A fluorescent "on-off-on" probe for sensitive detection of ATP based on ATP displacing DNA from nanoceria

Versatile, reusable and highly sensitive SERS-based point-of-care testing microplatform for reliable ATP detection

The advancement in miniaturized Raman spectrometers, coupled with the single-molecule-level sensitivity and unique fingerprint identification capability of surface-enhanced Raman scattering (SERS), offers great potential for point-of-care testing (POCT). Despite this, accurately quantifying analyte molecules, particularly in complex samples with limited sample volumes, remains difficult. Herein, we present a versatile and reusable SERS microplatform for highly sensitive and reliable quantitative detection of adenosine triphosphate (ATP) in biological fluids. The platform utilizes gold-Prussian blue core-shell nanoparticles modified with polyethyleneimine (Au@PB@PEI NPs), embedded within gold nanoparticle-immobilized capillary-based silica monolithic materials. PB acts as an internal standard, while PEI enhances molecular capture. The periodic, bimodal porous structure of the silica monolithic materials provides uniform and abundant sites for nanoparticle attachment, facilitating rapid liquid permeation, intense SERS enhancement, and efficient enrichment. The platform regulates ATP capture and release through magnesium ions in the liquid phase, eliminating matrix interferences and enabling platform reuse. Integrating efficient molecular enrichment, separation, an interference-free internal standard, a liquid flow channel, and a detection chamber, our platform offers simplicity in operation, exceptional sensitivity and accuracy, and rapid analysis (∼10 min). Employing PB as an internal calibration standard, ratiometric Raman signals (I732/I2123) facilitate precise ATP quantification, achieving a remarkable limit of detection down to 0.62 pM. Furthermore, this platform has been proven to be highly reproducible and validated for ATP quantification in both mouse cerebrospinal fluid and human serum, underscoring its immense potential for POCT applications.

β-Cyclodextrin Stabilized Nanoceria for Hydrolytic Cleavage of Paraoxon in Aqueous and Cationic Micellar Media

Beta-cyclodextrin (β-CD) stabilized cerium oxide nanoparticles (β-CD@CeO₂ NPs) were synthesized through a hydrothermal route. The electronic properties, surface functional group, surface composition, size, and morphologies of the as-synthesized β-CD@CeO₂ NPs were characterized using UV-visible spectroscopy, FTIR analysis, high resolution X-ray photoelectron spectroscopy (HRXPS), high resolution transmission electron microscopy (HRTEM), and field emission scanning electron microscopy (FESEM). The pH-dependent variation of the ζ-potential of β-CD@CeO₂ NPs and the catalytic activity of the NPs for the hydrolysis of paraoxon were investigated. The observed pseudo-first-order rate constant (k_obs) for the hydrolysis of paraoxon is increased with increasing pH and the ζ-potential of β-CD@CeO₂ NPs. The kinetics and mechanism of hydrolysis of paraoxon in the aqueous and cationic micellar media have been discussed.

Enzyme-Free Colorimetric Method for Fast Detection of PIK3CA Gene Mutation by Praseodymia Nanorods

The frequently mutated phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) gene is associated with multiple tumors and endocytosis of viruses. Identification of muted nucleotides at the hotspot can help in finding the susceptible people who are vulnerable to cancers and viruses. Herein, a simple enzyme-free colorimetric method is developed for the quick detection of PIK3CA gene mutations. The main mechanism lies in the dissimilar interactions between praseodymia nanorods and different nucleotides, as well as the underlying oxidase-mimicking characteristics of praseodymia. With rational designs of probes and processes, this method has great potential for expanded applications in the screening of mutations in other genes of interest.

Antifouling Electrochemical Biosensor Based on Conductive Hydrogel of DNA Scaffold for Ultrasensitive Detection of ATP

As an energy supplier, ATP plays an important role in various life activities, and there is an urgent need to develop an effective means of detecting ATP. However, the traditional sensors face serious nonspecific adsorption. In this work, an antifouling electrochemical biosensor based on the interpenetrating network of Y-DNA scaffold and polyaniline hydrogel was designed for ATP detection. The polyaniline hydrogel was conducive to the transport of electrons and ions, the structure of Y-DNA cross-linked by ATP aptamers in the polyaniline hydrogel achieved the effect of signal amplification. Super hydrophilic cellulose nanocrystals (CNCs) and zwitterion polypeptide sequence (Pep) were doped to play a synergistic antifouling effect. The hydrogel sensor we have built has a wide linear range of 0.1 pM-1 μM for ATP detection and a low detection limit of 0.025 pM (S/N = 3). For ATP detection in actual serum samples, the recovery of this sensor was 99.5%-106%, and the relative standard deviation was 0.4%-2.88%. It is proven that the sensor has good ATP detection performance, and it will provide a certain reference value for the detection of other biological small molecules.

Advances in chilling injury of postharvest fruit and vegetable: Extracellular ATP aspects

Due to the global use of cold chain, the development of postharvest technology to reduce chilling injury (CI) in postharvest fruits and vegetables during storage and transport is needed urgently. Considerable evidence shows that maintaining intracellular adenosine triphosphate (iATP) in harvested fruits and vegetables is beneficial to inhibiting CI occurrence. Extracellular ATP (eATP) is a damage-associated signal molecule and plays an important role in CI of postharvest fruits and vegetables through its receptor and subsequent signal transduction under low-temperature stress. The development of new aptasensors for the simultaneous determination of eATP level allows for better understanding of the roles of eATP in a myriad of responses mediated by low-temperature stress in relation to the chilling tolerance of postharvest fruits and vegetables. The multiple biological functions of eATP and its receptors in postharvest fruits and vegetables were attributed to interactions with reactive oxygen species (ROS) and nitric oxide (NO) in coordination with phytohormones and other signaling molecules via downstream physiological activities. The complicated interconnection among eATP in relation to its receptors, eATP/iATP homeostasis, ROS, NO, and heat shock proteins triggered by eATP recognition has been emphasized. This paper reviews recent advances in the beneficial effects of energy handling, outlines the production and homeostasis of eATP, discusses the possible mechanism of eATP and its receptors in chilling tolerance, and provides future research directions for CI in postharvest fruits and vegetables during low-temperature storage.

A 3D-printed, multi-modal microfluidic device for measuring nitric oxide and ATP release from flowing red blood cells

In this paper, a 3D-printed multi-modal device was designed and fabricated to simultaneously detect nitric oxide (NO) and adenosine triphosphate (ATP) in red blood cell suspensions prepared from whole blood. Once a sample was injected into the device, NO was first detected (via amperometry) using a three-electrode, dual-opposed, electrode configuration with a platinum-black/Nafion coated gold working electrode. After in-line amperometric detection of NO, ATP was detected via a chemiluminescence reaction, with a luciferin/luciferase solution continuously pumped into an integrated mixing T and the resulting light being measured with a PMT underneath the channel. The device was optimized for mixing/reaction conditions, limits of detection (40 nM for NO and 30 nM for ATP), and sensitivity. This device was used to determine the basal (normoxic) levels of NO and ATP in red blood cells, as well as an increase in concentration of both analytes under hypoxic conditions. Finally, the effect of storing red blood cells in a commonly used storage solution was also investigated by monitoring the production of NO and ATP over a three-week storage time.

A fluorescence nanoplatform for the determination of hydrogen peroxide and adenosine triphosphate via tuning of the peroxidase-like activity of CuO nanoparticle decorated UiO-66

A novel nanocomposite of CuO nanoparticle-modified Zr-MOF (CuO/UiO-66) was synthesized and developed as a fluorescence nanoplatform for H₂O₂ and adenosine triphosphate (ATP) via the "turn-on-off" mode in the presence of terephthalic acid (TA). The structure of CuO/UiO-66 was thoroughly characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), and other techniques. The CuO/UiO-66 with enhanced peroxidase-like (POD) activity obtained due to the Zr⁴⁺ in UiO-66 is beneficial to the aggregation of CuO NPs on its surface. As a result, the strengthened fluorescence at 425 nm with the excitation of 300 nm was found due to the highly fluorescent species of TAOH. This is produced by the oxidation of TA by ·OH that came from the catalysis of H₂O₂ via the peroxidase mimic of CuO/UiO-66. Hence the modification of CuO NPs on porous UiO-66 can provide a friendly and sensitive physiological condition for H₂O₂ detection. However, upon addition of ATP, the fluorescence intensity of TAOH at 425 nm effectively declined owing to the formation of complexation of Zr⁴⁺-ATP and the interaction of CuO to ATP which hampers the catalytic reaction of CuO/UiO-66 to H₂O₂. The specific interaction induced "inhibition of the peroxide-like activity" endows the sensitive and selective recognition of ATP. The detection limits were 16.87 ± 0.2 nM and 0.82 ± 0.1 nM, and linear analytical ranges were 0.02-100 μM and 0.002-30 μM for H₂O₂ and ATP, respectively. The novel strategy was successfully applied to H₂O₂ and ATP determination in serum samples with recoveries of 97.2-103.8% for H₂O₂ and 97.6-101.7% for ATP, enriching the avenue to design functional MOFs and providing new avenue of multicomponent bioanalysis.

Nanoceria, the versatile nanoparticles: Promising biomedical applications

Nanotechnology has been a boon for the biomedical field due to the freedom it provides for tailoring of pharmacokinetic properties of different drug molecules. Nanomedicine is the medical application of nanotechnology for the diagnosis, treatment and/or management of the diseases. Cerium oxide nanoparticles (CNPs) are metal oxide-based nanoparticles (NPs) which possess outstanding reactive oxygen species (ROS) scavenging activities primarily due to the availability of "oxidation switch" on their surface. These NP have been found to protect from a number of disorders with a background of oxidative stress such as cancer, diabetes etc. In fact, the CNPs have been found to possess the environment-dependent ROS modulating properties. In addition, the inherent catalase, SOD, oxidase, peroxidase and phosphatase mimetic properties of CNPs provide them superiority over a number of NPs. Further, chemical reactivity of CNPs seems to be a function of their surface chemistry which can be precisely tuned by defect engineering. However, the contradictory reports make it necessary to critically evaluate the potential of CNPs, in the light of available literature. The review is aimed at probing the feasibility of CNPs to push towards the clinical studies. Further, we have also covered and censoriously discussed the suspected negative impacts of CNPs before making our way to a consensus. This review aims to be a comprehensive, authoritative, critical, and accessible review of general interest to the scientific community.

Nanostructured Ceria: Biomolecular Templates and (Bio)applications

Ceria (CeO2) nanostructures are well-known in catalysis for energy and environmental preservation and remediation. Recently, they have also been gaining momentum for biological applications in virtue of their unique redox properties that make them antioxidant or pro-oxidant, depending on the experimental conditions and ceria nanomorphology. In particular, interest has grown in the use of biotemplates to exert control over ceria morphology and reactivity. However, only a handful of reports exist on the use of specific biomolecules to template ceria nucleation and growth into defined nanostructures. This review focusses on the latest advancements in the area of biomolecular templates for ceria nanostructures and existing opportunities for their (bio)applications.

Colorimetric and fluorometric dual-readout protein kinase assay by tuning the active surface of nanoceria

Herein, we demonstrate that the active surface of nanoceria can be fine-tuned by phosphorylated peptides. Accordingly, a colorimetric and fluorometric dual-readout strategy is rationally developed for assaying protein kinase activity. This feature not only enables the versatile monitoring of peptide phosphorylation but also broadens the application scope of nanoceria.

A Novel Electrochemical Aptasensor for the Ultrasensitive Detection of Adenosine Triphosphate Based on DNA-Templated Copolymers

Adenosine triphosphate (ATP) is a small but significant biological molecule that plays an important role in regulating cellular metabolism processes. Accurate and sensitive analytical techniques for detecting ATP are urgently needed. Herein, a new electrochemical aptasensor was designed in light of DNA-templated copolymers that parallel to the electrode for sensitive gauging of ATP. The ATP aptamer decorated by the electronic medium ferrocene can be regarded as a ″bridge″ connecting two DNA-templated copolymers. When ATP exists, because of the extraordinary binding selectivity of DNA-templated copolymers for target ATP, the rapid electron transfer of ferrocene was beneficial to the sensitive detection of target ATP. Specifically, our parallel DNA copolymers are more stable than upright DNA copolymers and have a faster signal transmission because of the close distance to the electrode; meanwhile, the nonspecific pollution is less. Consequently, the developed novel aptasensor exhibited a wide range of linear response toward ATP that was from 0.1 to 10 000 pM and high selectivity with a detection limit down to 11.5 fM. The electrochemical aptasensor has a broad application prospect in the detection of small biological molecules.

Fluorescence on-off-on with small and charge-tunable nanoparticles enables highly sensitive intracellular microRNA imaging in living cells

Nanomaterial-based on-off-on fluorescence sensing strategies are significant particularly in intracellular nucleic acids imaging assay. There still remains challenge to rationally balance fluorescence quenching efficiency and recovery dynamics. We assume that the performance of on-off-on fluorescence sensing strategy can be fundamentally improved on small zero-dimensional (0D) nanomaterial with precisely modulated surface charge. For a proof-of-concept demonstration, silicon nanoparticle (SiNP) with ~4 nm was synthesized and used as the quencher model, of which the surface charge density was modulated by modification of triphenylphosphonium (TPP). The influence of particle size, surface charge and charge density of the nanomaterials on sensing performance was systematically investigated. The strategy showed a low limit of detection (LOD) as 26 pM for target model miR-494, which is one of the lowest in nanomaterial-based on-off-on sensing platforms. And the LOD is even comparable to amplification-based methods in a greatly shortened assay time (2.5 h). The miR-494 expresses in cancerous and normal living cells of human cervical carcinoma (HeLa), human lung carcinoma (A549), human breast cancer (MCF-7), and normal human mammary epithelial (MCF-10A) cells were imaged and localized with significantly improved sensitivity and specificity. These excellent performances insure it a promising candidate as convenient and non-enzymatic sensing platform for miRNA-associated disease detection and early diagnosis.

Nanomaterial and Aptamer-Based Sensing: Target Binding versus Target Adsorption Illustrated by the Detection of Adenosine and ATP on Metal Oxides and Graphene Oxide

Target molecule-induced desorption of aptamer probes from nanomaterials has been a very popular sensing method, taking advantage of the fluorescence quenching or catalytic activity of nanomaterials for signal generation. While it is generally conceived that aptamers desorb due to binding to target molecules, in this work, we examined the effect of competitive target adsorption. From five metal oxide nanoparticles including CeO₂, ZnO, NiO, Fe₃O₄, and TiO₂, only ATP was able to induce desorption of its aptamer. Adenosine could not, even though it had an even higher affinity than ATP to the aptamer. The same conclusion was also observed with a random DNA that cannot bind ATP, indicating that the desorption of DNA was due to competitive adsorption of ATP instead of aptamer binding. On graphene oxide, however, adenosine produced slightly more aptamer desorption than ATP under most of the conditions, and this can be partially attributed to the weaker interaction of negatively charged ATP with negatively charged graphene oxide. For such surface-based biosensors, it is recommended that a nonaptamer control DNA be tested side-by-side to ensure the sensing mechanism to be related to aptamer binding instead of target adsorption.

Phosphate-sensing with (di-(2-picolyl)amino)quinazolines based on a fluorescence on–off system

Detection and visualization of phosphates such as ATP in living organisms can facilitate the elucidation of various biological events. Although substantial efforts had been made in this area, present methods have disadvantages such as the need for specialized equipment and poor sensitivities. To address these limitations, novel fluorescent probes, (di-(2-picolyl)amino)quinazolines, were developed for application in ATP detection. They selectively recognized copper ions by fluorescence quenching, and their copper complexes displayed fluorescence enhancement in the presence of phosphoric acid derivatives. This fluorescence on–off system enabled highly sensitive fluorescence detection of ATP when combined with a phenyl boronic acid-modified γ-cyclodextrin through a plausible multipoint recognition system.

Supramolecular probe Cu-dpa-QZ2/FPB-γ-CyD recognized ATP with high sensitivity.

A self-powered origami paper analytical device with a pop-up structure for dual-mode electrochemical sensing of ATP assisted by glucose oxidase-triggered reaction

A self-powered origami paper-based analytical device (oPAD), being with a pop-up structure as mechanical valve to first realize dual-mode of differential pulse voltammery (DPV)/supercapacitor amplified signal read out systems, was designed for detecting adenosine 5'-triphosphate (ATP) assisted by glucose oxidase (GOx)-triggered reaction. In order to accommodate the alternative step for dual-mode detection, a pop-up structure inspired by pop-up greeting cards was developed, making it possible to change the fluidic path with good registration and repeatability. To realize supercapacitor detection mode, a sandwich structure of a DNA sequence (DNA1), aptamer and a DNA sequence modified with GOx (GOx-DNA2) was formed on detection zone by hybridization reaction. With the addition of ATP, the GOx-DNA2 could be released with the specific binding between ATP and aptamer, and flowed into the reaction zone to catalyze the oxidation of glucose. Due to the difference in concentrations of [Fe(CN)₆]^3- and [Fe(CN)₆]^4- caused by the GOx-triggered reaction, a voltage could be produced to charge a paper supercapacitor which could provide a high instantaneous current with a digital multimeter to transduce the result of the assay, and realize the self-generation of an amplified electrical signal. By simply varying the direction of pop-up structure, the electrochemical signal from DPV read out mode could be achieved through catalytic oxidation of glucose by the remaining GOx-DNA2 on the detection zone. The proposed self-powered oPAD enabled the sensitive diagnosis of ATP in a linear range of 10-5000 nM with a limit of detection of 3 nM and 1.4 nM, respectively.

A label-free fluorometric aptasensor for adenosine triphosphate (ATP) detection based on aggregation-induced emission probe

Based on Aggregation-Induced Emission (AIE), the development of a label-free, simple and sensitive fluorometric aptasensor for adenosine triphosphate (ATP) detection is described. With ATP present, the aptamers will combine with ATP and the conformation of the aptamer will switch from a random coil to an antiparallel G-quadruplex, which impedes the digestion by exonuclease I (Exo I). Addition of 4,4 -(1E,1E)-2,2-(anthracene-9,10-diyl) bis (ethene-2,1-diyl) bis (N,N, N-trimethyl-benzenaminium iodide) (DSAI) into the solution will cause aggregation of DSAI on the surface of the aptamer/ATP complex and consequently give rise to strong emission. Additionally, a good linear relationship was observed under optimized conditions between the fluorescence intensities and the logarithm of ATP concentrations (R² = 0.9908). The established aptamer sensor was highly sensitive and exhibited a low limit of detection of 32.8 nM, with superior specificity for ATP. It was also used in the quantification of ATP levels in human serum samples and demonstrated satisfactory recoveries in the scope of 93.2%-107.6%. The cellular ATP assay results indicated that the developed method can be used for monitoring ATP concentrations in cell extracts without the interference of other substances in the cells. This method offers several advantages such as simplicity, rapidity, low cost and excellent selectivity, which make it hold great potential for the detection of ATP in bioanalytical and biological studies.

Ligation-Based qPCR-Amplification Assay for Radiolabel-Free Detection of ATP and NAD+ with High Selectivity and Sensitivity

We have developed a new sensing system based on quantitative real-time polymerase chain reaction assay (qPCR) to detect adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NAD⁺) with high sensitivity and selectivity. T4 DNA ligase can catalyze the ligation of two short oligonucleotides (DNA1 and DNA2), which complement a template (cDNA), in the presence of its cofactor, ATP, resulting in increased template concentration and decreased Ct values in qPCR assays. Similarly, the Escherichia coli DNA ligase is also able to catalyze the ligation of DNA1 and DNA2 upon the addition of NAD⁺. Moreover, this approach has potential for detecting other important cofactors in related systems. Therefore, as a convenient and sensitive strategy, the method may light new beacons and find broad application in biological fields.

A Label-Free Fluorescent DNA Machine for Sensitive Cyclic Amplification Detection of ATP

In this study, a target recycled amplification, background signal suppression, label-free fluorescent, enzyme-free deoxyribonucleic acid (DNA) machine was developed for the detection of adenosine triphosphate (ATP) in human urine. ATP and DNA fuel strands (FS) were found to trigger the operation of the DNA machine and lead to the cyclic multiplexing of ATP and the release of single stranded (SS) DNA. Double-stranded DNA (dsDNA) was formed on graphene oxide (GO) from the combination of SS DNA and complementary strands (CS′). These double strands then detached from the surface of the GO and in the process interacted with PicoGreen dye resulting in amplifying fluorescence intensity. The results revealed that the detection range of the DNA machine is from 100 to 600 nM (R² = 0.99108) with a limit of detection (LOD) of 127.9 pM. A DNA machine circuit and AND-NOT-AND-OR logic gates were successfully constructed, and the strategy was used to detect ATP in human urine. With the advantage of target recycling amplification and GO suppressing background signal without fluorescent label and enzyme, this developed strategy has great potential for sensitive detection of different proteins and small molecules.

A Label-Free Fluorescent DNA Calculator Based on Gold Nanoparticles for Sensitive Detection of ATP

Herein we described a deoxyribonucleic acid (DNA) calculator for sensitive detection of the determination of adenosine triphosphate (ATP) using gold nanoparticles (GNP) and PicoGreen fluorescence dye as signal transducer, and ATP and single-stranded DNA (DNA-M′) as activators. The calculator-related performances including linearity, reaction time, logic gate, and selectivity were investigated, respectively. The results revealed that this oligonucleotide sensor was highly sensitive and selective. The detection range was 50–500 nmol/L (R² = 0.99391) and the detection limit was 46.5 nmol/L. The AND DNA calculator was successfully used for the ATP detection in human urine. Compared with other methods, this DNA calculator has the characteristics of being label-free, non-enzymic, simple, and highly sensitive.