A label-free electrochemiluminescent sensor for ATP detection based on ATP-dependent ligation

Colorimetric detection of ATP by inhibiting the Peroxidase-like activity of carbon dots

Adenosine triphosphate (ATP) is the main energy currency for cells and an important biomolecule involved in cellular reactions, whose abnormal levels are closely related to physical disease, thus it is extremely important to establish a convenient, fast and simple ATP monitoring method. Toward this end, we developed a facile method for colorimetric detection of ATP on the basis of the inhibiting effect of ATP on the peroxidase-like activity of carbon dots (CDs). The detection principle of this method was utilizing the peroxidase-like activity of CDs, which catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H₂O₂ to generate blue products. However, the introduction of ATP in the system can inhibit the generation of blue products, so ATP can be colorimetric detected. This method exhibited high sensitivity with a detection limit of 34 nM and a wide linear range (0.050-2.0 μM). The as-proposed colorimetric ATP sensor was capable of detecting ATP in real samples accurately.

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 electrochemiluminescence sensor for 17β-estradiol detection based on resonance energy transfer in α-FeOOH@CdS/Ag NCs

An electrochemiluminescence (ECL) resonance energy transfer system is constructed for 17β-estradiol (E2) detection using α-FeOOH@CdS nanospheres as the ECL-active substrates and Ag NCs as an efficient quencher. CdS QDs loaded onto three-dimensional (3D) urchin-like α-FeOOH nanospheres (α-FeOOH@CdS nanospheres) exhibited excellent ECL responses, which is attributed to dual-amplification of α-FeOOH frameworks. The 3D hierarchical structure of the α-FeOOH nanospheres provided abundant sites for loading ECL-active species, thus significantly improving the ECL performance of substrates; While Fe³⁺ presented on surface of α-FeOOH nanospheres could be reduced to Fe²⁺ in negative potentials, after which might activate persulfate in a Fenton-like process, resulting in more sulfate free radicals for more effective ECL responses via electron transfer reactions. Additionally, Ag nanoclusters (Ag NCs) stabilized by single stranded oligonucleotide were introduced as quenching probes for CdS QDs owing to the well-matched donor-acceptor spectrum for efficient energy transfer, which makes them appropriate for detection of E2. The proposed strategy displayed a desirable dynamic range from 0.01 to 10 pg mL^-1 with a limit of detection of 0.003 pg mL^-1. The proposed strategy based on the ECL-RET strategy offered an ideal way for E2 detection, and also revealed an alternative platform for detection of other small molecules.

Proximity-enabled bidirectional enzymatic repairing amplification for ultrasensitive fluorescence sensing of adenosine triphosphate

A novel fluorescence sensing strategy for ultrasensitive and highly specific detection of adenosine triphosphate (ATP) has been developed by the combination of the proximity ligation assay with bidirectional enzymatic repairing amplification (BERA). The strategy relies on proximity binding-triggered the release of palindromic tail that initiates bidirectional cyclic enzymatic repairing amplification reaction with the aid of polymerase and two DNA repairing enzymes, uracil-DNA glycosylase (UDG) and endonuclease IV (Endo IV). A fluorescence-quenched hairpin probe with a palindromic tail at the 3' end is skillfully designed that functions as not only the recognition element, primer, and polymerization template for BERA but also the indicator for fluorescence signal output. On the basis of the amplification strategy, this biosensor displays excellent sensitivity and selectivity for ATP detection with an outstanding detection limit of 0.81 pM. Through simultaneously enhancing the target response signal value and reducing nonspecific background, this work deducted the background effect, and showed high sensitivity and reproducibility. Moreover, our biosensor also shows promising potential in real sample analysis. Therefore, the proximity-enabled BERA strategy indeed creates a simple and valuable fluorescence sensing platform for ATP identification and related disease diagnosis and biomedical research.

Target-activated DNA nanomachines for the ATP detection based on the SERS of plasmonic coupling from gold nanoparticle aggregation

The self-assembly of plasmonic nanoparticles provides a powerful approach to generate surface-enhanced Raman scattering (SERS), which promotes the actual applications in chemical and biomolecular analyses. Herein, we developed a facile SERS sensing strategy for an ATP assay with a 3-D DNA nanomachine that walks by the Exo III cleavage, leading to the formation of AuNP aggregates, which resulted in the enhancement of the electromagnetic field. Depending on the target-activated Exo III cleavage, the 3-D nanomachine can walk along the 3-D track on the surface of AuNPs and generate self-assembled hot-spots to enhance the SERS signal of a Raman dye, allowing a homogenous assay of the ATP concentration with high sensitivity and reproducibility. Under optimized experimental conditions, the biosensor detected ATP with a widened dynamic range from 1 pM to 1 × 10⁵ pM with a limit of detection of up to 0.29 pM. Hence, the novel strategy provides a useful and practical platform for the SERS assay of ATP with high sensitivity and repeatability. Besides, this platform shows great potential for applications in high-throughput assays for drug screening and clinical diagnostics.

Monitoring of dynamic ATP level changes by oligomycin-modulated ATP synthase inhibition in SW480 cancer cells using fluorescent "On-Off" switching DNA aptamer

Adenosine triphosphate (ATP) is the main energy source in cells and an important biomolecule participating in cellular reactions in living organisms. Since the ATP level changes dynamically reflecting the development of a debilitating disease or carcinogenesis, we have focused in this work on monitoring of the oligomycin (OMC)-modulated ATP synthase inhibition using a fluorescent-switching DNA aptamer designed for the detection of ATP (Apt(ATP)), as the model for studies of dynamic ATP level variation. The behavior of the ATP aptamer has been characterized using fluorescence spectroscopy. The Intramolecular fluorescence resonance energy transfer (iFRET) operates in the proposed aptamer from the FAM dye moiety to guanines of the aptamer G-quadruplex when the target ATP is present and binds to the aptamer changing its conformation. The iFRET process enables the detection of ATP down to the limit of detection, LOD = 17 μM, without resorting to any extra chemi-amplification schemes. The selectivity coefficients for relevant interferent triphosphates (UTP, GTP, and CTP) are low for the same concentration as that of ATP. We have demonstrated an efficient transfection of intact cells and OMC-treated SW480 colon cancer cells with Apt(ATP), using microscopic imaging, iFRET measurements, and cell viability testing with MTT method. The applicability of the switching DNA aptamer for the analysis of real samples, obtained by lysis of SW480 cells, was also tested. The proposed Apt(ATP) may be considered as a viable candidate for utilization in measurements of dynamic ATP level modulation in cells in different stages of cancer development and testing of new drugs in pharmacological studies.

A Nucleic Acid Nanostructure Built through On-Electrode Ligation for Electrochemical Detection of a Broad Range of Analytes

For an assay to be most effective in point-of-care clinical analysis, it needs to be economical, simple, generalizable, and free from tedious workflows. While electrochemistry-based DNA sensors reduce instrumental costs and eliminate complicated procedures, there remains a need to address probe costs and generalizability, as numerous probes with multiple conjugations are needed to quantify a wide range of biomarkers. In this work, we have opened a route to circumvent complicated multiconjugation schemes using enzyme-catalyzed probe construction directly on the surface of the electrode. With this, we have created a versatile DNA nanostructure probe and validated its effectiveness by quantification of proteins (streptavidin, anti-digoxigenin, anti-tacrolimus) and small molecules (biotin, digoxigenin, tacrolimus) using the same platform. Tacrolimus, a widely prescribed immunosuppressant drug for organ transplant patients, was directly quantified with electrochemistry for the first time, with the assay range matching the therapeutic index range. Finally, the stability and sensitivity of the probe was confirmed in a background of minimally diluted human serum.

A label-free hairpin aptamer probe for colorimetric detection of adenosine triphosphate based on the anti-aggregation of gold nanoparticles

A facile and rapid colorimetric approach was described for selective and sensitive determination of adenosine triphosphate (ATP) based on a hairpin aptamer probe and the anti-aggregation of AuNPs. Poly(diallyldimethylammonium chloride) (PDDA) can induce the aggregation of AuNPs due to the electrostatic interaction causing a red to blue color change. Upon the addition of ATP, aptamer-based hairpin probe is opened and releases flexible ssDNA ends. The released flexible ssDNA ends can interact with PDDA and prevent PDDA-induced AuNPs aggregation. Thus, a visible color change from blue to red and a decrease in the absorption ratio (A₆₁₀/A₅₂₀) are observed. Under the optimal conditions, the hairpin aptamer-based colorimetric assay exhibits high sensibility and selectivity for the detection of ATP with a detection limit of 1.7nM. Moreover, this assay is successfully used in the rapid determination of ATP in spiked human serum samples with good recoveries in the range of 102.88 to 104.07%.

Size-controlled DNA-cross-linked hydrogel coated silica nanoparticles served as a ratiometric fluorescent probe for the detection of adenosine triphosphate in living cells

Herein, we have designed a ratiometric fluorescent nanoprobe for adenosine triphosphate sensing and imaging in living cells, based on silica nanoparticles and a DNA-functionalized hybrid hydrogel. This ratiometric detecting method could validly avoid false-positive signals. Due to its controllable size, favorable biocompatibility and biostability, the nanohydrogel exhibited high cellular permeability and fast response in living cells.

Advances in the design of nanomaterial-based electrochemical affinity and enzymatic biosensors for metabolic biomarkers: A review

This review (with 340 refs) focuses on methods for specific and sensitive detection of metabolites for diagnostic purposes, with particular emphasis on electrochemical nanomaterial-based sensors. It also covers novel candidate metabolites as potential biomarkers for diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis. Following an introduction into the field of metabolic biomarkers, a first major section classifies electrochemical biosensors according to the bioreceptor type (enzymatic, immuno, apta and peptide based sensors). A next section covers applications of nanomaterials in electrochemical biosensing (with subsections on the classification of nanomaterials, electrochemical approaches for signal generation and amplification using nanomaterials, and on nanomaterials as tags). A next large sections treats candidate metabolic biomarkers for diagnosis of diseases (in the context with metabolomics), with subsections on biomarkers for neurodegenerative diseases, autism spectrum disorder and hepatitis. The Conclusion addresses current challenges and future perspectives. Graphical abstract This review focuses on the recent developments in electrochemical biosensors based on the use of nanomaterials for the detection of metabolic biomarkers. It covers the critical metabolites for some diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis.

A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer-magnetic nanoparticles and its single-stranded complementary DNA labeled carbon dots

A new fluorimetric aptasensor was designed for the determination of adenosine triphosphate (ATP) based on magnetic nanoparticles (MNPs) and carbon dots (CDs). In this analytical strategy, an ATP aptamer was conjugated on MNPs and a complementary strand of the aptamer (CS) was labeled with CDs. The aptamer and its CS were hybridized to form a double helical structure. The hybridized aptamers could be used for the specific recognition of ATP in a biological complex matrix using a strong magnetic field to remove the interfering effect. In the absence of ATP, no CDs-CS could be released into the solution and this resulted in a weak fluorescence signal. In the presence of ATP, the target binds to its aptamer and causes the dissociation of the double helical structure and liberation of the CS, such that a strong fluorescence signal was generated. The increased fluorescence signal was proportional to ATP concentration. The limit of detection was estimated to be 1.0 pmol L^-1 with a dynamic range of 3.0 pmol L^-1 to 5.0 nmol L^-1 . The specific aptasensor was applied to detect ATP in human serum samples with satisfactory results. Moreover, molecular dynamic simulation (MDS) studies were used to analyze interactions of the ATP molecule with the aptamer.

Target-activated cascaded digestion amplification of exonuclease III aided signal-on and ultrasensitive fluorescence detection of ATP

In this work, a rapid, one-step and ultrasensitive signal-on fluorescence sensing for the detection of adenosine triphosphate (ATP) based on target-activated cascaded digestion amplification with Exo III aid was developed.

Use of a small molecule as an initiator for interchain staudinger reaction: A new ATP sensing platform using product fluorescence

We demonstrated that a small molecule induced interchain Staudinger reaction can be employed for highly selective detection of adenosine triphosphate (ATP), an important energy-storage biomolecule. A designed ATP split aptamer (A1) was first functionalized with a weakly fluorescent coumarin derivative due to an azide group (azido-coumarin). The second DNA strand (A2) was covalently linked with triphenylphosphine, which could selectively and efficiently reduce azido to amino group through the Staudinger reaction. The A2 was then hybridized with a half of another designed longer DNA strand (T1). The second half of T1 was a split aptamer and selectively recognized ATP with A1 to form a sandwich structure. The specific interaction between ATP and the aptamers drew the two functionalized DNA strands (A1 and A2) together to initiate the interchain Staudinger reduction at fmol-nmol concentration level, hence produced fluorescent 7-aminocoumarin which could be used as an indicator for the presence of trace ATP. The reaction process had a concentration dependent manner with ATP in a large concentration range. Such a strategy of interchain Staudinger reaction can be extended to construct biosensors for other small functional molecules on the basis of judiciously designed aptamers.

Label-free Electrochemical Detection of ATP Based on Amino-functionalized Metal-organic Framework

A sensitive, selective and recyclable electrochemical sensor is designed for ATP detection based on amino-functionalized metal-organic framework. The functional MOF as the sensor is constructed by one-step synthesis Ce-MOF and sequentially modified on the Au electrode and conjugated with the aptamer of ATP. The presence of target ATP leads to the conformational change of aptamer strands and strong electrochemical impedance. The electrochemical sensor can detect ATP down to 5.6 nM with the linear range of 10 nm to 1000 μM. The present study is the first report on the use of MOF as an electrochemical sensor for ATP at nM level. This strategy has been successfully applied in detection of ATP in serum of cancer patients, which reveals its potential application in clinical diagnosis.

Ternary Interactions and Energy Transfer between Fluorescein Isothiocyanate, Adenosine Triphosphate, and Graphene Oxide Nanocarriers

The interactions of fluorescent probes and biomolecules with nanocarriers are of key importance to the emerging targeted drug delivery systems. Graphene oxide nanosheets (GONs) as the nanocarriers offer biocompatibility and robust drug binding capacity. The interactions of GONs with fluorophores lead to strong fluorescence quenching, which may interfere with fluorescence bioimaging and biodetection. Herein, we report on the interactions and energy transfers in a model ternary system: GONs-FITC-ATP, where FITC is a model fluorophore (fluorescein isothiocyanate) and ATP is a common biomolecule (adenosine-5'-triphosphate). We have found that FITC fluorescence is considerably quenched by ATP (the quenching constant K_SV = 113 ± 22 M^-1). The temperature coefficient of K_SV is positive (α_T = 4.15 M^-1deg^-1). The detailed analysis of a model for internal self-quenching of FITC indicates that the temperature dependence of the net quenching efficiency η for the FITC-ATP pair is dominated by FITC internal self-quenching modes with their contribution estimated at 79%. The quenching of FITC by GONs is much stronger (K_SV = 598 ± 29 M^-1) than that of FITC-ATP and is associated with the formation of supramolecular assemblies bound with hydrogen bonding and π-π stacking interactions. For the analysis of the complex behavior of the ternary system GONs-FITC-ATP, a model of chemisorption of ATP on GONs, with partial blocking of FITC quenching, has been developed. Our results indicate that ATP acts as a moderator for FITC quenching by GONs. The interactions between ATP, FITC, and GONs have been corroborated using molecular dynamics and quantum mechanical calculations.

Highly Selective Cerebral ATP Assay Based on Micrometer Scale Ion Current Rectification at Polyimidazolium-Modified Micropipettes

Development of new principles and methods for cerebral ATP assay is highly imperative not only for determining ATP dynamics in brain but also for understanding physiological and pathological processes related to ATP. Herein, we for the first time demonstrate that micrometer scale ion current rectification (MICR) at a polyimidazolium brush-modified micropipette can be used as the signal transduction output for the cerebral ATP assay with a high selectivity. The rationale for ATP assay is essentially based on the competitive binding ability between positively charged polyimidazolium and ATP toward negatively charged ATP aptamer. The method is well responsive to ATP with a good linearity within a concentration range from 5 nM to 100 nM, and high selectivity toward ATP. These properties essentially enable the method to determine the cerebral ATP by combining in vivo microdialysis. The basal dialysate level of ATP in rat brain cortex is determined to be 11.32 ± 2.36 nM (n = 3). This study demonstrates that the MICR-based sensors could be potentially used for monitoring neurochemicals in cerebral systems.

Progress and challenges in electrochemiluminescent aptasensors

The importance of developing new diagnostic and detection technologies for the growing number of sensing challenges is rising each year. Here, we present a comprehensive and concise review on electrochemiluminescent (ECL) aptasensors by putting special emphasis on its characteristic features, advances, challenges, and applications of ECL based aptasensors. ECL is an ideal tool for constructing such sensors because of its inherent characteristics and can be easily integrated into aptamer based sensing platforms. This review summarizes the "synergistic benefits" of ECL aptamer-based sensors; classifications of ECL aptamer-based assay designs, and signal amplification strategies. This critical review highlights the effects of integration of nanomaterials, immobilization techniques, and amplification/detection strategies on the analytical performance of ECL based aptasensors. Moreover, several proof-of-concepts with appropriate figures and explanations have been shown to provide a general guide for the design of ECL aptasensors, and to stimulate further application of these ECL aptasensors. Finally, we conclude with the remaining challenges and opportunities to inspire further developments in ECL aptasensors.

Terbium ion-coordinated carbon dots for fluorescent aptasensing of adenosine 5'-triphosphate with unmodified gold nanoparticles

This work reports on a novel time-resolved fluorescent aptasensing platform for the quantitative monitoring of adenosine 5'-triphosphate (ATP) by interaction of dispersive/agglomerate gold nanoparticles (AuNPs) with terbium ion-coordinated carbon dots (Tb-CDs). To construct such a fluorescent nanoprobe, Tb-CDs with high-efficient fluorescent intensity are first synthesized by the microwave method with terbium ions (Tb(3+)). The aptasensing system consists of ATP aptamer, AuNP and Tb-CD. The dispersive/agglomerate gold nanoparticles are acquired through the reaction of the aptamer with target ATP. Upon target ATP introduction, the aptamers bind with the analytes to form new aptamer-ATP complexes and coat on the surface of AuNPs to inhibit their aggregation in the high salt solution. In this case, the fluorescent signal of Tb-CDs is quenched by the dispersive AuNPs on the basis of the fluorescence resonance energy transfer (FRET). At the absence of target analyte, gold nanoparticles tend to aggregate in the high salt state even if the aptamers are present. Thus, the added Tb-CDs maintain their intrinsic fluorescent intensity. Experimental results indicated that the aptasensing system exhibited good fluorescent responses toward ATP in the dynamic range from 40nM to 4.0μM with a detection limit of 8.5nM at 3sblank criterion. The repeatability and intermediate precision is less than 9.5% at three concentrations including 0.04, 0.4 and 2.0μM ATP. The selectivity was acceptable toward guanosine 5'-triphosphate, uridine 5'-triphosphate and cytidine 5'-triphosphate. The methodology was applied to evaluate the blank human serum spiked with target ATP, and the recoveries (at 3 concentration levels) ranged between 97.0% and 103.7%. Importantly, this detection scheme is rapid, simple, cost-effective, and does not require extensive sample preparation or separation.