A universal aptasensing platform based on cryonase-assisted signal amplification and graphene oxide induced quenching of the fluorescence of labeled nucleic acid probes: application to the detection of theophylline and ATP

Advanced aptamer-based sensors for monitoring theophylline

Theophylline is a widely used bronchodilator for treating asthma-related symptoms like shortness of breath and chest tightness. However, its narrow therapeutic plasma range (20-200 μM) necessitates careful monitoring of blood levels to prevent toxicity. Various clinical laboratory techniques have been developed for detecting theophylline, including spectroscopy, high-performance liquid chromatography (HPLC), fluorescence polarization immunoassay, and radioimmunoassay. Despite their utility, these methods are limited by complex sample preparation, long processing times, large sample volumes, and high costs. Aptamer-based biosensors have emerged as a promising alternative, offering superior selectivity and specificity compared to conventional methods. This review evaluates the performance of aptamer-based sensors in terms of sensitivity, specificity, and limit of detection, comparing them to traditional techniques. Recent studies demonstrate the advantages of aptamer-based sensors, including their simplicity, rapid response time, and cost-effectiveness, which make them ideal for point-of-care applications. The review also explores the methodologies used in aptamer-based detection, highlighting key innovations and advances in the field. Findings from the literature show how aptamer-based sensors enhance the monitoring of theophylline levels, overcoming the limitations of traditional techniques. This is the first review dedicated to discussing aptamer-based techniques for theophylline monitoring, addressing a gap in current literature.

A novel fluorescent aptasensor for the detection of theophylline based on cryonase-driven signal amplification strategy

In the study, we have developed an expedient and efficient method for the detection of theophylline based on the amplification of the signal intensity of fluorescence based on oxidized single-walled carbon nanohorns (oxSWCNHs)/cryonase. When theophylline was not present in the system, oxSWCNHs can adequately adsorb nucleic acid probes labeled by carboxyfluorescein (FAM). In the presence of theophylline, the nucleic acid probe forms the tertiary probe-theophylline complex, which detaches from the surface of the oxSWCNHs. Then, upon reaction with cryonase, the complex can release the FAM and theophylline into the next cycle. The fluorescence signal of the system exhibits a 1:N magnification, enabling quantitative detection of theophylline. The linear range was 30-150 ng/mL, and the limit of detection (LOD) was 6.04 ng/mL. At the same time, it can also be used to detect theophylline in mouse serum.

Silver/copper bimetallic nanoclusters integrating with cryonase-assisted target recycling amplification detection of Salmonella typhimurium

An unsophisticated fluorescence-enabled strategy is brought forward to process the highly sensitive fluorescence detection of Salmonella typhimurium (S. typhimurium) which based on polyethyleneimine (PEI)-templated silver/copper nanoclusters (Ag/CuNCs) (λ excitation = 334 nm and λ emission = 466 nm) with cryonase-assisted target recycling amplification. The Ag/CuNCs nanoclusters are synthesized as fluorescent materials due to their strong and stable fluorescence characteristics and are modified with S. typhimurium aptamers to form aptamer-Ag/CuNCs probes. The probes can be adsorbed on the surface of quenching agents-polydopamine nanospheres (PDANSs), thereby inducing fluorescence quenching of the probes. Once the aptamers are bound to the target, the aptamers/targets complexes are separated from the PDANSs surface, and the Ag/CuNCs recover the fluorescence signal. The released complexes will immediately be transformed into a substrate digested by cryonase (an enzyme that can digest all types of nucleic acids), and the released targets are bound to another aptamers to initiate the next round of cleavage. This reaction will be repeated continuously until all relevant aptamers are consumed and all Ag/CuNCs are released, resulting in a significant amplification of the fluorescence signal and improved sensitivity. Using Ag/CuNCs as fluorescent probes combined with cryonase-assisted amplification strategy, the fluorescence aptasensor is constructed with detection limits as low as 3.8 CFU mL-1, which is tenfold better than without the cryonase assistance. The method developed has been applied to milk, orange juice, chicken, and egg white samples with excellent selectivity and accuracy providing an approach for the early and rapid detection of S. typhimurium in food.

Highly sensitive and stable fluorescent aptasensor based on an exonuclease III-assisted amplification strategy for ATP detection

Fluctuations in intracellular adenosine triphosphate (ATP) concentration are closely associated with some cancer diseases. Thus, it is a worthwhile undertaking to predict sickness by monitoring changes in ATP levels. However, the detection limits of current fluorescent aptamer sensors for ATP detection are in the range of nmol L^-1 to μmol L^-1. It has become crucial to employ amplification strategies to increase the sensitivity of fluorescent aptamer sensors. In the current paper, a duplex hybrid aptamer probe was developed based on exonuclease III (Exo III)-catalyzed target recycling amplification for ATP detection. The target ATP forced the duplex probe configuration to change into a molecular beacon that can be hydrolyzed with Exo III to achieve the target ATP cycling to amplify the fluorescence signal. Significantly, many researchers ignore that FAM is a pH-sensitive fluorophore, leading to the fluorescence instability of FAM-modified probes in different pH buffers. The negatively charged ions on the surface of AuNPs were replaced by new ligands bis(p-sulfonatophenyl)phenylphosphine dihydrate dipotassium salt (BSPP) to improve the drawback of FAM instability in alkaline solutions in this work. The aptamer probe was designed to eliminate the interference of other similar small molecules, showing specific selectivity and providing ultra-sensitive detection of ATP with detection limits (3σ) as low as 3.35 nM. Such detection limit exhibited about 4-500-fold better than that of the other amplification strategies for ATP detection. Thus, a relatively general high sensitivity detection system can be established according to the wide target adaptability of aptamers, which can form specific binding with different types of targets.

Acid-accelerated hydrolysis of NaBH4: a gas-generation reaction for diverse gas pressure biosensing

Gas pressure biosensing is a promising portable analysis method. The gas-generation reaction is crucial to its sensitivity, speed, repeatability, and usability. However, very few gas-generation reactions are available for sensitive, safe, and diverse biosensing. Herein, acid-accelerated hydrolysis of sodium borohydride (NaBH₄) was explored for the first time to achieve portable and diverse gas pressure biosensing. The slow hydrolysis and hydrogen generation of NaBH₄ in alkaline medium is accelerated with increasing acidity, which increased the gas pressure in a small and sealed tube within 10 min. Thus, a label-free bioassay is easily and specifically achieved once analytes can in-situ generate acid to accelerate the hydrolysis rate of NaBH₄, such as glucose, acetylcholine (ACh), adenosine triphosphate (ATP) and others. More importantly, analytes without acid generation could be quantitatively and selectively detected by combining target recognition with acid-generated biochemical reactions for enzyme-linked gas pressure biosensing. Inspired by this, aflatoxin B1 (AFB1)-aptamer interaction-triggered strand displacement reaction was combined with glucose oxidation by glucose oxidase (GOD) to detect AFB1 as low as 7.1 pM. Therefore, acid-accelerated hydrolysis of NaBH₄ is powerful for developing portable, cheap, and diverse gas pressure biosensing. It opens up a new way for cheap, universal, and portable biosensing.

Bio-inspired aptamers decorated gold nanoparticles enable visualized detection of malathion

Biosensors always respond to the targets of interest in a specific manner, employing biological or bio-mimic recognition elements such as antibodies and aptamers. Inspired by target recognition in nature, an aptamer-mediated, gold nanoparticle-based sensing approach is developed in this work for effective determination of malathion. The sensing system consists of negatively charged aptamer probes, and polycationic proteins, protamine, as well as exceptional colorimetric nanoprobes, barely gold nanoparticles (AuNPs). Protamine molecules bound to aptamer probes hinder the aggregation of AuNPs, while no such inhibition is maintained when aptamer-specific malathion is introduced into the solution, thus leading to the solution colour change from red to blue observable by the naked eye. The assay is accomplished via a mix-and-measure step within 40 min with a detection limit as low as 1.48 μg/L (3σ/s rule). The assay method also exhibits high selectivity and good applicability for the quantification of malathion in tap water with recovery rates of 98.9%-109.4%. Additionally, the good detection accuracy is also confirmed by the high-performance liquid chromatography method. Therefore, the non-enzymatic, label- and device-free characteristics make it a robust tool for malathion assay in agricultural, environmental, and medical fields.

Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection

The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.

Nano optical and electrochemical sensors and biosensors for detection of narrow therapeutic index drugs

For the first time, a comprehensive review is presented on the quantitative determination of narrow therapeutic index drugs (NTIDs) by nano optical and electrochemical sensors and biosensors. NTIDs have a narrow index between their effective doses and those at which they produce adverse toxic effects. Therefore, accurate determination of these drugs is very important for clinicians to provide a clear judgment about drug therapy for patients. Routine analytical techniques have limitations such as being expensive, laborious, and time-consuming, and need a skilled user and therefore  the nano/(bio)sensing technology leads to high interest.

Ligation-dependent rolling circle amplification method for ATP determination with high selectivity and sensitivity

It is highly demanded to develop methods for the reliable detection of ATP, which plays an extremely important role in clinical diagnosis, biomedical engineering, and food chemistry. However, the methods currently available for ATP sensing strongly rely on the utilization of expensive and sophisticated instruments or the use of ATP aptamers with mediocre sensitivity and selectivity. To circumvent these drawbacks, we herein propose an efficient method for ATP detection by integrating highly specific ATP-dependent ligation reaction with dual-stage signal amplification techniques executed by rolling circle amplification (RCA) and the subsequently fabricated DNAzymes ready for the catalytic cleavage and fluorescence signal generation from molecular beacons (MBs). The detection limit is down to 35 pM with a linear range from 0.05 nM to 200 nM. More importantly, the sensing strategy can effectively discriminate ATP from its analogues and the results from the spiked human serum albumin (HSA) samples further confirm the reliability for practical applications. Considering the high sensitivity and selectivity, wash-free and isothermal convenience, and the simplicity in probe design, the strategy reported herein paves a new avenue for the effective determination of ATP and other biomolecules in fundamental and applied research.

The Application of Nucleic Acid Probe-Based Fluorescent Sensing and Imaging in Cancer Diagnosis and Therapy

It is well known that cancer incidence and death rates have been growing, but the development of cancer theranostics and therapeutics has been a challenging work. Recently, nucleic acid probe-based fluorescent sensing and imaging have achieved remarkable improvements in a variety of cancer management techniques, credited to their high sensitivity, good tolerance to interference, fast detection, and high versatility. Herein, nucleic acid probe-based fluorescent sensing and imaging are labeled with advanced fluorophores, which are essential for fast and sensitive detection of aberrant nucleic acids and other cancer-relevant molecules, consequently performing cancer early diagnosis and targeted treatment. In this review, we introduce the characteristics of nucleic acid probes, summarize the development of nucleic acid probe-based fluorescent sensing and imaging, and prominently elaborate their applications in cancer diagnosis and treatment. In discussion, some challenges and perspectives are elaborated in the field of nucleic acid probe-based fluorescent sensing and imaging.

2'-O-Methyl molecular beacon: a promising molecular tool that permits elimination of sticky-end pairing and improvement of detection sensitivity

An innovative 2'-O-methyl molecular beacon (MB) has been designed and prepared with improved thermal stability and unique nuclease resistance. The employment of 2'-O-methyl MBs helps efficiently suppress the background signal, while DNase I is responsible for the signal amplification and elimination of sticky-end pairing. The coupled use of 2'-O-methyl MBs and DNase I makes it possible to develop an enzyme-aided strategy for amplified detection of DNA targets in a sensitive and specific fashion. The analysis requires only mix-and-measure steps that can be accomplished within half an hour. The detection sensitivity is theoretically determined as 27.4 pM, which is nearly 200-fold better than that of the classic MB-based assay. This proposed sensing system also shows desired selectivity. All these features are of great importance for the design and application of MBs in biological, chemical, and biomedical fields.

Carbon based nanomaterials for the detection of narrow therapeutic index pharmaceuticals

Precise detection of important pharmaceuticals with narrow therapeutic index (NTI) is very critical as there is a small window between their effective dose and the doses at which the adverse reactions are very likely to appear. Regarding the fact that various pharmacokinetics will be plausible while considering pharmacogenetic factors and also differences between generic and brand name drugs, accurate detection of NTI will be more important. Current routine analytical techniques suffer from many drawbacks while using novel biosensors can bring up many advantages including fast detection, accuracy, low cost with simple and repeatable measurements. Recently the well-known carbon Nano-allotropes including carbon nanotubes and graphenes have been widely used for development of different Nano-biosensors for a diverse list of analytes because of their great physiochemical features such as high tensile strength, ultra-light weight, unique electronic construction, high thermo-chemical stability, and an appropriate capacity for electron transfer. Because of these exceptional properties, scientists have developed an immense interest in these nanomaterials. In this case, there are important reports to show the effective Nano-carbon based biosensors in the detection of NTI drugs and the present review will critically summarize the available data in this field.

Enzyme-free and protein-assisted dual-amplified fluorescence anisotropy for sensitive miRNA detection in tumor cells

We here report a double amplification strategy to construct a fluorescence anisotropy sensor for microRNA analysis in practical biological samples. In this strategy, one target can trigger cyclic catalyzed hairpin assembly (CHA), with streptavidin incorporated as an amplifier of molar mass to enhance the signal intensity. The proposed strategy has a good linearity in the range of 5 pM - 0.5 nM with a detection limit down to 2.3 pM. More importantly, by using fluorescence anisotropy as the signal output, the strategy can be used directly for detection of miRNA in practical samples without any tedious sample pretreatment, holding the practical value in real biological systems.

A feasible sonochemical approach to synthesize CuO@CeO2 nanomaterial and their enhanced non-enzymatic sensor performance towards neurotransmitter

A nanostructured and high conductive cupric oxide (CuO NPs) with hierarchical CeO₂ sheets-like structure was synthesized by a facile sonochemical approach. Furthermore, CuO/CeO₂ nanostructure is synthesized by high-intensity ultrasonic probe (Ti-horn, 50 kHz and 100 W) at ambient air. Moreover, the synthesized CuO/CeO₂ material was characterized by various analytical techniques including FESEM, EDX, XRD and electrochemical methods. Then, the synthesized CuO/CeO₂ composite was applied for the electrocatalytic detection of dopamine using CV and DPV techniques. In addition, the CuO/CeO₂ modified electrode has good electrocatalytic performance with high linear range from 0.025 to 98.5 µM towards the determination of dopamine drug and high sensitivity of the CuO/CeO₂ modified drug sensor was calculated as 16.34 nM and 4.823 μA·µM^-1·cm^-2, respectively. Moreover, a repeatability, reproducibility and stability of the CuO@CeO₂ mixture modified electrode were analyzed towards the determination of dopamine biomolecule. Interestingly, the real time application of CuO@CeO₂ modified electrode was established in different serum and drug samples.

Facile sonochemical synthesis of rutile-type titanium dioxide microspheres decorated graphene oxide composite for efficient electrochemical sensor

In this reports the facile and green synthesis of rutile-type titanium dioxide nanoparticles decorated graphene oxide nanocomposite via the ultrasonication process (frequency: 50 kHz, Power: 100 W/cm² and Ultrasonic type: Ti-horn). Because, the sonochemical synthesis method is simple, non-explosive and harmless method than other conventional technique. Furthermore, the synthesized material was characterized by various analytical techniques including FESEM, EDX, XRD, EIS and electrochemical methods. Then, the synthesized TiO₂ MPs@GOS composite was applied for the electrocatalytic detection of theophylline (TPL) using CV and amperometric (current-time) techniques. Captivatingly, the modified sensor has excellent electrocatalytic performance with the wider linear range from 0.02 to 209.6 µM towards the determination of theophylline and the LOD and sensitivity of the modified sensor was calculated as 13.26 nM and 1.183 μA·µM^-1·cm^-2, respectively. In addition, a selectivity, reproducibility and stability of the TiO₂ MPs@GOS modified GCE were analyzed towards the determination of theophylline molecule. Finally, the real time application of TiO₂ MPs@GOS modified theophylline sensor was established in serum and drug samples.

Improving the sensitivity and selectivity of a DNA probe using graphene oxide-protected and T7 exonuclease-assisted signal amplification

The accurate analysis of single-nucleotide polymorphisms is of great significance for clinical detection and diagnosis. Based on the hybridization hindrance caused by graphene oxide (GO) and hairpin probe, we report a T7 Exo-assisted cyclic amplification technique to distinguish single-base mismatch for highly sensitive and selective detection of mutant-type DNA. When the mutant-type target is completely complementary to the probe, the T7 Exo hydrolyzes the probe and releases the fluorescent molecule from the GO surface, resulting in a fluorescence signal. Conversely, when the wild-type mismatch target is present, the weak hybridization prevents the release of FAM-labeled probe from the GO surface. Therefore, the FAM-labeled probe cannot be degraded efficiently by T7 Exo, and the fluorescence is still quenched by GO. The detection limit of the proposed method can be as low as 34 fM due to the cyclic signal amplification. The experimental results showed that the established method could be used to detect single-nucleotide polymorphisms accurately and sensitively at low cost.

Graphene/aptamer probes for small molecule detection: from in vitro test to in situ imaging

Small molecules are key targets in molecular biology, environmental issues, medicine and food industry. However, small molecules are challenging to be detected due to the difficulty of their recognition, especially in complex samples, such as in situ in cells or animals. The emergence of graphene/aptamer probes offers an excellent opportunity for small molecule quantification owing to their appealing attributes such as high selectivity, sensitivity, and low cost, as well as the potential for probing small molecules in living cells or animals. This paper (with 130 refs.) will review the application of graphene/aptamer probes for small molecule detection. We present the recent progress in the design and development of graphene/aptamer probes enabling highly specific, sensitive and rapid detection of small molecules. Emphasis is placed on the success in their development and application for monitoring small molecules in living cells and in vivo systems. By discussing the key advances in this field, we wish to inspire more research work of the development of graphene/aptamer probes for both on-site or in situ detection of small molecules and its applications for investigating the functions of small molecules in cells in a dynamic way. Graphical abstract Graphene/aptamer probes can be used to construct different platforms for detecting small molecules with high specificity and sensitivity, both in vitro and in situ in living cells and animals.

A carbon nanoparticle and DNase I-Assisted amplified fluorescent biosensor for miRNA analysis

Nucleic acid-based biosensors have become powerful tools in biomedical applications. But the stability issue seriously limits their wide applications. Fortunately, the emergence of carbon nanoparticles (CNPs), which can effectively protect DNA probes from enzymatic digestion and unspecific protein binding, provides a good solution. In this work, a DNase I-aided cyclic enzymatic amplification method (CEAM) for microRNA analysis has been developed based on the coupling use of nucleic acid probes with specific molecular recognition ability as well as CNPs with excellent biostability. The method is simple and sensitive, with a detection limit down to 3.2 pM. Furthermore, satisfactory results are achieved for miRNA analysis in breast cancer cell lysate, demonstrating the applicability in disease diagnosis. The ingenious combination of CNPs and nucleic acid probes can open a new chapter in the development of versatile analytical strategies that holds great potentials for clinical diagnosis, food safety, and environmental monitoring.

Graphene Oxide: A Smart (Starting) Material for Natural Methylxanthines Adsorption and Detection

Natural methylxanthines, caffeine, theophylline and theobromine, are widespread biologically active alkaloids in human nutrition, found mainly in beverages (coffee, tea, cocoa, energy drinks, etc.). Their detection is thus of extreme importance, and many studies are devoted to this topic. During the last decade, graphene oxide (GO) and reduced graphene oxide (RGO) gained popularity as constituents of sensors (chemical, electrochemical and biosensors) for methylxanthines. The main advantages of GO and RGO with respect to graphene are the easiness and cheapness of synthesis, the notable higher solubility in polar solvents (water, among others), and the higher reactivity towards these targets (mainly due to - interactions); one of the main disadvantages is the lower electrical conductivity, especially when using them in electrochemical sensors. Nonetheless, their use in sensors is becoming more and more common, with the obtainment of very good results in terms of selectivity and sensitivity (up to 5.4 × 10-10 mol L-1 and 1.8 × 10-9 mol L-1 for caffeine and theophylline, respectively). Moreover, the ability of GO to protect DNA and RNA from enzymatic digestion renders it one of the best candidates for biosensors based on these nucleic acids. This is an up-to-date review of the use of GO and RGO in sensors.

Carbon nanoparticle-protected RNA aptasensor for amplified fluorescent determination of theophylline in serum based on nuclease-aided signal amplification

A carbon nanoparticle (CNP) and Cryonase-aided method that realizes the amplified fluorescent detection of theophylline was proposed.