelation, adsorption) with gastric metals. In the present study, we tried to develop a rabbit model with low amounts of cationic metals in the stomach for preclinical oral bioavailability studies of chelating drugs. The elimination of gastric metals was achieved by preventing food intake and coprophagy and administering a low concentration of EDTA 2Na solution one day before experiments. Control rabbits were fasted but coprophagy was not prevented. The efficacy of rabbits treated with EDTA 2Na was evaluated by comparing the gastric contents, gastric metal contents and gastric pH between EDTA-treated and control rabbits. The treatment with more than 10 mL of 1 mg/mL EDTA 2Na solution decreased the amounts of gastric contents, cationic metals and gastric pH, without causing mucosal damage. The absolute oral bioavailabilities (mean values) of levofloxacin (LFX), ciprofloxacin (CFX) and tetracycline hydrochloride (TC), chelating antibiotics, were significantly higher in EDTA-treated rabbits than those in control rabbits as follows: 119.0 vs. 87.2%, 9.37 vs. 13.7%, and 4.90 vs. 2.59%, respectively. The oral bioavailabilities of these drugs were significantly decreased when Al(OH)₃ was administered concomitantly in both control and EDTA-treated rabbits. In contrast, the absolute oral bioavailabilities of ethoxycarbonyl 1-ethyl hemiacetal ester (EHE) prodrugs of LFX and CFX (LFX-EHE, CFX-EHE), which are non-chelating prodrugs at least in in vitro condition, were comparable between control and EDTA-treated rabbits irrespective of the presence of Al(OH)₃, although some variation was observed among rabbits. The oral bioavailabilities of LFX and CFX from their EHE prodrugs were comparable with LFX and CFX alone, respectively, even in the presence of Al(OH)₃. In conclusion, LFX, CFX and TC exhibited higher oral bioavailabilities in EDTA-treated rabbits than in control rabbits, indicating that the oral bioavailabilities of these chelating drugs are reduced in untreated rabbits. In conclusion, EDTA-treated rabbits were found to exhibit low gastric contents including metals and low gastric pH, without causing mucosal damage. Ester prodrug of CFX was effective in preventing chelate formation with Al(OH)₃ in vitro and in vivo, as well as in the case of ester prodrugs of LFX. EDTA-treated rabbits are expected to provide great advantages in preclinical oral bioavailability studies of various drugs and dosage formulations. However, a marked interspecies difference was still observed in the oral bioavailability of CFX and TC between EDTA-treated rabbits and humans, possibly due to the contribution of adsorptive interaction in rabbits. Further study is necessary to seek out the usefulness of the EDTA-treated rabbit with less gastric contents and metals as an experimental animal.

Graphene Oxide-Assisted Aptamer-Based Fluorescent Detection of Tetracycline Antibiotics

Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of tetracyclines was enhanced. This unique fluorescence enhancement was used to selectively detect the tetracyclines. The purpose of this study was to use graphene oxide (GO) to suppress the background fluorescence for enhanced detection. First, the adsorption of doxycycline on GO was studied. At pH 8.0, 82.7% of doxycycline was adsorbed by GO, and adding 2 µM aptamer desorbed 55.4% of doxycycline. With GO, the signal increase was comparable from pH 6 to 8, whereas without GO, the increase was significantly lower at pH 8. Under optimized condition, a detection limit of 1.6 nM doxycycline was achieved at pH 8.0 in the presence of GO, whereas without GO, the detection limit was 18.9 nM. This is an interesting example of the use of nanomaterials to enhance the performance of aptamer-based biosensors.

Surfactant-Assisted Label-Free Fluorescent Aptamer Biosensors and Binding Assays

Using DNA staining dyes such as SYBR Green I (SGI) and thioflavin T (ThT) to perform label-free detection of aptamer binding has been performed for a long time for both binding assays and biosensor development. Since these dyes are cationic, they can also adsorb to the wall of reaction vessels leading to unstable signals and even false interpretations of the results. In this work, the stability of the signal was first evaluated using ThT and the classic adenosine aptamer. In a polystyrene microplate, a drop in fluorescence was observed even when non-binding targets or water were added, whereas a more stable signal was achieved in a quartz cuvette. Equilibrating the system can also improve signal stability. In addition, a few polymers and surfactants were also screened, and 0.01% Triton X-100 was found to have the best protection effect against fluorescence signal decrease due to dye adsorption. Three aptamers for Hg²⁺, adenosine, and cortisol were tested for their sensitivity and signal stability in the absence and presence of Triton X-100. In each case, the sensitivity was similar, whereas the signal stability was better for the surfactant. This study indicates that careful control experiments need to be designed to ensure reliable results and that the reliability can be improved by using Triton X-100 and a long equilibration time.

An aptamer array for discriminating tetracycline antibiotics based on binding-enhanced intrinsic fluorescence

Tetracyclines are a class of antibiotics with a similar four-ringed structure. Due to this structural similarity, they are not easily differentiated from each other. We recently selected aptamers using oxytetracycline as a target and focused on an aptamer named OTC5, which has similar affinities for oxytetracycline (OTC), tetracycline (TC), and doxycycline (DOX). Tetracyclines exhibit an intrinsic fluorescence that is enhanced upon aptamer binding, allowing convenient binding assays and label-free detection. In this study, we analyzed the top 100 sequences from the previous selection library. Three other sequences were found to differentiate between different tetracyclines (OTC, DOX, and TC) by the selective enhancement of their intrinsic fluorescence. Among them, the OTC43 aptamer was more selective for OTC with a limit of detection (LOD) of 0.7 nM OTC, OTC22 was more selective for DOX (LOD 0.4 nM), and OTC2 was more selective for TC (0.3 nM). Using these three aptamers to form a sensor array, principal component analysis was able to discriminate between the three tetracyclines from each other and from the other molecules. This group of aptamers could be useful as probes for the detection of tetracycline antibiotics.

Dual fluorescent aptasensor for simultanous and quantitative detection of sulfadimethoxine and oxytetracycin residues in animal-derived foods tissues based on mesoporous silica

Herein, we developed a dual fluorescent aptasensor based on mesoporous silica to simultaneously detect sulfadimethoxine (SDM) and oxytetracycline (OTC) in animal-derived foods. We immobilized two types of aptamers modified with FAM and CY5 on the silica surface by base complementary pairing reaction with the cDNA modified with a carboxyl group and finally formed the aptasensor detection platform. Under optimal conditions, the detection range of the aptasensor for SDM and OTC was 3-150 ng/mL (R ² = 0.9831) and 5-220 ng/mL (R ² = 0.9884), respectively. The limits of detection for SDM and OTC were 2.2 and 1.23 ng/mL, respectively. The limits of quantification for SDM and OTC were 7.3 and 4.1 ng/mL, respectively. Additionally, the aptasensor was used to analyze spiked samples. The average recovery rates ranged from 91.75 to 114.65% for SDM and 89.66 to 108.94% for OTC, and all coefficients of variation were below 15%. Finally, the performance and practicability of our aptasensor were confirmed by HPLC, demonstrating good consistency. In summary, this study was the first to use the mesoporous silica-mediated fluorescence aptasensor for simultaneous detection of SDM and OTC, offering a new possibility to analyze other antibiotics, biotoxins, and biomolecules.