In situ simultaneous monitoring of ATP and GTP using a graphene oxide nanosheet-based sensing platform in living cells

Cu2Cl(OH)3 nanozyme-based colorimetric sensor array for phosphates discrimination and disease identification

The identification of phosphates holds significant importance in many physiological processes and disease diagnosis, and traditional detection techniques struggle to simultaneously detect and distinguish phosphates. The complexity of synthesizing sensing units restricts the construction of sensor arrays as well. In this study, a bifunctional dicopper chloride trihydroxide (Cu2Cl(OH)3) nanozyme with conspicuous laccase- and peroxidase-like activities has been synthesized in basic deep eutectic solvents (DES). Exploiting the various regulatory impacts of multiple phosphates on the dual-enzyme mimicking activities, the sensor array based on the laccase mimic and peroxidase mimic properties of Cu2Cl(OH)3 was designed, which has been successfully harnessed for the identification of eight phosphates (ATP, ADP, AMP, PPi, Pi, GTP, GDP, and GMP). This approach streamlines the creation of sensor arrays. Besides, the three simulated actual samples (healthy individuals, moderately ill patients, and severely ill patients) have been accurately distinguished. This work makes a substantial contribution to enhancing the highly effective construction of array channels and promoting discrimination of phosphates in intricate samples.

Construction of Smart DNA-Based Drug Delivery Systems for Cancer Therapy

Due to the disadvantages of poor targeting, slow action, and low effectiveness of current commonly used cancer treatments, including surgery, chemotherapy, and radiotherapy, researchers have turned to DNA as a biomaterial for constructing drug delivery nanocarriers. DNA is favored for its biocompatibility and programmability. In order to overcome the limitations associated with traditional drug delivery systems (DDSs), researchers have developed smart-responsive DNA DDSs that can control drug release in response to specific physical or chemical stimuli at targeted sites. In this review, a summary of multiple targeted ligand structures is provided, various shapes of stable DNA nanomaterials, and different stimuli-responsive drug release strategies in DNA DDSs. Specifically, targeted cell recognition, in vivo stable transport, and controlled drug release of smart DDSs are focused. Finally, the further development prospects and challenges of clinical application of DNA nanomaterials in the field of smart drug delivery are discussed. The objective of this review is to enhance researchers' comprehension regarding the potential application of DNA nanomaterials in precision drug delivery, with the aim of expediting the clinical implementation of intelligent DDSs.

Modular Engineering of Aptamer-Based Nanobiotechnology for Conditional Control of ATP Sensing

Dynamic changes of intracellular, extracellular, and subcellular adenosine triphosphates (ATPs) have fundamental interdependence with the physio-pathological states of cells. Spatially selective in situ imaging of such ATP dynamics offers valuable mechanistic insights into the related biological activities. Despite significant advances in the design of aptamer sensors for ATP detection, the dearth of methods that enable precise ATP imaging in specific cellular locations remains a challenge in this field. This review focuses on the modular engineering of regulatable sensing technology via the integration of aptamer probe designs with advanced functional nanomaterials, allowing conditional control of ATP sensing and imaging with high spatial precision from subcellular organelles to living animals. Highlighting the recent advances in the design of photo-triggered nanosensors for spatiotemporally controlled ATP imaging, endogenously-triggered ATP sensing in a cell-selective manner, and spatially-controlled nanodevices for ATP imaging in specific organelles and extracellular microenvironments. Emphasis will be put on elucidating the principles of how nanotechnology can be applied to regulate the spatial precision of aptamer-based ATP sensing activities. The authors envision that this perspective provides insights into the engineering of aptamer-based nanobiotechnology for opening new frontiers in precise molecular sensing and other bio-applications.

DNA-Based Fluorescent Nanoprobe for Cancer Cell Membrane Imaging

As an important barrier between the cytoplasm and the microenvironment of the cell, the cell membrane is essential for the maintenance of normal cellular physiological activities. An abnormal cell membrane is a crucial symbol of body dysfunction and the occurrence of variant diseases; therefore, the visualization and monitoring of biomolecules associated with cell membranes and disease markers are of utmost importance in revealing the biological functions of cell membranes. Due to their biocompatibility, programmability, and modifiability, DNA nanomaterials have become increasingly popular in cell fluorescence imaging in recent years. In addition, DNA nanomaterials can be combined with the cell membrane in a specific manner to enable the real-time imaging of signal molecules on the cell membrane, allowing for the real-time monitoring of disease occurrence and progression. This article examines the recent application of DNA nanomaterials for fluorescence imaging on cell membranes. First, we present the conditions for imaging DNA nanomaterials in the cell membrane microenvironment, such as the ATP, pH, etc. Second, we summarize the imaging applications of cell membrane receptors and other molecules. Finally, some difficulties and challenges associated with DNA nanomaterials in the imaging of cell membranes are presented.

Homogeneous luminescent quantitation of cellular guanosine and adenosine triphosphates (GTP and ATP) using QT-LucGTP&ATP assay

Guanosine triphosphate (GTP) and adenosine triphosphate (ATP) are essential nucleic acid building blocks and serve as energy molecules for a wide range of cellular reactions. Cellular GTP concentration fluctuates independently of ATP and is significantly elevated in numerous cancers, contributing to malignancy. Quantitative measurement of ATP and GTP has become increasingly important to elucidate how concentration changes regulate cell function. Liquid chromatography-coupled mass spectrometry (LC-MS) and capillary electrophoresis-coupled MS (CE-MS) are powerful methods widely used for the identification and quantification of biological metabolites. However, these methods have limitations related to specialized instrumentation and expertise, low throughput, and high costs. Here, we introduce a novel quantitative method for GTP concentration monitoring (GTP-quenching resonance energy transfer (QRET)) in homogenous cellular extracts. CE-MS analysis along with pharmacological control of cellular GTP levels shows that GTP-QRET possesses high dynamic range and accuracy. Furthermore, we combined GTP-QRET with luciferase-based ATP detection, leading to a new technology, termed QT-LucGTP&ATP, enabling high-throughput compatible dual monitoring of cellular GTP and ATP in a homogenous fashion. Collectively, GTP-QRET and QT-LucGTP&ATP offer a unique, high-throughput opportunity to explore cellular energy metabolism, serving as a powerful platform for the development of novel therapeutics and extending its usability across a range of disciplines.

Tumor Microenvironment-Responsive Hydrogel for Direct Extracellular ATP Imaging-Guided Surgical Resection with Clear Boundaries

Most solid tumors are clinically treated using surgical resection, and the presence of residual tumor tissues at the surgical margins often determines tumor survival and recurrence. Herein, a hydrogel (Apt-HEX/Cp-BHQ1 Gel, termed AHB Gel) is developed for fluorescence-guided surgical resection. AHB Gel is constructed by tethering a polyacrylamide hydrogel and ATP-responsive aptamers together. It exhibits strong fluorescence under high ATP concentrations corresponding to the TME (100-500 µm) but shows little fluorescence at low ATP concentrations (10-100 nm) such as those in normal tissues. AHB Gel can rapidly (within 3 min) emit fluorescence after exposure to ATP, and the fluorescence signal only occurs at sites exposed to high ATP, resulting in a clear boundary between the ATP-high and ATP-low regions. In vivo, AHB Gel exhibits specific tumor-targeting capacity with no fluorescence response in normal tissue, providing clear tumor boundaries. In addition, AHB Gel has good storage stability, which is conducive to its future clinical application. In summary, AHB Gel is a novel tumor microenvironment-targeted DNA-hybrid hydrogel for ATP-based fluorescence imaging. It can enable the precise imaging of tumor tissues, showing promising application in fluorescence-guided surgeries in the future.

Background-filtered telomerase activity assay with cyclic DNA cleavage amplification

Overexpression of telomerase incites the abnormal proliferation of cancer cells. Thus, it has been regarded as a cancer biomarker and a potential therapeutic target. Existing assays suggest a promising sensing scheme to detect telomerase activity. However, they are complicated in terms of assay preparation and implementation. We herein report a Quenching-Exempt invader Signal Amplification Test, termed 'QUEST'. The assay leverages on a high turnover, specific cleaving enzyme, flap endonuclease I (FEN1), and graphene oxide (GO) for background (BG) filtering. In response to the target, FEN1 significantly boosts the signal with invader signal amplification. To distinguish the target signal, GO filters out the BG. It captures residual reporter invader probes (RP) to quench undesired signals. QUEST is straightforward without any pre-preparatory steps and washing/separation. Its probe design is simple and cost-effective. With QUEST, we investigated telomerase activities in various cell lines. Notably, we discriminated cancer cell lines from normal cell lines. In addition, a candidate inhibitor for telomerase was screened, which showed the promising potential of QUEST in real applications.

Combination of multiple nucleic acid aptamers for precision detection of tumors based on optical methods

BACKGROUND AND PURPOSE

Nucleic acid aptamers are a novel molecular recognition tool that is functionally similar to antibodies but superior to antibodies in terms of thermal stability, structural modification, preparation, and cost, and therefore hold great promise for molecular detection. However, due to the limitations of a single aptamer in molecular detection, the multiple aptamer combination for bioanalysis has received much attention. Here, we reviewed the progress of tumor precision detection based on the combination of multiple nucleic acid aptamers and optical methods and discussed its challenges and prospects.

METHODS

The relevant literature in PubMed was collected and reviewed.

RESULTS

The combination of two or more aptamers with modern nanomaterials and analytical methods allows the fabrication of various detection systems for the simultaneous detection of different structural domains of a substance and/or different substances, including soluble tumor markers, tumor cell surface and intracellular markers, circulating tumor cells, and other tumor-related biomolecules, which has great potential for application in efficient and precise tumor detection.

CONCLUSION

The combination of multiple nucleic acid aptamers provides a new approach for the precise detection of tumors and will play an important role in precision medicine for tumors.

Construction of a simple dual-mode ATP-sensing system for reliable fish freshness evaluation

Adenosine triphosphate (ATP), the main carrier of chemical energy, plays a key role in various biochemical reactions such as cellular metabolism. Currently, ATP levels are considered important indicators of microbial content in food safety, and food freshness can be determined by detecting ATP content. Some ATP sensing strategies have been applied to evaluate food freshness. However, cumbersome nanomaterial preparation, low sensitivity, and low reliability hamper their widespread application. Herein, a simple, high-performance, and reliable dual-mode sensing system based on hemin-G-quadruplex (G4) DNAzyme was established to detect ATP and assess fish freshness. Two nucleic acid probes, including subunits of the hemin-G4 DNAzyme in inactive structures and anti-ATP aptamer, self-assemble upon the input of ATP into the active hemin-G4 DNAzyme unit. The generated DNAzyme acts as a biocatalyst for colorimetric or fluorescent readout of the sensing process. The colorimetric and fluorescent dual-mode sensing system enables highly sensitive and reliable analysis of target ATP with detection limits of 71 nM and 73 nM, respectively. Moreover, the biosensor exhibited good selectivity for differentiating ATP from other interfering analytes. The proposed system was used to detect ATP in perch samples, and a linear correlation between ATP level and microbial content was confirmed. The established ATP-sensing system reliably evaluated fish freshness. Notably, in comparison with microbiological counts, the proposed DNAzyme-based dual-mode strategy for freshness evaluation is facile, highly efficient, and cost-effective, thus providing a promising method for food safety and quality monitoring.

Recent progress of aptamer‒drug conjugates in cancer therapy

Aptamers are single-stranded DNA or RNA sequences that can specifically bind with the target protein or molecule via specific secondary structures. Compared to antibody-drug conjugates (ADC), aptamer‒drug conjugate (ApDC) is also an efficient, targeted drug for cancer therapy with a smaller size, higher chemical stability, lower immunogenicity, faster tissue penetration, and facile engineering. Despite all these advantages, several key factors have delayed the clinical translation of ApDC, such as in vivo off-target effects and potential safety issues. In this review, we highlight the most recent progress in the development of ApDC and discuss solutions to the problems noted above.

Enzyme Translocation-Mediated Signal Amplification for Spatially Selective Aptasensing of ATP in Inflammatory Cells

Amplified ATP imaging in inflammatory cells is highly desirable. However, the spatial selectivity of current amplification methods is limited, that is, signal amplification is performed systemically and not in a disease site-specific manner. Here we present a versatile strategy, termed enzymatically triggerable, aptamer-based signal amplification (ETA-SA), that enables inflammatory cell-specific imaging of ATP through spatially-resolved signal amplification. The ETA-SA leverages a translocated enzyme in inflammatory cells to activate DNA aptamer probes and further drive cascade reactions through the consumption of hairpin fuels, which, however, exerts no ATP response activity in normal cells, leading to a significantly improved sensitivity and spatial specificity for the inflammation-specific ATP imaging in vivo. Benefiting from the improved spatial selectivity, enhanced signal-to-background ratios were achieved for ATP imaging during acute hepatitis.

Poria cocos polysaccharide-functionalized graphene oxide nanosheet induces efficient cancer immunotherapy in mice

Introduction: Tumor vaccines that induce robust humoral and cellular immune responses have attracted tremendous interest for cancer immunotherapy. Despite the tremendous potential of tumor vaccines as an effective approach for cancer treatment and prevention, a major challenge in achieving sustained antitumor immunity is inefficient antigen delivery to secondary lymphoid organs, even with adjuvant aid. Methods: Herein, we present antigen/adjuvant integrated nanocomplexes termed nsGO/PCP/OVA by employing graphene oxide nanosheet (nsGO) as antigen nanocarriers loaded with model antigen ovalbumin (OVA) and adjuvant, Poria cocos polysaccharides (PCP). We evaluated the efficacy of nsGO/PCP/OVA in activating antigen-specific humoral as well as cellular immune responses and consequent tumor prevention and rejection in vivo. Results: The optimally formed nsGO/PCP/OVA was approximately 120-150 nm in diameter with a uniform size distribution. Nanoparticles can be effectively engulfed by dendritic cells (DCs) through receptor-mediated endocytosis, induced the maturation of DCs and improved the delivery efficiency both in vitro and in vivo. The nsGO/PCP/OVA nanoparticles also induced a significant enhancement of OVA antigen-specific Th1 and Th2 immune responses in vivo. In addition, vaccination with nsGO/PCP/OVA not only significantly suppressed tumor growth in prophylactic treatments, but also achieved a therapeutic effect in inhibiting the growth of already-established tumors. Conclusion: Therefore, this potent nanovaccine platform with nanocarrier nsGO and PCP as adjuvants provides a promising strategy for boosting anti-tumor immunity for cancer immunotherapy.

Catalytic nanozyme Zn/Cl-doped carbon quantum dots as ratiometric fluorescent probe for sequential on-off-on detection of riboflavin, Cu2+ and thiamine

A novel metal-doped Zn/Cl carbon quantum dots (Zn/Cl-CQDs) was developed successfully as ratiometric fluorescent probes for the sequential on-off-on detection of riboflavin, Cu²⁺ ion and thiamine. The excellent catalytic performance of the Zn/Cl-CQDs nanozyme serves as an ideal platform for sensitive detection of thiamine. Due to the addition of riboflavin to the Zn/Cl-CQDs, the blue emission peak of Zn/Cl-CQDs at 440 nm remains unaffected and used as an internal reference approach, while the green emission peak of riboflavin at 520 nm appeared and increased remarkably. Following the presence of Cu²⁺, a quenching blue fluorescence signal of Zn/Cl-CQDs was observed which resulted in consequent fluorescent 'turn-off' response toward Cu²⁺ ion. Finally, upon the addition of thiamine to the above solution under alkaline condition, the blue emission of Zn/Cl-CQDs was gradually recovered. The prepared Zn/Cl-CQDs could act as a nanozyme catalyst for directly catalyzing the oxidation of non-fluorescent substrate of thiamine to produce highly fluorescent substrate of thiochrome. As a result, the blue fluorescence emission peak at 440 nm was recovered. Eventually, the sequential detection properties of ratiometric probes for riboflavin, Cu²⁺ ion and thiamine were successfully applied in VB2 tablets, drinking water and VB1 tablet with good recoveries of 96.21%, 98.25% and 98.44%, respectively.

Interaction of Nucleic Acids with Metal-Organic Framework Nanosheets by Fluorescence Spectroscopy and Molecular Dynamics Simulations

The integration of nanomaterials and nucleic acids has attracted great attention in various research fields, especially biomedical applications. Designing two-dimensional nanomaterials and studying the mechanism of their interaction with nucleic acids are still attractive tasks. Herein, we designed and prepared a class of ultrathin two-dimensional metal-organic framework (MOF) nanosheets, named Zr-BTB MOF nanosheets, composed of Zr-O clusters and 1,3,5-benzenetribenzoate by a bottom-up synthesis strategy. The Zr-BTB MOF nanosheets possessed inherent excellent performance such as a high specific surface area, porosity, and biocompatibility. In addition, we clarified the interaction difference between the Zr-BTB MOF nanosheets and fluorophore-labeled double-stranded DNA and single-stranded DNA via molecular dynamics simulations and fluorescence measurement. Through molecular dynamics simulations, specific interactions between DNA and nanosheets such as forces, binding energies, and binding modes were deeply analyzed and clearly presented. Based on the affinity difference, the system showed the biosensing potential for target DNA detection with considerable specificity, sensitivity, and linearity. Our research results presented the Zr-BTB MOF nanosheet as a platform for nucleic acid detection, showing the potential for hybridization-based biosensing and related biological applications.

Recent Advances in Electrochemical Sensing of Hydrogen Peroxide (H2O2) Released from Cancer Cells

Cancer is by far the most common cause of death worldwide. There are more than 200 types of cancer known hitherto depending upon the origin and type. Early diagnosis of cancer provides better disease prognosis and the best chance for a cure. This fact prompts world-leading scientists and clinicians to develop techniques for the early detection of cancer. Thus, less morbidity and lower mortality rates are envisioned. The latest advancements in the diagnosis of cancer utilizing nanotechnology have manifested encouraging results. Cancerous cells are well known for their substantial amounts of hydrogen peroxide (H₂O₂). The common methods for the detection of H₂O₂ include colorimetry, titration, chromatography, spectrophotometry, fluorimetry, and chemiluminescence. These methods commonly lack selectivity, sensitivity, and reproducibility and have prolonged analytical time. New biosensors are reported to circumvent these obstacles. The production of detectable amounts of H₂O₂ by cancerous cells has promoted the use of bio- and electrochemical sensors because of their high sensitivity, selectivity, robustness, and miniaturized point-of-care cancer diagnostics. Thus, this review will emphasize the principles, analytical parameters, advantages, and disadvantages of the latest electrochemical biosensors in the detection of H₂O₂. It will provide a summary of the latest technological advancements of biosensors based on potentiometric, impedimetric, amperometric, and voltammetric H₂O₂ detection. Moreover, it will critically describe the classification of biosensors based on the material, nature, conjugation, and carbon-nanocomposite electrodes for rapid and effective detection of H₂O₂, which can be useful in the early detection of cancerous cells.

Aptamer based probes for living cell intracellular molecules detection

Biosensors have been employed for monitoring and imaging biological events and molecules. Sensitive detection of different biomolecules in vivo can reflect the changes of physiological conditions in real-time, which is of great significance for the diagnosis and treatment of diseases. The detection of intracellular molecules concentration change can indicate the occurrence and development of disease. But the analysis process of the existing detection methods, such as Western blot detection of intracellular protein, polymerase chain reaction (PCR) technique quantitative analysis of intracellular RNA and DNA, usually need to extract the cell lysis which is complex and time-consuming. Fluorescence bioimaging enables in situ monitoring of intracellular molecules in living cells. By combining the specificity of aptamer for intracellular molecules binding, and biocompatibility of fluorescent materials and nanomaterials, biosensors with different nanostructures have been developed to enter into living cells for analysis. This review summarizes the fluorescence detection methods based on aptamer for intracellular molecules detection. The principles, limit of detection, advantages, and disadvantages of different platforms for intracellular molecular fluorescent response are summarized and reviewed. Finally, the current challenges and future developments were discussed and proposed.

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

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

Multidimensional Imaging Reveals Mechanisms Controlling Multimodal Label-Free Biosensing in Vertical 2DM-Heterostructures

Two-dimensional materials and their van der Waals heterostructures enable a large range of applications, including label-free biosensing. Lattice mismatch and work function difference in the heterostructure material result in strain and charge transfer, often varying at a nanometer scale, that influence device performance. In this work, a multidimensional optical imaging technique is developed in order to map subdiffractional distributions for doping and strain and understand the role of those for modulation of the electronic properties of the material. As an example, vertical heterostructures comprised of monolayer graphene and single-layer flakes of transition metal dichalcogenide MoS₂ were fabricated and used for biosensing. Herein, the optical label-free detection of doxorubicin, a common cancer drug, is reported via three independent optical detection channels (photoluminescence shift, Raman shift, and graphene enhanced Raman scattering). Non-uniform broadening of components of multimodal signal correlates with the statistical distribution of local optical properties of the heterostructure. Multidimensional nanoscale imaging allows one to reveal the physical origin for such a local response and propose the best strategy for the mitigation of materials variability and future device fabrication, enabling multiplexed biosensing.

Fluorogenic "on-off" nanosensor based on dual-quenching effect for imaging intracellular metabolite of various microalgae

Sensing intracellular compounds such as ATP in living microalgal cells is of great importance in diverse fields. To achieve this, nanosensing platform composed of graphene oxide (GO) and ATP aptamer (APT) was applied to diverse microalgal cells (Chlamydomonas reinhardtii, Chlorella vulgaris, Anabaena flos-aquae, and Ochromonas danica). The nanosized GO was characterized with atomic force microscopy (AFM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). The nanosensing platform (GO-APT) was prepared by attaching fluorophore-labeled APT to GO. GO-APT was applicable to only cell wall-deficient species (O. danica and mutant strains of C. reinhardtii) and the existence of flagella did not affect the uptake of the GO-APT by the cells. These results indicate that the cell wall is the primary barrier of GO-APT internalization for sensing application. To reduce the background fluorescence signal elicited by nonspecific displacement of the fluorophore-labeled probe, APT was modified as molecular beacon (MB) type (APTMB). Owing to the double quenching effect (by GO and quencher-labeled complementary sequence), the background signal significantly reduced. Cytotoxicity of GO-APTMB on the microalgal species was also tested. The application of GO-APTMB had no effect on the growth of microalgae. Given that diverse aptamer sequences had been screened, the sensing platform is not limited for detecting ATP only, but also can be applied to other metabolite imaging by simply changing the aptamer sequences. Our research will contribute to broadening the application of GO and aptamer beacon complex for intracellular metabolite imaging and detecting.

CRISPR-Cas12a-based efficient electrochemiluminescence biosensor for ATP detection

CRISPR-Cas12a system exhibits tremendous potential in accurate recognition and quantitation of nucleic acids and non-nucleic-acid targets thanks to the discovery of its cleavage capability toward single-stranded DNA (ssDNA). In this study, we developed an efficient electrochemiluminescence (ECL) sensing platform based on CRISPR-Cas12a for the analysis of adenosine triphosphate (ATP). In the presence of the target, the successful release of the DNA activator is specially recognized by Cas12a-crRNA duplex and activates the cleavage of ferrocene (Fc) labeled-ssDNA (Fc-ssDNA) modified on the cathode of bipolar electrode (BPE), resulting in a decrease of ECL intensity of [Ru(bpy)₃]²⁺/TPrA in the anodic cell of BPE. By means of the unique combination of Cas12a with ECL technique based on BPE, it can convert the recognition of target ATP into a detectable ECL signal. The detection limit of ATP was determined to be 0.48 nM under the optimal conditions. This work will expand the application of CRISPR-Cas detection system and propose a potential method for the analysis of non-nucleic-acid targets.

A Cooperatively Activatable DNA Nanoprobe for Cancer Cell-Selective Imaging of ATP

DNA-based nanoprobes have attracted extensive interest in the field of bioanalysis. Notably, engineered DNA nanoprobes that can respond to multiple pathological parameters are desirable to detect targets precisely. Here we design a split aptamer/DNAzyme (aptazyme)-based DNA probe for fluorescence detection of ATP and further develop a cooperatively activatable DNA nanoprobe for tumor-specific imaging of ATP in vivo. The DNA nanoprobes comprising split aptazyme-coated MnO₂ nanovectors have high stability and are synergistically activated by multiple biomarkers, GSH and ATP. Upon stimuli by overexpressed GSH in tumor cells, this DNA nanoprobe can release the aptazyme and self-supply cofactor Mn²⁺ of the DNAzyme. Sequentially, intracellular ATP induces the proper folding of the split ATP aptamer and Mn²⁺-dependent DNAzyme, which activates the specific cleavage of substrate and generates the optical readout signal. This nanoprobe exhibits remarkable resistance to enzymatic degradation, satisfactory biosafety, identifies ATP specifically within cancer cells, and selectively lights up solid tumors. Our research provides a reliable method for ATP imaging in cancer cells and opens a new avenue for biochemical research and highly accurate disease diagnosis.

Rapid and Specific Imaging of Extracellular Signaling Molecule Adenosine Triphosphate with a Self-Phosphorylating DNAzyme

Adenosine 5'-triphosphate (ATP) is a central extracellular signaling agent involved in various physiological and pathological processes. However, precise measurements of the temporal and spatial components of ATP dynamics are lacking due primarily to the limitations of available methods for ATP detection. Here, we report on the first effort to design a self-phosphorylating DNAzyme (SPDz) sensor for fluorescence imaging of ATP. In response to ATP, SPDz sensors exhibit subsecond response kinetics, extremely high specificity, and micromolar affinities. In particular, we demonstrate cell-surface-anchored SPDz sensors for fluorescence imaging of both stress-induced endogenous ATP release in astrocytes and mechanical stimulation-evoked ATP release at the single-cell level. We also validated their utility for visualizing the rapid dynamic properties of ATP signaling upon electrical stimulation in astrocytes. Thus, SPDz sensors are robust tools for monitoring ATP signaling underlying diverse cellular processes.

Ex vivo and in vivo fluorescence detection and imaging of adenosine triphosphate

Background

Ex vivo and in vivo detection and imaging of adenosine triphosphate (ATP) is critically important for the diagnosis and treatment of diseases, which still remains challenges up to present.

Results

We herein demonstrate that ATP could be fluorescently detected and imaged ex vivo and in vivo. In particular, we fabricate a kind of fluorescent ATP probes, which are made of titanium carbide (TC) nanosheets modified with the ROX-tagged ATP-aptamer (TC/Apt). In the constructed TC/Apt, TC shows superior quenching efficiency against ROX (e.g., ~ 97%). While in the presence of ATP, ROX-tagged aptamer is released from TC surface, leading to the recovery of fluorescence of ROX under the 545-nm excitation. Consequently, a wide dynamic range from 1 μM to 1.5 mM ATP and a high sensitivity with a limit of detection (LOD) down to 0.2 μM ATP can be readily achieved by the prepared TC/Apt. We further demonstrate that the as-prepared TC/Apt probe is feasible for accurate discrimination of ATP in different samples including living cells, body fluids (e.g., mouse serum, mouse urine and human serum) and mouse tumor models.

Conclusions

Fluorescence detection and imaging of ATP could be readily achieved in living cells, body fluids (e.g., urine and serum), as well as mouse tumor model through a new kind of fluorescent ATP nanoprobes, offering new powerful tools for the treatment of diseases related to abnormal fluctuation of ATP concentration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-021-00930-4.

In Vivo Monitoring of Intracellular Metabolite in a Microalgal Cell Using an Aptamer/Graphene Oxide Nanosheet Complex

Real-time sensing and imaging of intracellular metabolites in living cells are crucial tools for the characterization of complex biological processes, including the dynamic fluctuation of metabolites. Therefore, additional efforts are required to develop in vivo detection strategies for the visualization and quantification of specific target metabolites, particularly in microalgae. In this study, we developed a strategy to monitor a specific microalgal metabolite in living cells using an aptamer/graphene oxide nanosheet (GOnS) complex. As a proof-of-concept, β-carotene, an antioxidant pigment that accumulates in most microalgal species, was chosen as a target metabolite. To achieve this, a β-carotene-specific aptamer was selected through graphene oxide-assisted systematic evolution of ligands by exponential enrichment (GO-SELEX) and characterized thereafter. The aptamer could sensitively sense the changes in the concentration of β-carotene (i.e., the target metabolite) and more specifically bind to β-carotene than to nontargets. The selected aptamer was labeled with a fluorophore (fluorescein; FAM) and allowed to form an aptamer/GOnS complex that protected the aptamer from nucleic cleavages. The aptamer/GOnS complex was delivered into the cells via electroporation, thus enabling the sensitive monitoring of β-carotene in the cell by quantifying the aptamer fluorescence intensity. The results suggest that our biocompatible strategy could be employed to visualize and semiquantify intracellular microalgae metabolites in vivo, which holds a great potential in diverse fields such as metabolite analysis and mutant screening.

Recent progress in developing fluorescent probes for imaging cell metabolites

Cellular metabolites play a crucial role in promoting and regulating cellular activities, but it has been difficult to monitor these cellular metabolites in living cells and in real time. Over the past decades, iterative development and improvements of fluorescent probes have been made, resulting in the effective monitoring of metabolites. In this review, we highlight recent progress in the use of fluorescent probes for tracking some key metabolites, such as adenosine triphosphate, cyclic adenosine monophosphate, cyclic guanosine 5'-monophosphate, Nicotinamide adenine dinucleotide (NADH), reactive oxygen species, sugar, carbon monoxide, and nitric oxide for both whole cell and subcellular imaging.

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.

Tunable graphdiyne for DNA surface adsorption: affinities, displacement, and applications for fluorescence sensing

Graphdiyne (GDY) adsorbed DNA probes have been used as a fluorescent sensing platform, but topics including DNA adsorption affinities, DNA probe displacement, and fluorescence quenching ability were rarely researched. Herein, the adsorption affinity of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) on a tremella-like GDY was tuned by modulating the surface chemistry of GDY. The fluorescence quenching ability of GDY with different oxidation degrees was compared. The nonspecific displacement of DNA probes on GDY was studied. Under the same concentrations, GDY with low oxidation degree exhibited stronger adsorption affinity and higher adsorption capacity to both ssDNA and dsDNA than highly oxidized GDY. DNA adsorbed on low-oxidized GDY was more resistant to displacement by other DNAs. Protein showed strong interaction with different GDY and could displace DNA probes on GDY. Based on these findings, an ideal GDY with proper oxidation degree, exhibiting high surface affinity for ssDNA and low affinity for dsDNA, was used as scavenger of redundant ssDNA fluorescent probe in an enzyme-assisted amplification system for sensitive ochratoxin (OTA) detection. This study has enhanced our fundamental understanding of DNA adsorption by GDY. It also provided a rational way to apply GDY for fluorescence sensing in a complicated system.

Graphene-nucleic acid biointerface-engineered biosensors with tunable dynamic range

Programmed biosensors with tunable quantification range and sensitivity would greatly broaden their application in medical diagnosis, food safety and environmental analysis. Herein, we proposed a graphene-nucleic acid biointerface-engineered biosensor, allowing target molecules to be detected with adjustable dynamic ranges and sensitivities. The biosensors were programmed by simply tuning the poly A tail of aptamer probes. The tuning of the poly A tail would allow the interaction between aptamer probes and graphene oxide (GO) to be modulated, in turn programing the competitive binding processes of aptamer probes to target molecules and GO. The biosensors, termed affinity-tunable aptasensors (atAptasensors) could be easily tuned with different dynamic ranges by using aptamer probes with different tail lengths, and the dynamic range could be extended to be over 3 orders by a combined use of multiple aptamer probes. Remarkably, the specificity of aptamer probes could be increased by increasing the interaction between aptamer probes and GO. Reliability of atAptasensor for ATP detection was tested in serum and milk samples, and we also applied atAptasensor for culture-independent analysis of microorganism pollution.

Tumor-Targeting Cholesterol-Decorated DNA Nanoflowers for Intracellular Ratiometric Aptasensing

Probing endogenous molecular profiles is of fundamental importance to understand cellular function and processes. Despite the promise of programmable nucleic-acid-based aptasensors across the breadth of biomolecular detection, target-responsive aptasensors enabling intracellular detection are as of yet infrequently realized. Several challenges remain, including the difficulties in quantification/normalization of quencher-based intensiometric signals, stability issues of the probe architecture, and complex sensor operations often necessitating extensive structural modeling. Here, the biomimetic crystallization-empowered self-assembly of a tumor-targetable DNA-inorganic hybrid nanocomposite aptasensor is presented, which enables Förster resonance energy transfer (FRET)-based quantitative interpretation of changes in the cellular target abundance. Leveraging the design programmability and high-throughput fabrication of rolling circle amplification-driven DNA nanoarchitecture, this designer platform offers a method to self-assemble a robust nanosensor from a multifunctionality-encoded template that includes a cell-targeting aptamer, a ratiometric aptasensor, and a cholesterol-decorating element. Taking prostate cancer cells and intracellular adenosine triphosphate molecules as a model system, a synergistic effect in the targeted delivery by cholesterol and aptamers, and the feasibility of quantitative intracellular aptasensing are demonstrated. It is envisioned that this approach provides a highly generalizable strategy across wide-ranging target systems toward a biologically deliverable nanosensor that enables quantitative monitoring of the abundance of endogenous biomolecules.

Translational control of enzyme scavenger expression with toxin-induced micro RNA switches

Biological computation requires in vivo control of molecular behavior to progress development of autonomous devices. miRNA switches represent excellent, easily engineerable synthetic biology tools to achieve user-defined gene regulation. Here we present the construction of a synthetic network to implement detoxification functionality. We employed a modular design strategy by engineering toxin-induced control of an enzyme scavenger. Our miRNA switch results show moderate synthetic expression control over a biologically active detoxification enzyme molecule, using an established design protocol. However, following a new design approach, we demonstrated an evolutionarily designed miRNA switch to more effectively activate enzyme activity than synthetically designed versions, allowing markedly improved extrinsic user-defined control with a toxin as inducer. Our straightforward new design approach is simple to implement and uses easily accessible web-based databases and prediction tools. The ability to exert control of toxicity demonstrates potential for modular detoxification systems that provide a pathway to new therapeutic and biocomputing applications.

Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces

Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.

Fe3O4 NP@ZIF-8/MoS2 QD-based electrochemiluminescence with nanosurface energy transfer strategy for point-of-care determination of ATP

Herein, Fe₃O₄ NP@ZIF-8/MoS₂ QD-based electrochemiluminescence (ECL) biosensor with nanosurface energy transfer strategy was successfully developed for point-of-care determination of ATP. With the porous structure and poor electron transfer ability, Fe₃O₄ NP@ZIF-8 complex was first used as an excellent catalyst in ECL. The complex catalyzed the coreactant for more free radicals and hindered the quenching effect of Fe₃O₄ nanoparticles (NPs) on quantum dots (QDs). In ECL-nanosurface energy transfer (NSET) system, through the specific binding of complementary DNA linked to MoS₂ QDs (QDs-cDNA) and aptamer linked to Au NPs, interaction between the point dipole of MoS₂ QDs and the collective dipoles of Au NPs quenched ECL signal. When ATP was captured by aptamer, the ECL-NSET system was taken apart, which resulted in the recovery of ECL signal. Moreover, changes of the ECL imaging can be captured by a smartphone, which enabled point-of-care determination of ATP from 0.05 nmol L^-1 to 200 nmol L^-1 with LOD of 0.015 nmol L^-1. With superior specificity and stability, the sensing system showed significant potential about the application of catalysts coated with ZIF and NSET in point-of-care ECL determination.

Fluorescent Carbon Dots for in Situ Monitoring of Lysosomal ATP Levels

Monitoring the ATP levels in lysosomes in situ is crucial for understanding their involvement in various biological processes but remains difficult due to the interference of ATP in other organelles or the cytoplasm. Here, we report a lysosome-specific fluorescent carbon dot (CD), which can be used to detect ATP in acidic lysosomes with "off-on" changes of yellow fluorescence. These CDs were successfully applied in real-time monitoring of the fluctuating concentration of lysosomal ATP induced by drug stimulation (e.g., chloroquine, etoposide, and oligomycin). Because of the excellent specificity, these CDs are promising agents for drug screening and medical diagnostics through lysosomal ATP monitoring.

Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption

Graphene quantum dots (GQDs) are an allotrope of carbon with a planar surface amenable to functionalization and nanoscale dimensions that confer photoluminescence. Collectively, these properties render GQDs an advantageous platform for nanobiotechnology applications, including optical biosensing and delivery. Towards this end, noncovalent functionalization offers a route to reversibly modify and preserve the pristine GQD substrate, however, a clear paradigm has yet to be realized. Herein, we demonstrate the feasibility of noncovalent polymer adsorption to GQD surfaces, with a specific focus on single-stranded DNA (ssDNA). We study how GQD oxidation level affects the propensity for polymer adsorption by synthesizing and characterizing four types of GQD substrates ranging ~60-fold in oxidation level, then investigating noncovalent polymer association to these substrates. Adsorption of ssDNA quenches intrinsic GQD fluorescence by 31.5% for low-oxidation GQDs and enables aqueous dispersion of otherwise insoluble no-oxidation GQDs. ssDNA-GQD complexation is confirmed by atomic force microscopy, by inducing ssDNA desorption, and with molecular dynamics simulations. ssDNA is determined to adsorb strongly to no-oxidation GQDs, weakly to low-oxidation GQDs, and not at all for heavily oxidized GQDs. Finally, we reveal the generality of the adsorption platform and assess how the GQD system is tunable by modifying polymer sequence and type.

Chiral Interaction Is a Decisive Factor To Replace d-DNA with l-DNA Aptamers

Nucleic acid aptamers have been widely used in various fields such as biosensing, DNA chip, and medical diagnosis. However, the high susceptibility of nucleic acids to ubiquitous nucleases reduces the biostability of aptamers and limits their applications in biological contexts. Therefore, improving the biostability of aptamers becomes an urgent need. Herein, we present a simple strategy to resolve this problem by directly replacing the d-DNA-based aptamers with left-handed l-DNA. By testing several reported aptamers against respective targets, we found that our proposed strategy stood up well for nonchiral small molecule targets (e.g., Hemin and cationic porphyrin) and chiral targets whose interactions with aptamers are chirality-independent (e.g., ATP). We also found that the l-DNA aptamers were indeed endowed with greatly improved biostability due to the extraordinary resistance of l-DNA to nuclease digestion. With respect to other small-molecule targets whose interactions with aptamers are chirality-dependent (e.g., kanamycin) and biomacromolecules (e.g., tyrosine kinase-7), however, the proposed strategy was not entirely effective likely due to the participation of the DNA backbone chirality into the target recognition. In spite of this limitation, this strategy indeed paves an easy way to screen highly biostable aptamers important for the applications in many fields.

Nucleic-Acid Structures as Intracellular Probes for Live Cells

The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.

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

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

Aptamer-based Homogeneous Analysis for Food Control

Background:

Highly sensitive and rapid analysis of food contaminants is of great significance for food safety control. Aptamer is a new kind of recognition molecules which could be applied for constructing homogeneous analysis assays, potentially achieving highly sensitive, cheap and rapid profiling of food contaminants.

Methods:

An overview of the literature concerning the homogeneous analysis of food contaminations based on aptamers has been reviewed (focused on the most recent literature, 2000-2018).

Results:

Attributed to aptamer’s controllability, designability and feasibility for the adoption of nucleic acid amplification, rapid, highly sensitive homogeneous assay for various food contaminants could be constructed. The structure-switching aptamer probe would confer quick, efficient and specific response to target food contaminants. Besides, the capability of amplification of aptamer sequences or nucleic acid probes would lead to highly sensitive detection.

Conclusion:

Aptamer-based homogeneous analysis methods have already been applied to detect various food contaminations ranging from toxins, heavy metal and pesticide to allergen and pathogenic bacteria. However, it is still a challenge to achieve robust and accurate detection of food contaminants in complex food samples.

A label-free and ultrasensitive DNA impedimetric sensor with enzymatic and electrical dual-amplification

In this work, we report a facile, sensitive, selective, and reproducible DNA impedimetric sensor device. We demonstrate that, combined with exonuclease III, the easily prepared electrochemically reduced graphene oxide (rGO) could be a desirable platform to amplify signals in electrochemical impedance spectroscopy for ultrasensitive DNA detection. Guided by enzyme assisted target recycling, efficient interfacial tuning can be obtained, from the situation with high impedance caused by single-stranded DNA probes directly adsorbed onto rGO to the one with low impedance due to the continuous desorption of target-probe DNA hybrids and the consequent digestion of DNA probes. Just a few DNA targets can specifically trigger the enzymatic digestion of a large number of DNA probes. It is the excellent electrical conductivity of rGO that further enlarges the changes of electron transfer resistance after the removal of DNA probes. As a result of synergistically combining both enzymatic and electrical amplification, the enlarged changes of impedimetric signals can be measured to sensitively report DNA targets. The specificity has been guaranteed by the intrinsic recognition of hybrids through both rGO and exonuclease III. A limit of detection as low as 10 aM target DNA in the matrix of cell culture medium, as well as a wide linear range and good discrimination of mismatched sequences even at the one-base level, suggests its great application prospect in biosensing and biomedical analysis. It also has other advantages including easy operation, low cost, and convenient regeneration, with more competitive performance in developing impedimetric biosensors.

Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations

The integration of nucleic acids with nanomaterials has attracted great attention from various research communities in search of new nanoscale tools for a range of applications, from electronics to biomedical uses. MXenes are a new class of multielement 2D materials baring exciting properties mostly directed to energy-related fields. These advanced materials are now beginning to enter the biomedical field given their biocompatibility, hydrophilicity and near-infrared absorption. Herein, we elucidate the interaction of MXene Ti3C2T x with fluorophore-tagged DNA by fluorescence measurements and molecular dynamics simulations. The system showed potential for biosensing with unequivocal detection at picomole levels and single-base discrimination. We found that this material possesses a kinetically unique entrapment/release behavior, with potential implications in time-controlled biomolecule delivery. Our findings present MXenes as platforms for binding nucleic acids, contributing to their potential for hybridization-based biosensing and related bio-applications.

In situ Analysis of Cancer Cells Based on DNA Signal Amplification and DNA Nanodevices

Cancer is a global disease which has been disturbing researchers in medicine and seriously threatens patients' health and lifetime around the world in the past several decades. Due to the characteristics of cancer cells, such as uncontrollable cell proliferation, cell invasion and metastasis to surrounding tissues, lower grade of differentiation, higher telomerase activity and others, it has been one of the most usual lethal factors, next to heart disease in incidence. Cancer mortality can be decreased by early diagnosis, and the people who with treatment at an early stage have an obvious improved survival rate. Consequently, early detection is significant for better understanding the pathogenesis of cancer and improving the prognosis of patients. In situ detection technique is a vital tool for imaging and cellular pathology research, which can provide effective information about tumor markers in the early cancer detection. In view of low expression of most tumor markers in the early stage of cancers, detection techniques based on DNA signal amplification and DNA nanodevices can provide a strong support for the diagnosis and detection of cancers. In this review, we summarize the research progress of different analytical techniques for detecting various tumor markers that have been reported in recent years. We compare different DNA amplification and nanodevices, then provide guidance and suggestions for better understanding in situ analysis of cancer cells.