Fluorescent probes for recognition 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.

Rational construction of a self-assembled nanoprobe for specific imaging ATP in cancer cells

Adenosine triphosphate (ATP) serves as the energy currency unit and plays a crucial role in various cellular processes. While many small molecule fluorescent probes have been successfully developed for detecting ATP, their biological applications have been limited due to the restrictions of specificity of ATP response and targeting cancer cells. This study introduces a novel self-assembled polymer fluorescent nanoprobe, RdB-DETA-HA NPs, specifically designed for the monitoring and imaging of ATP in live cancer cells. The nanoprobe integrates diethylenetriamine-linked rhodamine B as a fluorescence recognition moiety for ATP, covalently incorporated with hyaluronic acid (HA). This innovative design enhances water dispersibility, prevents dye leakage, and significantly improves cancer cell targeting via CD44 receptor-mediated endocytosis. Our results demonstrate the nanoprobe's exceptional ability to specifically target cancer cells and dynamically monitor ATP levels, marking a substantial advancement over traditional small molecule probes. The RdB-DETA-HA NPs show great promise for widespread applications in biomedical research and diagnostic imaging.

A novel ratiometric luminescent probe based on a ruthenium(II) complex-rhodamine scaffold for ATP detection in cancer cells

Adenosine 5'-triphosphate (ATP) plays a pivotal role as an essential intermediate in energy metabolism, influencing nearly all biological metabolic processes. Cancer cells predominantly rely on glycolysis for ATP production, differing significantly from normal cells. Real-time in situ monitoring and rapid response to intracellular ATP levels offers more valuable insights into cancer cell physiology. Herein, we report a novel ratiometric luminescent probe, Ru-Rho, comprised of a ruthenium(II)-based complex and rhodamine 6G (Rho 6G) with excellent water solubility and photostability. Notably, Ru-Rho selectively responds to ATP at acidic conditions, matching the need of monitoring ATP under the acidic intracellular environment of cancer cells. Moreover, the fast ratiometric detection and imaging of ATP under single wavelength excitation improve the detection accuracy. Ru-Rho has been effectively utilized not only for ratio imaging ATP in cells and zebrafish, but also for assessing the efficacy of glycolysis-inhibiting anticancer drugs in intracellular levels, which accelerates the screening process for anticancer drugs and supports the development of new therapeutic agents. The design strategy based on transition metal ruthenium(II) complexes opens a new pathway for constructing ATP luminescent probes, allowing for better adaptation to complex detection requirements.

Multifunctional Fluorescent Probe for Simultaneous Detection of ATP, Cys, Hcy, and GSH: Advancing Insights into Epilepsy and Liver Injury

Adenosine triphosphate (ATP) is a critical intracellular energy currency that plays a key role in various cellular processes and is closely associated with numerous diseases. Similarly, biothiols such as glutathione (GSH), cysteine (Cys), and homocysteine (Hcy) are integral to many physiological and pathological processes due to their strong redox properties. Simultaneous discrimination and detection of ATP and biothiols offer valuable insights into the pathogenesis of conditions such as epilepsy and liver injury. This study introduces the first fluorescent probe, BCR, designed for multifunctional detection of ATP, GSH, Hcy, and Cys. With outstanding optical properties, excellent biocompatibility, high selectivity, and superior sensitivity, probe BCR enables effective imaging of ATP and biothiol dynamics in vivo. Moreover, probe BCR successfully visualizes changes in ATP, GSH, Hcy, and Cys levels in a PTZ-induced epileptic zebrafish model and an APAP-induced mouse liver injury tissue section model. These findings underscore the significant potential of probe BCR for early disease diagnosis and therapeutic applications.

Pyridine appended pyrimidine bis hydrazone: Zn2+/ATP detection, bioimaging and functional properties of its dinuclear Zn(II) complex

A pyridine functionalized pyrimidine-based system, H2P was successfully synthesized, characterized, and evaluated for its remarkable selective characteristics towards Zn2+ and ATP ions. The chemical sensing capabilities of H2P were demonstrated through absorption, fluorescence, and NMR spectroscopic techniques. The probe exhibited outstanding sensitivity when interacting with the ions, demonstrating relatively strong association constants and impressively low detection limits. The comprehensive binding mechanism of H2P with respect to Zn2+ and ATP ions was investigated using a combination of analytical methods, including Job's plot, NMR spectroscopy, mass spectrometry, and density functional theory (DFT) experiments. The interesting sensing ability of H2P for Zn2+/ATP ions was harnessed for live cell bioimaging and other diverse on-site detection purposes, including paper strips, cotton swabs, and applications involving mung bean sprouts. Further, the fluorescent probe demonstrated its effectiveness in detecting Zn2+ and ATP within live cells, indicating its significant potential in the realm of biological imaging applications. Moreover, the molecular configuration of the zinc complex (H2P-Zn2Cl4), derived from H2P, was elucidated using X-ray crystallography. This complex exhibited intriguing multifunctional attributes, encompassing its capability for detecting picric acid and for reversible acid/base sensing responses. The enhanced conducting behavior of the complex as well as its resistance properties were investigated by performing I-V characteristics and electrochemical impedance spectroscopic (EIS) experiments respectively.

Macrocyclic Conformational Switch Coupled with Pyridinium-Induced PET for Fluorescence Detection of Adenosine Triphosphate

The binding of nucleotides is crucial for signal transduction as it induces conformational protein changes, leading to downstream cellular responses. Synthetic receptors that bind nucleotides and transduce the binding event into global conformational rearrangements are highly challenging to design, especially those that operate in an aqueous solution. Much work is focused on evaluating functionalized dyes to detect nucleotides, whereas coupling of a nucleotide-induced conformational switching to a sensing event has not been reported to date. We disclose synthetic receptors that undergo a global conformational rearrangement upon nucleotide binding. Integrating naphthalimide and the pyridinium ion into the structure enables stabilization of the folded conformation and efficient fluorescence quenching. The binding of a nucleotide rearranges the receptor conformation and alters the strong fluorescence enhancement. The methylpyridinium-containing receptor demonstrated high sensing selectivity for adenosine 5'-triphosphate (ATP) and a record 160-fold fluorescence enhancement. It can detect fluctuations of ATP in HeLa cells and possesses low cytotoxicity. The developed systems present an attractive approach for designing ATP-responsive artificial molecular switches that operate in water and integrate a strong fluorescence response.

Metal Ion-Regulated Fluorescent Sensor Array Based on Gold Nanoclusters for Physiological Phosphate Sensing

The detection of physiological phosphates (PPs) is of great importance due to their essential roles in numerous biological processes, but the efficient detection of different PPs simultaneously remains challenging. In this work, we propose a fluorescence sensor array for detecting PPs based on metal-ion-regulated gold nanoclusters (AuNCs) via an indicator-displacement assay. Zn2+ and Eu3+ are selected to assemble with two different AuNCs, resulting in quenching or enhancing their fluorescence. Based on the competitive interaction of metal ions with AuNCs and PPs, the fluorescence of AuNCs will be recovered owing to the disassembly of AuNC-metal ion ensembles. Depending on different PPs' distinct fluorescence responses, a four-channel sensor array was established. The array not only exhibits good discrimination capability for eight kinds of PPs (i.e., ATP, ADP, AMP, GTP, CTP, UTP, PPi, and Pi) via linear discriminant analysis but also enables quantitative detection of single phosphate (e.g., ATP) in the presence of interfering PPs mixtures. Moreover, potential application of the present sensor array for the discrimination of different PPs in real samples (e.g., cell lysates and serum) was successfully demonstrated with a good performance. This work illustrates the great potential of a metal ion-regulated sensor array as a new and efficient sensing platform for differential sensing of phosphates as well as other disease-related biomolecules.

Water-Soluble Triazolium Covalent Cages for ATP Sensing

Water-soluble organic cages are attractive targets for their molecular recognition and sensing features of biologically relevant molecules. Here, we have successfully designed and synthesized a pair of water-soluble cationic cages employing click reaction as the fundamental step followed by the N-methylation of the triazole rings. The rigid and shape-persistent 3D hydrophobic cavity, positively charged surface, H-bonding triazolium rings, and excellent water solubility empower both cages to exhibit a superior affinity and selectivity for binding with adenosine-5'-triphosphate (ATP) compared to cyclophanes and other macrocyclic receptors. Both cage molecules (PCC⋅Cl and BCC⋅Cl) can bind a highly emissive dye HPTS (8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt) to form non-fluorescent complexes. The addition of ATP resulted in the stronger cage⊂ATP complexes with the retention of HPTS emission upon its displacement. The resultant indicator-displacement assay system can efficiently sense and quantify ATP in nanomolar detection limits in buffer solutions and human serum matrix. Spectroscopic and theoretical studies revealed the synergistic effect of π⋅⋅⋅π stacking interaction between the aromatic moiety of the cationic cages and the adenine moiety of ATP, as well as the electrostatic and hydrogen bonding interaction between the phosphate anion of ATP and triazole protons of cages, played the pivotal roles in the sensing process.

Gold Nanocluster-Based Fluorescent Microneedle Platform toward Visual Detection of ATP

Adenosine triphosphate (ATP) participates in the regulation of most biological processes, and the ATP level is closely associated with many diseases. However, it still remains challenging to achieve on-site monitoring of ATP in an equipment-free and efficient way. Microneedles, a minimally invasive technology that can extract biomarkers from liquid biopsies, have recently emerged as useful tools for early diagnosis of a broad range of diseases. In this work, we developed hydrogel microneedles that are loaded with ATP-specific dual-emitting gold nanoclusters (RhE-AuNCs) for fast sampling and on-needle detection of ATP. These RhE-AuNCs were photo-crosslinked to the hydrogel matrix to form a fluorescent microneedle patch. Based on the ATP-induced Förster resonance energy transfer in RhE-AuNCs, a highly selective, sensitive, and reliable ATP sensor was developed. Moreover, simultaneous capture and visual detection of ATP was achieved by the AuNC-loaded microneedle sensing platform, which exhibits promising sensing performance. This work provides a new approach to design a point-of-care ATP sensing platform, which also holds great potential for the further development of microneedle-based analytical devices.

Real-Time Visualization of Cytosolic and Mitochondrial ATP Dynamics in Response to Metabolic Stress in Cultured Cells

Adenosine 5' triphosphate (ATP) is the energy currency of life, which is produced in mitochondria (~90%) and cytosol (less than 10%). Real-time effects of metabolic changes on cellular ATP dynamics remain indeterminate. Here we report the design and validation of a genetically encoded fluorescent ATP indicator that allows for real-time, simultaneous visualization of cytosolic and mitochondrial ATP in cultured cells. This dual-ATP indicator, called smacATPi (simultaneous mitochondrial and cytosolic ATP indicator), combines previously described individual cytosolic and mitochondrial ATP indicators. The use of smacATPi can help answer biological questions regarding ATP contents and dynamics in living cells. As expected, 2-deoxyglucose (2-DG, a glycolytic inhibitor) led to substantially decreased cytosolic ATP, and oligomycin (a complex V inhibitor) markedly decreased mitochondrial ATP in cultured HEK293T cells transfected with smacATPi. With the use of smacATPi, we can also observe that 2-DG treatment modestly attenuates mitochondrial ATP and oligomycin reduces cytosolic ATP, indicating the subsequent changes of compartmental ATP. To evaluate the role of ATP/ADP carrier (AAC) in ATP trafficking, we treated HEK293T cells with an AAC inhibitor, Atractyloside (ATR). ATR treatment attenuated cytosolic and mitochondrial ATP in normoxia, suggesting AAC inhibition reduces ADP import from the cytosol to mitochondria and ATP export from mitochondria to cytosol. In HEK293T cells subjected to hypoxia, ATR treatment increased mitochondrial ATP along with decreased cytosolic ATP, implicating that ACC inhibition during hypoxia sustains mitochondrial ATP but may not inhibit the reversed ATP import from the cytosol. Furthermore, both mitochondrial and cytosolic signals decrease when ATR is given in conjunction with 2-DG in hypoxia. Thus, real-time visualization of spatiotemporal ATP dynamics using smacATPi provides novel insights into how cytosolic and mitochondrial ATP signals respond to metabolic changes, providing a better understanding of cellular metabolism in health and disease.

Approaches to monitor ATP levels in living cells: where do we stand?

ATP is the most universal and essential energy molecule in cells. This is due to its ability to store cellular energy in form of high-energy phosphate bonds, which are extremely stable and readily usable by the cell. This energy is key for a variety of biological functions such as cell growth and division, metabolism, and signaling, and for the turnover of biomolecules. Understanding how ATP is produced and hydrolyzed with a spatiotemporal resolution is necessary to understand its functions both in physiological and in pathological contexts. In this review, first we will describe the organization of the electron transport chain and ATP synthase, the main molecular motor for ATP production in mitochondria. Second, we will review the biochemical assays currently available to estimate ATP quantities in cells, and we will compare their readouts, strengths, and weaknesses. Finally, we will explore the palette of genetically encoded biosensors designed for microscopy-based approaches, and show how their spatiotemporal resolution opened up the possibility to follow ATP levels in living cells.

Rhodamine-thiourea Linked Naphthalimide Derivative to Image ATP in Mitochondria using Two Channels

Adenosine 5'-triphosphate (ATP), synthesized in mitochondria, is an energy molecule in all living things. ATP not only serves as an energy source for protein synthesis and muscle contraction, but also as an important indicator for various diseases, such as Parkinson's disease, cardiovascular disease, and others. Accordingly, detection and sensing of ATP, especially in mitochondria, are important. In this study, a unique ring-opening process of rhodamine was coupled to recognition of ATP via introduction of a thiourea moiety, which was further linked to a naphthalimide group. A strong fluorescent emission at ∼580 nm was accompanied by a color change from colorless to pink upon addition of ATP at pH 7.4. Fluorescent probe 1 successfully imaged mitochondrial ATP with a Pearson's coefficient of 0.8. In addition, green emission from the naphthalimide moiety at ∼530 nm was observed without any change upon addition of ATP. This emission can be considered equivalent to an internal standard to utilize probe 1 as a dual-channel probe for ATP. Furthermore, probe 1 showed negligible cytotoxicity based on MTT assays.

Recent Progress in Fluorescent Chemosensors for Protein Kinases

Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.

Development and Challenge of Fluorescent Probes for Bioimaging Applications: From Visualization to Diagnosis

Fluorescent probes have been used widely in bioimaging, including biological substance detection, cell imaging, in vivo biochemical reaction process tracking, and disease biomarker monitoring, and have gradually occupied an indispensable position. Compared with traditional biological imaging technologies, such as positron emission tomography (PET) and nuclear magnetic resonance imaging (MRI), the attractive advantages of fluorescent probes, such as real-time imaging, in-depth visualization, and less damage to biological samples, have made them increasingly popular. Among them, ultraviolet-visible (UV-vis) fluorescent probes still occupy the mainstream in the field of fluorescent probes due to the advantages of available structure, simple synthesis, strong versatility, and wide application. In recent years, fluorescent probes have become an indispensable tool for bioimaging and have greatly promoted the development of diagnostics. In this review, we focus on the structure, design strategies, advantages, representative probes and latest discoveries in application fields of UV-visible fluorescent probes developed in the past 3-5 years based on several fluorophores. We look forward to future development trends of fluorescent probes from the perspective of bioimaging and diagnostics. This comprehensive review may facilitate the development of more powerful fluorescent sensors for broad and exciting applications in the future.

Cell-membrane-targeted near-infrared fluorescent probe for detecting extracellular ATP

A fluorescent probe for detecting extracellular ATP.

Recent achievements and advances in optical and electrochemical aptasensing detection of ATP based on quantum dots

The design and fabrication of high sensitive and selective biosensing platforms areessential goals to precisely recognize biomaterials in biological assays. In particular, determination of adenosine triphosphate (ATP) as the main energy currency of the cells and one of the most important biomolecules in living organisms is a pressing need in advanced biological detection. Recently, aptamer-based biosensors are introduced as a new direct strategy in which the aptamers (Apts) directly bind to the different targets and detect them on the basis of conformational changes and physical interactions. They can also be conjugated to optical and electronic probes such as quantum dot (QD) nanomaterials and provide unique QD aptasensing platforms. Currently, these Apt-based biosensors with excellent recognition features have attracted extensive attention due to the high specificity, rapid response and facile construction. Therefore, in this review article, recent achievements and advances in aptasensing detection of ATP based on different detection methods and types of QDs are discussed. In this regard, the optical and electrochemical aptasensors have been categorized based on detection methods; fluorescence (FL), electrochemiluminescence (ECL) and photoelectrochemical (PEC) and they have been also divided to two main groups based on QDs; metal-based (M-based) and carbon-based (C-based) materials. Then, their advantages and limitations have been highlighted, compared and discussed in detail.

Azulene-based fluorescent chemosensor for adenosine diphosphate

AzuFluor® 435-DPA-Zn, an azulene fluorophore bearing two zinc(II)-dipicolylamine receptor motifs, exhibits fluorescence enhancement in the presence of adenosine diphosphate. Selectivity for ADP over ATP, AMP and PPi results from appropriate positioning of the receptor motifs, since an isomeric sensor cannot discriminate between ADP and ATP.

Theoretical Study on Storage and Release of Firefly Luciferin

Among numerous bioluminescent organisms, firefly is the most studied one. Recent experiment proposed that sulfoluciferin (SLH₂ ) may serve as a storage form of luciferin (LH₂ ). In the present article, we employed density functional theory calculation to uncover the mechanism and detailed process of the storage and release reactions. Due to lack of available crystallographic structure of the related enzyme, the calculation was performed on a model system. For the storage reaction, possible amino acid residues were used for imitating the protein environment. For the release reaction, the dielectric constant of 3.0 was employed to simulate the polarity of the protein cavity. The computational results indicated that the reactions from LH₂ to SLH₂ and from SLH₂ to LH₂ are both exergonic, which favor the storage and release processes and coincide with the experimental observation. Basing on experimental and current theoretical study, we supplemented the stages of LH₂ storage and release in the entire bioluminescent cycle of firefly. The current theoretical calculation could inspire the study on LH₂ storage and release of other bioluminescent organisms.

A Fluorescence Sensor Array Based on Zinc(II)-Carboxyamidoquinolines: Toward Quantitative Detection of ATP*

The newly prepared fluorescent carboxyamidoquinolines (1-3) and their Zn(II) complexes (Zn@1-Zn@3) were used to bind and sense various phosphate anions utilizing a relay mechanism, in which the Zn(II) ion migrates from the Zn@1-Zn@3 complexes to the phosphate, namely adenosine 5'-triphosphate (ATP) and pyrophosphate (PPi), a process accompanied by a dramatic change in fluorescence. Zn@1-Zn@3 assemblies interact with adenine nucleotide phosphates while displaying an analyte-specific response. This process was investigated using UV-vis, fluorescence, and NMR spectroscopy. It is shown that the different binding selectivity and the corresponding fluorescence response enable differentiation of adenosine 5'-triphosphate (ATP), adenosine 5'-diphosphate (ADP), pyrophosphate (PPi), and phosphate (Pi). The cross-reactive nature of the carboxyamidoquinolines-Zn(II) sensors in conjunction with linear discriminant analysis (LDA) was utilized in a simple fluorescence chemosensor array that allows for the identification of ATP, ADP, PPi, and Pi from 8 other anions including adenosine 5'-monophosphate (AMP) with 100 % correct classification. Furthermore, the support vector machine algorithm, a machine learning method, allowed for highly accurate quantitation of ATP in the range of 5-100 μM concentration in unknown samples with error <2.5 %.

Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds

Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.

Binding and Sensing Properties of a Hybrid Naphthalimide-Pyrene Aza-Cyclophane towards Nucleotides in an Aqueous Solution

Selective recognition of nucleotides with synthetic receptors is an emerging direction to solve a series of nucleic acid-related challenges in biochemistry. Towards this goal, a new aza-cyclophane with two different dyes, naphthalimide and pyrene, connected through a triamine linker has been synthesized and studied for the ability to bind and detect nucleoside triphosphates in an aqueous solution. The receptor shows Foerster resonance energy transfer (FRET) in fluorescence spectra upon excitation in DMSO, which is diminished dramatically in the presence of water. According to binding studies, the receptor has a preference to bind ATP (adenosine triphosphate) and CTP (cytidine triphosphate) with a “turn-on” fluorescence response. Two separate emission bands of dyes allow one to detect nucleotides in a ratiometric manner in a broad concentration range of 10⁻⁵–10⁻³ M. Spectroscopic measurements and quantum chemical calculations suggest the formation of receptor–nucleotide complexes, which are stabilized by dispersion interactions between a nucleobase and dyes, while hydrogen bonding interactions of nucleobases with the amine linkers are responsible for selectivity.

Fluorescence ‘off–on–off’ signaling with zinc ensemble: a new array of investigating prevalence of ATP in liver cancer cells

2-Hydroxy naphthaldehyde–picolylamine conjugate (NPAC) ensemble with Zn²⁺ (NPAC–Zn2+) has been synthesized for the selective recognition and estimation of ATP in human liver cancer cells.

Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes

The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.

Ratiometric Detection of ATP by Fluorescent Cyclophanes with Bellows-Type Sensing Mechanism

Pyrene-based cyclophanes have been synthesized with the aim to realize a bellows-type sensing mechanism for the ratiometric detection of nucleotide concentrations in a buffered aqueous solution. The sensing mechanism involves the encapsulation of a nucleobase between two pyrene rings, which affects the monomer-excimer equilibrium of the receptor in the excited state. The nature of the spacer and its connection pattern to pyrene rings have been varied to achieve high selectivity for ATP. The 1,8-substituted pyrene-based cyclophane with the 2,2'-diaminodiethylamine spacer demonstrates the best selectivity for ATP showing a 50-fold increase in the monomer-excimer emission ratio upon saturation with the nucleotide. The receptor can detect ATP within the biological concentrations range over a wide pH range. NMR and spectroscopic studies have revealed the importance of hydrogen bonding and stacking interactions for achieving a required receptor selectivity. The probe has been successfully applied for the real-time monitoring of creatine kinase activity.

Supramolecular Assembly of Acriflavine on Graphene Oxide for the Sensing of Adenosine Phosphates

An acriflavine-graphene oxide (GAF) supramolecular assembly has been prepared from water-soluble graphene oxide (GO) and a fluorescent dye, acriflavine (AF). Upon binding this non-covalently to the GO, the fluorescence of acriflavine has been "turned off" effectively, competitive binding potential of the sensor substrates such as ATP, ADP, AMP and the pyrophosphate weakens the supramolecular assembly of GAF, which allows the release of acriflavine quantitatively, which also "turns-on" the fluorescence of the dye under UV irradiation. Interestingly, GAF displayed the highest sensitivity towards ATP within the family of adenosine phosphates. We have developed a naked eye detection method for the adenosine phosphates biomolecules. For the first time, acriflavine has been utilized for the sensing of adenosine phosphates in combination with GO, which can be useful for the detection of other biomolecules.

A Quinoline-Appended Cyclodextrin Derivative as a Highly Selective Receptor and Colorimetric Probe for Nucleotides

The design and development of specific recognition and sensing systems for biologically important anionic species has received growing attention in recent years, as they play significant roles in biology, pharmacy, and environmental sciences. Herein, a new supramolecular sensing probe L1 was developed for highly selective differentiation of nucleotides. L1 displayed extremely marked absorption and emission differentiation upon binding with nucleotide homologs of AMP, ADP, and ATP, due to the divergent spatial orientations of guests upon binding, which allowed for a naked-eye colorimetric differentiation for nucleotides. A differentiating mechanism was unambiguously rationalized by using various spectroscopic studies and theoretical calculations. Furthermore, we successfully demonstrated that L1 can be applied to the real-time monitoring of the enzyme-catalyzed phosphorylation/dephosphorylation processes and thus demonstrated an unprecedented visualizable strategy for selectively differentiating the structurally similar nucleotides and real-time monitoring of biological processes via fluorescent and colorimetric changes.

Engineering a Reversible Fluorescent Probe for Real-Time Live-Cell Imaging and Quantification of Mitochondrial ATP

Real-time imaging and quantification of adenosine triphosphate (ATP) fluctuation in cells are significant for understanding the relationship between energy metabolism and cell functions. However, few synthetic fluorescent probes have been reported to tackle this challenge due to lack of accurate fluorescence readout and suitable response concentration. Herein we designed and synthesized a ratiometric fluorescent probe (Rh6G-ACFPN) for quantitatively detecting the fluctuation of mitochondrial ATP in living cells. Rh6G-ACFPN selectively and reversibly responds to ATP with an ideal dissociation constant (K_d) of 4.65 mM (3-10 mM: the range of mitochondrial ATP concentrations). Live-cell imaging allows us to directly monitor the dynamic changes of mitochondrial ATP in high temporal resolution. Moreover, for the first time, mitochondrial ATP in normal and cancer cells lines was successfully quantified and discriminated. These results demonstrate the versatility of Rh6G-ACFPN as a useful imaging tool to elucidate the function of mitochondrial ATP in living cells.

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.

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 Coumarin-Benzothiazole Derivative as a FRET-Based Chemosensor of Adenosine 5′-Triphosphate

A coumarin-benzothiazole ratiometric probe of ATP was designed and synthesized. The probe is based on incorporation of benzothiazole scaffold as a donor and coumarin nucleus as an acceptor in a single Förster resonance energy transfer/fluorescence resonance energy transfer (FRET) sensing platform. The sensor can detect ATP in aqueous solution with high selectivity over other nucleotide polyphosphate (NPP) anions. Binding of ATP to the sensor results in modulation of FRET efficiency between the donor and the acceptor which afforded a linear relationship between FRET signal and ATP (0.1–10 μM). A limit of detection (LOD) of 94.5 nM was quantified for FRET sensing of ATP by the probe. In addition, Job plot analysis revealed 1:1 binding interaction between the probe and ATP. The FRET probe was successfully utilized in monitoring ATP hydrolysis by apyrase in aqueous solution.

Self-assembling nanoprobes that display two-dimensional fluorescent signals for identification of surfactants and bacteria

The imidazolium-pyrene self-assembling nanoprobes can rapidly discriminate four types of surfactants.

Molecular Receptors for Recognition and Sensing of Nucleotides

Nucleotides are constituents of nucleic acids and they have a variety of functions in cellular metabolism. Synthetic receptors and sensors are required to reveal the role of nucleotides in living organisms and mechanisms of signal transduction events. In recent years, a large number of nucleotide-selective synthetic receptors have been devised, which utilize different molecular designs and sensing mechanisms. This Minireview presents recent progress in the design of synthetic molecular receptors for selective recognition of nucleotides in aqueous solution. The binding properties of receptors and the origins of their selectivity for a particular nucleotide are discussed.