Cascaded signal amplification via target-triggered formation of aptazyme for sensitive electrochemical detection of ATP

Triple-signal strategy utilizing a colorimetric, fluorescence, and chromogenic paper-based sensor for rapid detection of ATP at neutral pH

This study presents a novel triple signal amplification strategy for paper-based colorimetric/fluorescence/chromogenic detection of adenosine triphosphate (ATP). Fluorescent gold nanoclusters (BSA-AuNCs) induce a redshift in the absorbance of quercetin (QCT), and the paper substrate displays a yellow color. Simultaneously, BSA-AuNCs activated QCT to emit fluorescence through the surface plasmon resonance (SPR) effect, producing a strong fluorescence signal at 541 nm, while the red fluorescence of BSA-AuNCs at 636 nm remained stable, resulting in a yellowish-green fluorescence of the paper. Upon the addition of ATP, the absorbance appeared to blue shift, and the paper substrate transitioned from yellow to colorless within 30 s. Concurrently, the fluorescence intensity of QCT decreased significantly, while the fluorescence intensity of BSA-AuNCs at 636 nm was almost unchanged, leading the fluorescence of the paper substrate to gradually shift to red. The QCT/BSA-AuNC paper-based system functions as a dual-signal sensor, enabling rapid ATP detection through both colorimetric and fluorescence modes with limits of detection (LOD) of 0.72 μM and 0.68 μM, respectively. Additionally, ATP enhances the peroxidase-like catalytic activity of BSA-AuNCs, promoting the chromogenic reaction of TMB and turning the paper sensor dark blue, with a LOD of 0.43 μM. This triple signal amplification method enables sensitive ATP screening using paper-based test strips, providing high sensitivity, selectivity, and reliable quantitative results. Notably, this three-mode sensing strategy holds significant potential for development into a quantitative method for ATP detection in normal and tumor cell samples, aiding in cell identification.

A Fluorescence Enhancement Sensor Based on Silver Nanoclusters Protected by Rich-G-DNA for ATP Detection

In this study, a turn-on fluorescence sensor for the detection of adenosine 5'-triphosphate (ATP) was developed and tested using ATP-DNA2-Ag NCs. The results showed that the fluorescence of ATP-DNA2-Ag NCs was significantly enhanced with the addition of ATP. The fluorescence enhancement was a result of the specific binding activity of the ATP aptamer and ATP, which caused G-rich sequences to approach the dark DNA-Ag NCs, owing to the alteration in ATP aptamer conformation. The proposed sensor demonstrated a good linear range of 18-42 mM and a limit of detection (LOD) of 2.8 μM. The sensor's features include sensitivity, selectivity, and simple operation. In addition, the proposed sensor successfully measured ATP in 100-fold diluted fetal bovine serum.

Enhancing the substrate selectivity of enzyme mimetics in biosensing and bioassay: Novel approaches

A substantial development in nanoscale materials possessing catalytic activities comparable with natural enzymes has been accomplished. Their advantages were owing to the excellent sturdiness in an extreme environment, possibilities of their large-scale production resulting in higher profitability, and easy manipulation for modification. Despite these advantages, the main challenge for artificial enzyme mimetics is the lack of substrate selectivity where natural enzymes flourish. This review addresses this vital problem by introducing substrate selectivity strategies to three classes of artificial enzymes: molecularly imprinted polymers, nanozymes (NZs), and DNAzymes. These rationally designed strategies enhance the substrate selectivity and are discussed and exemplified throughout the review. Various functional mechanisms associated with applying enzyme mimetics in biosensing and bioassays are also given. Eventually, future directives toward enhancing the substrate selectivity of biomimetics and related challenges are discussed and evaluated based on their efficiency and convenience in biosensing and bioassays.

Turn-on fluorescent nanoprobe for ATP detection based on DNA-templated silver nanoclusters

A turn-on fluorescence nanoprobe was constructed for the determination of adenosine 5'-triphosphate (ATP) based on DNA-templated silver nanoclusters (DNA-AgNCs). The significant enhancement fluorescence intensity of DNA-AgNCs in the presence of ATP is due to the high special binding affinity between ATP and the aptamer, resulting in the environment of DNA-AgNCs with darkish fluorescence lying at one terminus of DNA slightly altering owing to the change of ATP aptamer conformation. A good linear range runs from 9 to 24 mM with a satisfactory detection limit of 3 μM. Furthermore, the proposed nanoprobe exhibited good performance for ATP detection in diluted fetal bovine serum.

Portable and Recyclable Luminescent Lanthanide Coordination Polymer Film Sensors for Adenosine Triphosphate in Urine

Adenosine triphosphate (ATP) is a small molecule that is released to the urine from bladder urothelial cells and the bladder mucosal band of the human body. In certain cases, ATP can serve as a biomarker in bladder disease. For the practical applicability of luminescent sensors for ATP in urine, it is significant to find a new strategy for making the detection progress simple and available for in-field urine analysis. Here, a novel luminescent lanthanide coordination polymer (Tb-BPA) was designed and synthesized for quick and sensitive detection of ATP through luminescence quenching with a quenching constant of 4.90 × 103 M-1 and a detection limit of 0.55 × 10-6 M. Besides, Tb-BPA has excellent anti-interference ability and can detect ATP in simulated urine with a small relative standard deviation (<4%). Moreover, the luminescent polyacrylonitrile nanofiber films modified by Tb-BPA were prepared by electrospinning and were used for ATP visual detection. Notably, this film is easy to recover and reuse, and maintains good detection performance after at least 7 cycles.

SERS Immunoassay Based on an Enzyme-Catalyzed Cascade Reaction and Metal-Organic Framework/Alkaline Phosphatase for Ultrasensitive Detection of Adenosine Triphosphate

Herein, an adenosine triphosphate (ATP)-induced enzyme-catalyzed cascade reaction system based on metal-organic framework/alkaline phosphatase (MOF/ALP) nanocomposites was designed to establish a surface-enhanced Raman spectroscopy (SERS) biosensor for use in rapid, sensitive ATP detection. Numerous ALP molecules were first encapsulated using ZIF-90 to temporarily deactivate the enzyme activity, similar to a lock. Au nanostars (AuNSs), as SERS-enhancing substrates, were combined with o-phenylenediamine (OPD) to form AuNSs@OPD, which could significantly improve the Raman signal of OPD. When the target ATP interacted with the MOF/ALP nanocomposites, ATP could act as a key to open the MOF structure, releasing ALP, which should further catalyze the conversion of OPD to oxOPD with the aid of ascorbic acid 2-phosphate. Therefore, with the increasing concentrations of ATP, more ALP was released to catalyze the conversion of OPD, resulting in the reduced intensity of the Raman peak at 1262 cm-1, corresponding to the level of OPD. Based on this principle, the ATP-induced enzyme-catalyzed cascade reaction SERS biosensor enabled the ultrasensitive detection of ATP, with a low detection limit of 0.075 pM. Consequently, this study provides a novel strategy for use in the ultrasensitive, rapid detection of ATP, which displays considerable potential for application in the fields of biomedicine and disease diagnosis.

An intelligent "chemical tongue" for high-order monitoring ATP-related physiological phosphates and ATP hydrolysis through diverse transduction principles

For discriminating diverse analytes and monitoring a specific chemical reaction, the emerging multi-channel "chemical nose/tongue" is challenging multi-material "chemical nose/tongue". The former contributes greatly to integrating different transduction principles from a single sensing material, avoiding the need for complex design, high cost, and tedious operation involved with the latter. Therefore, this high-order sensing puts a particular emphasis on the effects of encapsulation. Herein, the plasmonic gold nanoparticles (Au NPs) are encapsulated as a core into the fluorescent guanine monophosphate-Tb3+ infinite coordination polymer nanoparticles (GMP-Tb ICPs) to obtain a core-shell nanocomposite named Au NPs@GMP-Tb ICPs. Hence, a dual-channel "chemical tongue" based on Au NPs@GMP-Tb ICPs is present to realize high-order sensing of adenosine triphosphate (ATP)-related physiological phosphates and the monitoring of ATP hydrolysis. Considering the affinity of Tb3+ towards P-O bonds, four inorganic phosphates and three nucleotide phosphates with different phosphate group numbers and steric hindrance effect directly regulate two stimulus responses (fluorescence intensity and UV-vis absorbance) of Au NPs@GMP-Tb ICPs. Robust statistical methods, such as linear discriminant analysis and hierarchical cluster analysis, are used to recognize each phosphate by the developed sensor array either in the aqueous solution or in complex media such as serum, together with efficiently monitored ATP hydrolysis at different intervals. These findings and blind test clarify that the designed "chemical tongue" guarantees interference resistance and strengthens analytical capacity, together with offering valuable insight into "lab-on-a-nanoparticle" development for monitoring specific chemical reactions.

Split aptazyme-based signal amplification for AβO analysis

Aptazyme is a chimera of functional nucleic acids, which integrates recognition and amplification elements to simplify the assay process and improve sensing efficiency. However, its application may be limited by signal leakage. In this work, we innovatively integrate the AβO aptamer and an MNAzyme (multicomponent nucleic acid enzyme) for highly efficient detection of AβO. The aptamer and half of the MNAzyme are positioned at one strand, and the other half of the MNAzyme is integrated with a toehold sequence. These two sequences cannot hybridize to activate the MNAzyme until the target is added. The background signal is significantly reduced by the split format and the secondary structure of DNA probes formed in the absence of the target. The proposed aptazyme can not only achieve amplification through enzymatic catalysis but also greatly improve the efficiency of signal transduction and output. We systematically investigated the influence of different DNA probes on the detection performance, and the optimized aptazyme can detect as low as 26.5 pM targets in 1h. The stability of this method was also investigated by detection targets in real biological samples.

Halloysite nanotubes-loaded conductive polymer as substrate and label material for sensitive detection of amyloid-β protein by electrochemical immunosensor

Amyloid-beta protein (Aβ) is a unique biomarker for Alzheimer's disease (AD). The sandwich-type electrochemical immunosensor, one of the key tools for detecting biomarkers, relies on a high-performance signal amplification approach to enhance its sensitivity. Ni/PdH nanodendrites (Ni/PdH NDs) have increased catalytic activity due to their unique interaction with palladium hydride and their nickel-rich surface, tunable shape and high specific surface area. Modified halloysite nanotubes (mHNT)-loaded with polypyrrole (PPy@mHNT) possess excellent dispersion and a large surface area. This enables the formation of a conductive network to prevent the accumulation of Ni/PdH NDs. Additionally, it exposes more electrocatalytic active centers, effectively amplifying electrical signals. By utilizing Ni/PdH@PPy@mHNT as the labeling material, it shows a consistent and remarkable electrocatalytic activity in H2O2 reduction, leading to signal amplification. The acid-etched HNT coated with polyaniline (PANI@eHNT) exhibits an exceptionally low background signal and outstanding conductivity. This not only accelerates electron transfer on the electrode surface, but also ensures the stable incubation of biomolecules post-amino grafting. Utilizing NH2-PANI@eHNT as a substrate material can guarantee stable biomolecule incubation, offer a stable sensing platform and enhance immunosensor performance. The signal can be amplified and the immunosensor's sensitivity can be raised through the efficient cooperation of the aforementioned nanomaterials. Under optimum circumstances, the electrochemical immunosensor had the lowest detection limit of 5.53 fg mL-1 and a linear range of 50 fg mL-1 to 100 ng mL-1. Based on the outstanding performance previously mentioned, this immunosensor is anticipated to aid in the early detection of AD.

Overcoming Debye length limitations: Three-dimensional wrinkled graphene field-effect transistor for ultra-sensitive adenosine triphosphate detection

Adenosine triphosphate (ATP) is closely related to the pathogenesis of certain diseases, so the detection of trace ATP is of great significance to disease diagnosis and drug development. Graphene field-effect transistors (GFETs) have been proven to be a promising platform for the rapid and accurate detection of small molecules, while the Debye shielding limits the sensitive detection in real samples. Here, a three-dimensional wrinkled graphene field-effect transistor (3D WG-FET) biosensor for ultra-sensitive detection of ATP is demonstrated. The lowest detection limit of 3D WG-FET for analyzing ATP is down to 3.01 aM, which is much lower than the reported results. In addition, the 3D WG-FET biosensor shows a good linear electrical response to ATP concentrations in a broad range of detection from 10 aM to 10 pM. Meanwhile, we achieved ultra-sensitive (LOD: 10 aM) and quantitative (range from 10 aM to 100 fM) measurements of ATP in human serum. The 3D WG-FET also exhibits high specificity. This work may provide a novel approach to improve the sensitivity for the detection of ATP in complex biological matrix, showing a broad application value for early clinical diagnosis and food health monitoring.

Electronic supplementary materials

The online version contains supplementary material available at 10.1007/s11467-023-1281-7 and https://journal.hep.com.cn/fop/EN/10.1007/s11467-023-1281-7.

Colorimetric Detection of ATP by a Chlorophosphonazo III -based Mg2+ Complex in Aqueous Solution via Indicator Displacement Approach

A simple and effective colorimetric detection of adenosine 5-triphosphate (ATP) in 100% aqueous media was developed based on an indicator displacement approach (IDA). A commercially available dye, Chlorophosphonazo III (CPA), was utilized as the indicator and the ATP detection was achieved using the complex of CPA with Mg²⁺ in a 2:1 stoichiometric ratio (CPA₂-Mg²⁺) through the regeneration of CPA by the binding of ATP to Mg²⁺. Upon addition of a series of anions to the CPA₂-Mg²⁺ complex, only the appearance of the solution of the complex with ATP exhibited a color change from blue to purple which can be detected by the naked eye. Moreover, the ATP recognition was not hampered by the presence of other anions. Hence, CPA₂-Mg²⁺ is efficient in ATP highly selective and sensitive colorimetric detection in 100% aqueous media.

Ratiometric ECL sensor based on Apt-AuNS@Lu nanoprobe for analyzing cell swelling-induced ATP release

A novel ratiometric electrochemiluminescence (ECL) system based on gold nanostars (AuNSs) support was constructed for the determination of hypotonicity-induced ATP release from HepG2 cells. AuNS@Lu nanoprobe was used as anodic luminophore and K₂S₂O₈ as cathodic luminophore as well as anodic co-reactant. AuNS with the large specific surface was adopted to adsorb plentiful luminol to form solid-state probe and as affinity support to immobilize ATP aptamer (Apt). The obtained nanocomposite (Apt-AuNS@Lu) generated a strong ECL signal at + 0.4 V (vs. Ag/AgCl) with co-reactant K₂S₂O₈, because of excellent conductivity and catalytic activity of AuNS. Furthermore, graphene oxide was reduced onto indium tin oxide (ITO) electrodes to facilitate the electron transfer. Following, polydopamine (PDA) film was formed via self-polymerization, improving stability and adhesion of the electrode surface. To immobilize ATP capture aptamer (Apt_C), abounding AuNSs were attached to RGO/PDA surface. When the sensor was incubated in the mixture solution of Apt-AuNS@Lu and target ATP, the ECL signal of Apt-AuNS@Lu increased with the increase of ATP concentration, meanwhile, the signal of K₂S₂O₈ declined. The ratio of the two luminophores was used for the quantitative determination of ATP. The linear range was 5 to 250 nM, and the limit of detection was 1.4 nM at (3σ)/S. The method was successfully applied to analyze ATP release from HepG2 cells stimulated by 0.45% NaCl hypotonic solution. The results showed that the release kinetics profile of ATP had a sigmoidal shape with rapid release within 10 min and then slowed. Compared to the isotonic groups, the intracellular ATP concentration was 3.7 ± 0.3 µM (n = 3) decreasing by 40.3% and the extracellular was 23.4 ± 1.2 nM (n = 3) increasing by 9.2 times in the hypotonicity for 10 min, which showed ATP release from cells and good agreement with commercial ELISA test. The proposed strategy would be beneficial to broadening application of ECL technology in studying cell biological functions.

A label-free aptasensor for the detection of ATP based on turn-on fluorescence DNA-templated silver nanoclusters

A label-free aptasensor has been fabricated in order to detect adenosine triphosphate (ATP) using turn-on fluorescence DNA-Ag NCs. The fluorescence of the DNA-Ag NCs could increase remarkably with the addition of ATP mainly because ATP specifically interacts with its aptamer to change the microenvironment of the darkish DNA-Ag NCs located at one terminus or two termini due to the conformational alteration of the aptamer structure. The proposed sensor can detect ATP in a linear range of 6-27 mM with a good detection limit of 5.0 μM. Additionally, the proposed method succeeded in detecting ATP in fetal bovine serum.

Facile fabrication of highly sensitive and non-label aptasensors based on antifouling amyloid-like protein aggregates

In this paper, we present a robust and versatile method for developing non-label aptasensors with high sensitivity. Amyloid-like protein aggregates were facilely synthesized with the commonly used passivating agent bovine serum albumin (BSA) in developing biosensors, and the produced amyloid-like phase-transited BSA (PTB) exhibited excellent antifouling performances and robust interfacial adhesion with the electrode surface. In order to improve the detection sensitivity of electrochemical measurements, reduced graphene oxide was electrochemically deposited onto the electrode surface. Moreover, gold nanoparticles were introduced to enhance the conductivity of the PTB film and facilitate subsequent aptamer modification. Two common biological species, adenosine triphosphate (ATP) and cytochrome c (cyt c), were chosen as detection targets, and their corresponding aptasensors were successfully constructed and systematically evaluated. The proposed aptasensors based on the PTB-Au antifouling composite exhibited high sensitivity and specificity towards ATP and cyt c detection, and the detection limits were calculated to be 0.26 nM and 0.64 nM for ATP and cyt c, respectively. Hence, this work provides a simple approach to develop highly sensitive aptasensors without any labeling process, and thus promises its great application in biological analysis.

A genetically encoded fluorescent biosensor for monitoring ATP in living cells with heterobifunctional aptamers

Visualizing the dynamics of ATP in living cells is key to understanding cellular energy metabolism and related diseases. However, the live-cell applications of current methods are still limited due to challenges in biological compatibility and sensitivity to pH. Herein, a novel label-free fluorescent " turn-on " biosensor for monitoring ATP in living bacterias and mammalian cells was developed. This biosensor (Broc-ATP) employed heterobifunctional aptamers to detect ATP with high sensitivity in vitro. In our system, a very useful tandem method was established by combining four Broc-ATPs with 3 × F30 three-way junction scaffold to construct an intracellular biosensor that achieves sufficient fluorescence to respond to intracellular ATP. This intracellular biosensor can be used for sensitive and specific dynamic imaging of ATP in mammalian cells. Hence, this genetically encoded biosensor provides a robust and efficient tool for the detection of intracellular ATP dynamics and 3 × F30 tandem method expands the application of heterobifunctional aptamers in mammalian cells.

Ultrasensitive Glutathione-Mediated Facile Split-Type Electrochemiluminescence Nanoswitch Sensing Platform

Seeking for an advanced electrochemiluminescence (ECL) platform is still an active and continuous theme in the ECL-sensing realm. This work outlines a femtomolar-level and highly selective glutathione (GSH) and adenosine triphosphate (ATP) ECL assay strategy using a facile split-type gold nanocluster (AuNC) probe-based ECL platform. The system utilizes GSH as an efficient etching agent to turn on the MnO₂/AuNC-based ECL nanoswitch platform. This method successfully achieves an ultrasensitive detection of GSH, which significantly outperformed other sensors. Based on the above excellent results, GSH-related biological assays have been further established by taking ATP as a model. Combined with the high catalytic oxidation ability of DNAzyme, this ECL sensor can realize ATP assay as low as 1.4 fmol without other complicated exonuclease amplification strategies. Thus, we successfully achieved an ultrahigh sensitivity, extremely wide dynamic range, great simplicity, and strong anti-interference detection of ATP. In addition, the actual sample detection for GSH and ATP exhibits satisfactory results. We believe that our proposed high-performance platform will provide more possibilities for the detection of other GSH-related substances and show great prospect in disease diagnosis and biochemical research.

Simultaneous preconcentration and fluorescence detection of ATP by a hybrid nanocomposite of magnetic nanoparticles incorporated in mixed metal hydroxide

A new approach for increasing the sensitivity of adenosine triphosphate (ATP) detection was demonstrated. The assay was based on the synergetic function of a hybrid nanocomposite (MNPs@MMH) composed of magnetic nanoparticles (MNPs) incorporated in a mixed metal hydroxide (MMH). MNPs@MMH can be utilized as an efficient green extractant and peroxidase catalyst. The trace level of ATP in the sample solution was first extracted by the MNPs@MMH hybrid nanocomposite through the ion exchange properties of MMH and adsorbed on the surface of the MNPs@MMH. The concentration of ATP was related to the fluorescence intensity of 2,3-diaminophenazine (DAP) generated from peroxidase-like activity of the MNPs in the presence of H₂O₂ and o-phenylenediamine (OPD). In the presence of ATP, the active surface of the MNPs was diminished, and the amount of DAP generated was reduced. Thus, the concentration of ATP was related to the degree of fluorescence decrease compared to the fluorescence intensity of the system without ATP. Based on the proposed strategy, a highly sensitive assay for ATP was achieved. This assay exhibited good selectivity for detection of ATP over derivatives and other common anions. The proposed assay allowed the detection of ATP in a concentration range of 2.5-20 μM with a detection limit of 0.41 μM.

Recent Advances on Functional Nucleic-Acid Biosensors

In the past few decades, biosensors have been gradually developed for the rapid detection and monitoring of human diseases. Recently, functional nucleic-acid (FNA) biosensors have attracted the attention of scholars due to a series of advantages such as high stability and strong specificity, as well as the significant progress they have made in terms of biomedical applications. However, there are few reports that systematically and comprehensively summarize its working principles, classification and application. In this review, we primarily introduce functional modes of biosensors that combine functional nucleic acids with different signal output modes. In addition, the mechanisms of action of several media of the FNA biosensor are introduced. Finally, the practical application and existing problems of FNA sensors are discussed, and the future development directions and application prospects of functional nucleic acid sensors are prospected.

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.

An "off-on" electrochemiluminescence biosensor coupled with strand displacement-powered 3D micromolecule walking nanomachine for ultrasensitive detection of adenosine triphosphate

A three-dimensional (3D) micromolecule walking nanomachine propelled by strand displacement was developed to establish a novel switching electrochemiluminescence (ECL) biosensor for ultrasensitive detection of adenosine triphosphate (ATP). Generally, walking nanomachines reported previously were limited to DNA walkers, while the proposed 3D walking nanomachine focused on the micromolecule walker. Firstly, TiO₂ and silver nanoparticles (Ag NPs) functionalized N-(4-aminobutyl)-N-(ethylisoluminol) (Ag-ABEI) were deposited onto the electrode surface to offer an enhanced ECL signal, resulting from the double catalytic effect of TiO₂ and Ag NPs for H₂O₂. Following, dopamine (DA)-labeled DNA duplex probes (S1/S2-DA) immobilized onto the modified electrode cut down the original ECL signal due to the quenching of DA toward ABEI (signal-off). Target ATP walker moved along the 3D DNA track, simultaneously releasing numerous DNA3, which was applied to displace S2-DA, resulting in the quenched ECL intensity recovery (signal-on). As a result, the biosensor showed a low limit of detection down to 0.5 nM (S/N = 3) and was successfully employed to determine ATP in human serum samples. Thus, the established biosensing strategy holds great potential for biochemical studies and clinical diagnosis.

Recent advances of functional nucleic acids-based electrochemiluminescent sensing

Electroluminescence (ECL) has been used in extensive applications ranging from bioanalysis to clinical diagnosis owing to its simple device requirement, low background, high sensitivity, and wide dynamic range. Nucleic acid is a significant theme in ECL bioanalysis. The inherent versatile selective molecular recognition of nucleic acids and their programmable self-assembly make it desirable for the robust construction of nanostructures. Benefiting from their unique structures and physiochemical properties, ECL biosensing based on nucleic acids has experienced rapid growth. This review focuses on recent applications of nucleic acids in ECL sensing systems, particularly concerning the employment of nucleic acids as molecular recognition elements, signal amplification units, and sensing interface schemes. In the end, an outlook of nucleic acid-based ECL biosensing will be provided for future developments and directions. We envision that nucleic acids, which act as an essential component for both bioanalysis and clinical diagnosis, will provide a new thinking model and driving force for developing next-generation sensing systems.

Application of tetrahedral -deoxyribonucleic acid electrochemistry platform coupling aptazymes and hybridized hairpin reactions for the measurement of extracellular adenosine triphosphate in plants

Extracellular ATP (eATP) is an important biological signal transduction molecule. Although a variety of detection methods have been extensively used in ATP sensing and analysis, accurate detection of eATP remains difficult due to its extremely low concentration and spatiotemporal distribution. Here, an eATP measurement strategy based on tetrahedral DNA (T-DNA)-modified electrode sensing platform and hybridization chain reaction (HCR) combined with G-quadruplex/Hemin (G4/Hemin) DNAzyme dual signal amplification is proposed. In this strategy, ATP aptamer and RNA-cleaving DNAzyme were combined to form a split aptazyme. In the presence of ATP, this aptazyme hydrolyzes the cleaving substrate strand with high selectivity, releasing cleaved ssDNA, which are captured by the T-DNA assembled on the electrode surface, triggering an HCR on the electrode surface to form numerous linker sequences of the HCR dsDNA product. When G-quadruplex@AuNPs (G4) spherical nucleic acid enzymes (SNAzymes) with other linkers are used as nanocatalyst tags, they are captured by HCR dsDNA through sticky linkers present on the electrode surface. An amplified electrochemical redox current signal is generated through SNAzyme-mediated catalysis of H₂O₂, enabling easy detection of picomole amounts of ATP. Using this strategy, eATP levels released by tobacco suspension cells were accurately measured and the distribution and concentration of eATP released on the surface of an Arabidopsis leaf was determined.

ATP-responsive laccase@ZIF-90 as a signal amplification platform to achieve indirect highly sensitive online detection of ATP in rat brain

A novel electrochemical online system for indirect, highly sensitive and selective online monitoring of ATP in the cerebral microdialysate is presented based on the particular reaction of ATP with zeolitic imidazole framework-90 (ZIF-90) encapsulated laccase microcrystals (laccase@ZIF-90) and the natural catalytic activity of laccase.

Target-induced activation of polymerase activity for recycling signal amplification cascades for sensitive aptamer-based detection of biomarkers

It is of great importance to develop biosensing methods for the sensitive and selective analysis of biomarkers at very low levels in biological samples. Using a new target-induced activation of the DNA polymerase activity for recycling amplification cascades, we describe an aptamer-based method for highly sensitive detection of platelet-derived growth factor BB (PDGF-BB) in human serums. The polymerase activity is initially inhibited by the binding of the polymerase to the enzyme aptamer sequence. PDGF-BB associates with and switches a PDGF-BB binding aptamer to trigger the release of an active polymerase, which further initiates the simultaneous recycling of the target PDGF-BB molecules and the enzyme aptamer sequence for the subsequent displacement of the fluorescently quenched probes to recover the fluorescence. Due to two recycling cascades, substantial fluorescence magnification is obtained for the highly sensitive detection of PDGF-BB with a low detection limit of 5.1 pM. Moreover, the potential applicability of this method for real samples was verified by determining PDGF-BB in diluted human serums, relying on the excellent specificity and selectivity of the aptamer. The demonstration of the PDGF-BB assay method here thus can be expanded for the construction of diverse sensing platforms for detecting different trace biomarkers with the integration of an elaborate design of the aptamer probes.

Nucleic acid therapeutics: a focus on the development of aptamers

INTRODUCTION

Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches.

AREAS COVERED

In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed.

EXPERT OPINION

Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.

A near-infrared-II fluorescence anisotropy strategy for separation-free detection of adenosine triphosphate in complex media

Fluorescence anisotropy (FA) has been widely applied for detecting and monitoring special targets in life sciences. However, matrix autofluorescence restricted its further application in complex biological samples. Herein, we report a near-infrared-II (NIR-II) FA strategy for detecting adenosine triphosphate (ATP) in human serum samples and breast cancer cell lysate, which employed NIR-II fluorescent Ag₂Se quantum dots (QDs) as tags to reduce matrix autofluorescence effect and applied graphene oxide (GO) to enhance fluorescence anisotropy signals. In the presence of ATP, the recognition between NIR-II Ag₂Se QDs labeled aptamer (QD-pDNA) and ATP led to the release of QD-pDNA from GO, resulting in the obvious decrease of FA values. ATP could be quantitatively detected in concentrations ranged from 3 nM to 2500 nM, with a detection limit down to 1.01 nM. This study showed that the developed NIR-II FA strategy could be applied for detecting targets in complex biological samples and had great potential for monitoring interactions between biomolecules in biomedical research.

A nanoprobe based on molybdenum disulfide nanosheets and silver nanoclusters for imaging and quantification of intracellular adenosine triphosphate

Adenosine triphosphate (ATP), as a high-energy phosphate compound that stores and releases energy in living cells, has an irreplaceable role in many physiological processes and maintenance of biological functions, and can be used as an indicator of many diseases. In this work, a composite nanoprobe, silver nanocluster (AgNC) @ molybdenum disulfide (MoS₂), was designed to achieve in situ fluorescence imaging and quantitative analysis of intracellular ATP in HeLa cells by fluorescence spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). The probe was constructed based on the adsorption of DNA-AgNCs by MoS₂ nanosheets, and the DNA-AgNCs were prepared with the ATP aptamer as a template, whose fluorescence was initially quenched by MoS₂. When the probe was incubated into the cells, intracellular ATP recognized the aptamer sequence and caused the DNA-AgNCs to fall off the MoS₂ nanosheets, resulting in fluorescence recovery. Here, AgNCs not only acted as a fluorescence label for imaging, but also as an element tag for quantitative analysis of intracellular ATP with the detection of ¹⁰⁷Ag by ICP-MS. The ATP in HeLa cells detected by this method was 24.6 ± 1.7 nmol L^-1, which was in good agreement with the test result of the ATP test kit (20.4 ± 0.8 nmol L^-1). The proposed method has potential application in medical clinical diagnosis and evaluation of the body's metabolic level via fluorescence imaging and ICP-MS detection of intracellular ATP.

Aptamer-integrated nucleic acid circuits for biosensing: Classification, challenges and perspectives

Owing to their high programmability and modularity, autonomous enzyme-free nucleic acid circuits are attracting ever-growing interest as signal amplifiers with potential applications in developing highly sensitive biosensing techniques. Besides nucleic acid input, the biosensing scope of aptamer-integrated nucleic acids could be further expanded to non-nucleic targets by integrating nucleic acid circuits with aptamers-a class of functional oligonucleotides with binding capabilities toward specific targets. By coupling upstream target recognition with downstream signal amplification, aptamer-integrated nucleic acid circuits enable aptasensors with increased sensitivity and enhanced performances, which may act as powerful tools in various fields including environment monitoring, personal care, clinical diagnosis, etc. In designing aptamer-integrated nucleic acid circuits, smart integration between aptamer and nucleic acid circuits plays a crucial role in developing reliable circuits with good performances. To date, although there are plenty of published researches adopting aptamer-integrated nucleic acid circuits as amplifiers in biosensing systems, deep discussion or systematic review on rational design strategies for aptamer-integrated nucleic acid circuits is still lacking. To fill this gap, rational aptamer-nucleic acid circuits integration modes were classified and summarized for the first time based on reviewing the state of art of existing aptamer-integrated nucleic acid circuits. Moreover, theoretical updates in nucleic acid circuits designs and major challenges to be overcome in developing highly sensitive aptamer-integrated nucleic acids based biosensing systems are discussed in this review.

An electrochemical aptasensor for ATP based on a configuration-switchable tetrahedral DNA nanostructure

A novel electrochemical aptasensor for ATP was developed based on an aptamer-embedded configuration-switchable tetrahedral DNA nanostructure (TDN) and the formation of a G-quadruplex. This unique TDN was formed through the self-assembly of four specially designed single-stranded DNA (ssDNA) sequences (S1, S2, S3 and S4). The TDN was immobilized on the surface of a Au electrode through the thiol groups at the 5'-end of S1, S2 and S3. Five edges of the TDN were designed to form a double helix to preserve the structural robustness of the tetrahedron, while the ATP aptamer embedded sequence (S3) was designed to be located at the rest edge. The two terminals of S4 at the same edge were composed of two split G-quadruplex-forming sequences, which were non-complementary to the aptamer. This edge offered the configuration-switchable characteristic of the TDN. In the absence of ATP, the TDN remained in a relaxed state, and the G-quadruplex cannot form due to the large distance between the split G-quadruplex-forming sequences. However, in the presence of ATP, the aptamer combined with ATP and shortened the distance between the split sequences, resulting in the taut state of the TDN and the formation of a G-quadruplex at the edge. After the addition of hemin, the differential pulse voltammograms (DPVs) were used to quantify ATP. The sensor revealed a dynamic response range from 0.1 nM to 1 μM, with a detection limit of 50 pM. In addition, the specificity and practicability in real samples were also verified, indicating its potential applications.

One-Step Synthesis of Methylene Blue-Encapsulated Zeolitic Imidazolate Framework for Dual-Signal Fluorescent and Homogeneous Electrochemical Biosensing

In vitro diagnosis requires target biomarkers to be reliably detected at an ultralow level. A dual-signal strategy permits self-calibration to overcome the interferences of experimental and environmental factors, and thus is regarded as a promising approach. However, currently reported works mainly concentrated on the same forms of energy of output signals. Herein, we propose a one-step strategy for synthesis of methylene blue-encapsulated zeolitic imidazolate framework-90 (MB@ZIF-90) with high loading, unique dual-signal property, exceptional recognition capability, and good stability, and we further pioneer MB@ZIF-90 as a dual-signal biosensor for label-free, enzyme-free, and ultrasensitive detection of adenosine triphosphate (ATP) by integration of fluorescence and homogeneous electrochemical techniques. The recognition of MB@ZIF-90 by target ATP spurs the decomposition of ZIF-90, subsequently permitting MB to be released into a supernatant. As compared to the case where ATP does not exist, obviously increased intensities in fluorescence and differential pulse voltammetry current are observed and both signals are directly proportional to ATP concentrations. Thus, the MB@ZIF-90-based biosensor achieved dual-signal detection of ATP in an ultrasensitive manner and displayed a more reliable diagnosis result than previously reported ATP biosensors. This dual-signal strategy provides a new opportunity to develop high-performance biosensors for in vitro diagnosis and demonstrates great potential for future applications in bioinformatics and clinical medicine.

Cascaded multiple recycling amplifications for aptamer-based ultrasensitive fluorescence detection of protein biomarkers

Highly sensitive detection of molecular biomarkers plays a significant role in diagnosing various types of diseases at the early stage. We demonstrated in this paper an ultrasensitive aptamer-based fluorescence method for detecting mucin 1 (MUC1) in human serum via a cascaded multiple recycling signal amplification strategy. The MUC1 target molecules present in the samples cause structure switching of the hairpin aptamer probes, which initiates three cascaded recycling cycles for the cleavage of the fluorescently quenched signal probes to recover significant fluorescence for highly sensitive detection of MUC1. The developed method has a linear range from 100 fM to 1 nM for MUC1 detection. Besides, owing to the substantial signal amplification by the integrated and cascaded recycling cycles, a low detection limit of 35 fM is achieved with high selectivity. Moreover, the monitoring of trace MUC1 in human serum can also be realized with such a method, indicating its great potential for highly sensitive detection of different disease biomarkers.

Ultrasensitive and label-free detection of ATP by using gold nanorods coupled with enzyme assisted target recycling amplification

Abnormal concentration of adenosine triphosphate (ATP) is directly asscociate with several diseases. Thus, sensitive detection of ATP is essential to early diagnosis of disease. Herein, we described an ultrasensitive strategy for ATP detection by using positively charged gold nanorods ((+)AuNRs) as an efficient fluorescence quenching platform, coupled with exonuclease Ⅲ (Exo Ⅲ) assisted target recycling amplification. To construct the sensor, DNA template that contained ATP aptamer was used for the formation of Ag nanoclusters signal probe (DNA/AgNCs), the structure of it could change to duplex after the interaction of it with ATP. Such DNA template or duplex DNA product could electrostatically adsorb onto (+)AuNRs surface, resulting in the quenching of the fluorescence signal due to the vicinity of AgNCs to (+)AuNRs. With the addition of Exo Ⅲ, DNA duplex could be hydrolyzed and released from (+)AuNRs surface, leading to the recovery of a strong fluorescent signal, while ATP could be regenerated for next target recycling. Combing the good fluorescence quenching ability of (+)AuNRs and the Exo Ⅲ assisted signal amplification, a low detection limit of 26 pM was achieved for ATP detection. Notably, the proposed method can be successfully applied for detecting ATP in serum samples, indicating a potential application value in early cancer diagnosis.

Coupling strand extension/excision amplification with target recycling enables highly sensitive and aptamer-based label-free sensing of ATP in human serum

Detection of aberrant ATP concentrations with high sensitivity and selectivity is of critical importance for monitoring many biological processes and disease stages. By coupling extension/excision amplification with target recycling, we have established an aptamer-based method for label-free fluorescence ATP detection in human serum with high sensitivity. The ATP target molecules associate with the aptamer-containing double hairpin probes and cause conformational changes of the probes to initiate the cyclic strand extension/excision processes in the presence of polymerase, endonuclease and assistance sequences for the recycling of ATP and the production of a large number of G-quadruplex sequences. The organic dye thioflavin T subsequently binds these G-quadruplex sequences to yield substantially enhanced fluorescence emission for achieving highly sensitive detection of ATP down to 2.2 nM in the range of 5 to 200 nM without using any labels. The developed aptamer sensing method also exhibits high selectivity and allows the monitoring of ATP at low concentrations in diluted real samples, which offers promising opportunities to establish effective signal magnification means for the detection of various biomolecules at trace levels.

Coupling aptazyme and catalytic hairpin assembly for cascaded dual signal amplified electrochemiluminescence biosensing

Developing reliable and sensitive detection methods for adenosine triphosphate (ATP) is vital for both clinical diagnosis and food safety. In this work, by coupling aptazyme- and catalytic hairpin assembly (CHA)-based signal amplification and electrochemiluminescence (ECL), an ultrasensitive biosensor for sensing ATP was fabricated using Ru(bpy)₃²⁺-doped silica nanoparticles (RuSiO₂) as ECL probes and a ferrocene-functionalized hairpin DNA (hairpin-Fc) as quencher. The aptazyme-triggered cleavage of the DNA substrate and the CHA reaction both led to the circular release of trigger DNA, resulting in a significant dual signal amplification, with unprecedented enhancement up to 940-fold. Moreover, the bioconjugation of the DNA substrate with Au@Fe₃O₄ facilitated the separation and purification of the released trigger DNA, and effectively reduced the background signal. As a result, the as-prepared ECL biosensor exhibited a much lower detection limit of 0.054 pM for ATP, compared to those in previous reports, and showed high reliability for ATP detection in both spiked serum samples and Staphylococcus aureus. This work offers a new perspective for designing nucleic acid-based signal amplification for detecting ATP in bacterial analysis and clinical diagnosis.

Programmable mismatch-fueled high-efficiency DNA signal converter

Herein, by directly introducing mismatched reactant DNA, high-reactivity and high-threshold enzyme-free target recycling amplification (EFTRA) is explored. The developed high-efficiency EFTRA (HEEFTRA) was applied as a programmable DNA signal converter, possessing higher conversion efficiency than the traditional one with perfect complement owing to the more negative reaction standard free energy (ΔG). Once traces of input target miRNA interact with the mismatched reactant DNA, amounts of ferrocene (Fc)-labeled output DNA could be converted via the EFTRA. Impressively, the Fc-labeled output DNA could be easily captured by the DNA tetrahedron nanoprobes (DTNPs) on the electrode surface to form triplex-forming oligonucleotide (TFO) at pH = 7.0 for sensitive electrochemical signal generation and the DTNPs could be regenerated at pH = 10.0, from which the conversion efficiency (N) will be accurately obtained, benefiting the selection of suitable mismatched bases to obtain high-efficiency EFTRA (HEEFTRA). As a proof of concept, the HEEFTRA as an evolved DNA signal converter is successfully applied for the ultrasensitive detection of miRNA-21, which gives impetus to the design of other signal converters with excellent efficiency for ultimate applications in sensing analysis, clinical diagnosis, and other areas.

Fluorometric determination of ssDNA based on functionalized magnetic microparticles and DNA supersandwich self-assemblies

A method is described for the determination of DNA via nucleic acid amplification by using nucleic acid concatemers that result from DNA supersandwich self-assemblies (SSAs). The method employs two auxiliary probes to form self-assembled biotin SSAs. These exhibit strong fluorescence if labeled with intercalator SYBR Green I. In the presence of the target (as exemplified for a 30-mer), streptavidin is released from the surface of the functionalized magnetic microparticles (FMMPs) by competitive hybridization on the surface. However, the SSA products do not conjugate to the FMMPs. This leads to a large amount of SYBR Green I intercalated into the concatemers and eventually results in amplified fluorescence in the supernate. The SSA products can be prepared beforehand, and amplification therefore can be completed within 50 min. The method is more efficient than any other conventional amplification. The detection limit for the 30-mer is 26.4 fM which is better by a factor of 10 compared to other amplification methods. Conceivably, the method can be further extended to the determination of a wide variety of targets simply by replacing the sequences of the probes. Finally, this rapid and highly sensitive method was employed for detection of Ebola virus gene (≈30-mer) and ATP in spiked serum with satisfactory results. Graphical abstract A high sensitivity and efficiency bioassay is described based on functionalized magnetic microparticles and DNA supersandwich self-assemblies.

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme-free, high-efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single-stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in-depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000-fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.