Aptamer based fluorometric determination of ATP by exploiting the FRET between carbon dots and graphene oxide

Fabrication of a ratiometric fluorescent probe based on Tb3+ doped dual-emitting carbon dots for the detection of cytochrome c

Cytochrome c (Cyt-c) was commonly an intrinsic biomarker for a variety of cellular characteristics, such as respiration, energy levels, and apoptosis. Herein, a simple fluorescence sensor was constructed for the detection of Cyt-c in buffer and real serum samples. The carbon dots doped with Tb3+ on the premise of 1-(2-pyridylazo)-2-naphthol (PAN) were fabricated and used as a dual-emission ratiometric fluorescent probe for detecting Cyt-c based on the internal filtering effect (IFE). As a fluorescent probe for ultra-sensitive detection, Cyt-c was quantitatively detected at different concentrations from 1 to 1000 nM. The fluorescent detection method for Cyt-c showed a good linear relationship from 1 to 50 nM, and the limit of detection (LOD) was 0.35 nM. In the recovery range of 101.27-103.39 % in human serum samples, the relative standard deviation (RSD) was less than 3.27 % (n = 3). In the end, the possible structures of CDs were predicted by DFT theoretical simulation calculations. All the results proved the ability of carbon dots as fluorescent probes to detect biomarkers and the application prospects in bioanalysis.

Luminescent carbon dots versus quantum dots and gold nanoclusters as sensors

Ultra-small nanoparticles, including quantum dots, gold nanoclusters (AuNCs) and carbon dots (CDs), have emerged as a promising class of fluorescent material because of their molecular-like properties and widespread applications in sensing and imaging. However, the fluorescence properties of ultra-small gold nanoparticles (i.e., AuNCs) and CDs are more complicated and well distinguished from conventional quantum dots or organic dye molecules. At this frontier, we highlight recent developments in the fundamental understanding of the fluorescence emission mechanism of these ultra-small nanoparticles. Moreover, this review carefully analyses the underlying principles of ultra-small nanoparticle sensors. We expect that this information on ultra-small nanoparticles will fuel research aimed at achieving precise control over their fluorescence properties and the broadening of their applications.

A Microfluidic Chip-Based Automated System for Whole-Course Monitoring the Drug Responses of Organoids

Tumor patients-derived organoids, as a promising preclinical prediction model, have been utilized to evaluate ex vivo drug responses for formulating optimal therapeutic strategies. Detecting adenosine triphosphate (ATP) has been widely used in existing organoid-based drug response tests. However, all commercial ATP detection kits containing the cell lysis procedure can only be applied for single time point ATP detection, resulting in the neglect of dynamic ATP variations in living cells. Meanwhile, due to the limited number of viable organoids from a single patient, it is impractical to exhaustively test all potential time points in search of optimal ones. In this work, a multifunctional microfluidic chip was developed to perform all procedures of organoid-based drug response tests, including establishment, culturing, drug treatment, and ATP monitoring of organoids. An ATP sensor was developed to facilitate the first successful attempt on whole-course monitoring the growth status of fragile organoids. To realize a clinically applicable automatic system for the drug testing of lung cancer, a microfluidic chip based automated system was developed to perform entire organoid-based drug response test, bridging the gap between laboratorial manipulation and clinical practices, as it outperformed previous methods by improving data repeatability, eliminating human error/sample loss, and more importantly, providing a more accurate and comprehensive evaluation of drug effects.

Advancements in the synthesis of carbon dots and their application in biomedicine

As a sort of fluorescent carbon nanomaterial with a particle size of less than 10 nm, carbon dots (CDs) have their own merits of good dispersibility in water, stable optical properties, strong chemical inertness, stable optical properties, and good biosecurity. These excellent peculiarities facilitated them like sensing, imaging, medicine, catalysis, and optoelectronics, making them a new star in the field of nanotechnology. In particular, the development of CDs in the fields of chemical probes, imaging, cancer therapy, antibacterial and drug delivery has become a hot topic in current research. Although the biomedical applications in CDs have been demonstrated in many research articles, a systematic summary of their role in biomedical applications is scarce. In this review, we introduced the basic information of CDs in detail, including synthesis approaches of CDs as well as their favorable properties including photoluminescence and low cytotoxicity. Subsequently, the application of CDs in the field of biomedicine was emphasized. Finally, the main challenges and research prospects of CDs in this field were proposed, which might provide some detailed information in designing new CDs in this promising biomedical field.

A dual-functional microfluidic chip for guiding personalized lung cancer medicine: combining EGFR mutation detection and organoid-based drug response test

Many efforts have been paid to advance the effectiveness of personalized medicine for lung cancer patients. Sequencing-based molecular diagnosis of EGFR mutations has been widely used to guide the selection of anti-lung-cancer drugs. Organoid-based assays have also been developed to ex vivo test individual responses to anti-lung-cancer drugs. After addressing several technical difficulties, a new combined strategy, in which anti-cancer medicines are first selected based on molecular diagnosis and then ex vivo tested on organoids, has been realized in a single dual-functional microfluidic chip. A DNA-based nanoruler has been developed to detect the existence of EGFR mutations and shrink the detection period from weeks to hours, compared with sequencing. The employment of the DNA-based nanoruler creates a possibility to purposively test anti-cancer drugs, either EGFR-TKIs or chemotherapy drugs, not both, on limited amounts of organoids. Moreover, a DNA-based nanosensor has been developed to recognize intracellular ATP variation without harming cell viability, realizing in situ monitoring of the whole course growth status of organoids for on-chip drug response test. The dual-functional microfluidic chip was validated by both cell lines and clinical samples from lung cancer patients. Furthermore, based on the dual-functional microfluidic chip, a fully automated system has been developed to span the divide between experimental procedures and therapeutic approaches. This study constitutes a novel way of combining EGFR mutation detection and organoid-based drug response test on an individual patient for guiding personalized lung cancer medicine.

Fluorescent nanostructured carbon dot-aptasensor for chlorpyrifos detection: Elucidating the interaction mechanism for an environmentally hazardous pollutant

Chlorpyrifos (CPF) is a commonly used insecticide found in many water sources and is related to several health and environmental effects. Biosensors based on aptamers (single-stranded nucleic acid oligonucleotides) are promising alternatives to achieve the detection of CPF and other pesticides in natural waters. However, several challenges need to be addressed to promote the real application of functional aptasensing devices. In this work, an ssDNA aptamer (S1) is combined with carbon quantum dots (CD) and graphene oxide (GO) to produce a stable fluorescent aptasensor characterized through spectrophotometric and electrophoretic techniques. For a deeper understanding of the system, the mechanism of molecular interaction was studied through docking modeling using free bioinformatic tools like HDOCK, showing that the stem-loops and the higher guanine (G) content are crucial for better interaction. The model also suggests the possibility of generating a truncated aptamer to improve the binding affinity. The biosensor was evaluated for CPF detection, showing a low LOD of 0.01 μg L-1 and good specificity in tap water, even compared to other organophosphates pesticides (OPs) like profenofos. Finally, the recovery of the proposed aptasensor was evaluated in some natural water using spiked samples and compared with UPLC MS-MS chromatography as the gold standard, showing a good recovery above 2.85 nM and evidencing the need of protecting ssDNA aptamers from an erratic interaction with the aromatic groups of dissolved organic matter (humic substances). This work paves the way for a better aptasensors design and the on-site implementation of novel devices for environmental monitoring.

Fluorescence Sensor for Zearalenone Detection Based on Oxidized Single-walled Carbon Nanohorns/N-doped Carbon Quantum Dots-aptamer

Zearalenone (ZEN), a resorcinolactone toxin, which has been a potential threat to agricultural production and human health. In this study, a sample and rapid fluorescence sensor was established for the detection of ZEN, which is based on the fluorescence properties of N-doped carbon dots-aptamer (NCDs-apt) and the quenching ability of oxidized single-walled carbon nanohorns (oxSWCNHs). NCDs synthesized by one-step hydrothermal method were connected with ZEN-aptamer (ZEN-apt), and oxSWCNHs were added to quench the fluorescence of NCDs-apt. Therefore, an oxSWCNHs/NCDs-apt aptasensor based on fluorescence "on-off" for the determination of ZEN in food was formed. Under optimum conditions, the limit of detection (LOD) of this method was 18 ng/mL and the linear range was 20 ~ 100 ng/mL. The possible interfering substances were investigated, and the results showed excellent selectivity. The recoveries were in the range of 99.5%~114.3%, and the relative standard deviations (RSDs) were not more than 6.5%, which demonstrated that this aptasensor was successfully applied for the detection of ZEN in food samples with satisfactory result.

Real-time monitoring ATP variation in human cancer organoids for a long term by DNA-based nanosensor

Cancer organoids have become promising tools for predicting drug responses on many different types of cancer. Detecting the adenosine triphosphate (ATP) has currently been considered as a decisive test to profile the growth status and drug responses of organoids. ATP profiling using commercial ATP detection kits, which involve cell lysis, can be performed at a single time spot, causing a clinical dilemma of selecting the optimal time spot to adopt diverse cancer types and patients. This study provides a feasible solution to this dilemma by developing a DNA-based ATP nanosensor to realize real-time ATP monitoring in organoids for a long term. The employment of DNA materials ensures high biocompatibility and low cytotoxicity, which are crucial for fragile organoids; The usage of tetrahedral DNA framework ensures cell permeability and intracellular ATP detection; The introduction of ATP-mediated molecular replacement ensures the high sensitivity and selectivity of ATP recognition. These features result in the first successful attempt on real-time monitoring ATP in organoids for up to 26 days and gaining growth status curves for the whole duration of a drug sensitivity test on human lung cancer organoids.

A fluorescent probe for protein tyrosine kinase 7 detection in serum and cell imaging

Tyrosine protein kinase 7 (PTK7) is overexpressed in breast cancer, which is considered as a cancer marker for breast cancer diagnosis. Therefore, a simple fluorescent probe for PTK7 detection and cell imaging was developed. In the developed probe, Fe₃O₄ magnetic nanoparticles were used as the fluorescent separator, and the fluorescence of carbon dots were used as the detection signal. The probe was worked by control the configurations of the aptamer of PTK7, the aptamer would be open chains by recognition of PTK7, which bond with carbon dots and show fluorescent signal. Based on the remarkably high affinity and selectivity of aptamer for PTK7, the excellent fluorescence property of carbon dots and the outstanding magnetism of Fe₃O₄ magnetic nanoparticles, the developed probe showed satisfied results for PTK7 detection in serum and MCF-7 cell imaging. The probe detected PTK7 in the range of 0.2-200 ng mL^-1 with a detection limit of 0.0347 ng mL^-1, and successfully imaged the cancer cell expressed PTK7. The results indicate that the nano-fluorescent probe has great potential for clinical applications.

Microfluidic biosensor for one-step detection of multiplex foodborne bacteria ssDNA simultaneously by smartphone

As a major threat to food safety due to their pathogenicity, foodborne bacteria have received much attention. In this paper, we present a one-step and wash-free microfluidic biosensor platform by smartphone for simultaneous multiple foodborne bacteria target single-stranded DNA (ssDNA) detection. This technology is based on the fluorescence resonance energy transfer (FRET) between the graphene oxide (GO) and fluorescence molecules modified capture ssDNA of the target bacteria ssDNA (ctDNA) which were coated on the microfluidic chips. The fluorescence recovery was recorded by a smartphone fluorescent detector. With an optimal analytical performance, the platform realized the detection of four kinds of bacteria ssDNA simultaneously within 5 min, with the limits of detection (LODs) of 0.17, 0.18, 0.27, and 0.17 nM, respectively. And the throughput analysis of trace amounts of foodborne bacteria ssDNA in milk and water samples were successfully detected. This one-step and wash-free microfluidic biosensor can be used as a tool for food safety analysis.

Preparation of Fluorescent Carbon Dots Composites and Their Potential Applications in Biomedicine and Drug Delivery-A Review

Carbon dots (CDs), a new member of carbon nanostructures, rely on surface modification and functionalization for their good fluorescence phosphorescence and excellent physical and chemical properties, including small size (<10 nm), high chemical stability, biocompatibility, non-toxicity, low cost, and easy synthesis. In the field of medical research on cancer (IARC), CDs, a new material with unique optical properties as a photosensitizer, are being applied to heating local apoptosis induction of cancer cells. In addition, imaging tools can also be combined with a drug to form the nanometer complex compound, the imaging guidance for multi-function dosage, so as to improve the efficiency of drug delivery, which also plays a big role in genetic diagnosis. This paper mainly includes three parts: The first part briefly introduces the synthesis and preparation of carbon dots, and summarizes the advantages and disadvantages of different preparation methods; The second part introduces the preparation methods of carbon dot composites. Finally, the application status of carbon dot composites in biomedicine, cancer theranostics, drug delivery, electrochemistry, and photocatalysis is summarized.

A highly sensitive strategy for glypican-3 detection based on aptamer/gold carbon dots/magnetic graphene oxide nanosheets as fluorescent biosensor

Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths in China. Glypican-3 (GPC3) is a specific antigen related to HCC, which is widely used in clinical detection as a reliable marker of HCC. In this paper, a highly sensitive homogeneous apatasensor was designed for GPC3 detection based on fluorescence resonance energy transfer (FRET) where the GPC3 aptamer labelled gold carbon dots (AuCDs-GPC3_Apt) are used as a donor and magnetic graphene oxide (Fe₃O₄/GO) nanosheets are used as an acceptor. A one-step hydrothermal method was used to synthesize AuCDs to provide sufficient fluorescence. The FRET phenomenon exists between AuCDs-GPC3_Apt and Fe₃O₄/GO, which weakens the fluorescence intensity of the whole system. When the target GPC3 is added to the FRET system, the fluorescent AuCDs-GPC3_Apt binds to the GPC3 and forms a folded structure, which leads to AuCDs-GPC3_Apt separation from Fe₃O₄/GO nanosheets. The Fe₃O₄/GO is then magnetically separated so that the fluorescence of free labelled AuCDs-GPC3_Apt is restored. Under the optimum conditions, the fluorescence recovery rate is linearly correlated with the concentration of GPC3 (5-100 ng·mL^-1) and the detection limit is 3.01 ng·mL^-1 (S/N = 3). This strategy shows recoveries from 98.76 to 101.29% in real human serum samples and provides an immediate and effective detection method for the quantification of GPC3 with great potential applications for early diagnosis of HCC. A sensitive homogeneous FRET-based apatasensor was designed for GPC3 detection where the AuCDs-GPC3_Apt is a donor and Fe₃O₄/GO nanosheets are an acceptor. The GPC3 fluorescent aptasensor combines wider output range with low cost, high specificity, and good anti-interference.

Development of a graphene oxide nanosheet and double-stranded DNA structure based fluorescent "signal off" aptasensor for ochratoxin A detection in malt

A "signal off" fluorescent aptasensor based on graphene oxide (GO) nanosheet and double-stranded DNA structure was fabricated for OTA detection. In the absence of OTA, the aptamer and its complementary DNA (cDNA) formed double-stranded conjugates that could coexist with GO, presenting fluorescence responses. Then, the presented OTA was captured by the aptamers, causing the release of cDNA-FAM probes. The free probes were adsorbed by GO, leading to an OTA concentration-dependent fluorescence quenching through fluorescence resonance energy transfer. Under optimum conditions, the fluorescent aptasensor exhibited outstanding sensitivity with a LOD of 11 pg/mL and a wide dynamic range of 0.04-30 ng/mL. The selectivity of the aptasensor was confirmed against other four mycotoxins, and the feasibility and reliability were verified by determining OTA in the spiked malt samples with satisfactory recovery of 95.50%-112.05%. This aptasensing platform could be adapted to measure other mycotoxins by replacing the aptamer sequences for food safety.

Branched poly(ethylenimine) carbon dots-MnO2 nanosheets based fluorescent sensory system for sensing of malachite green in fish samples

Malachite green (MG) is an organic dye compound that is frequently used as a fungicide and antiseptic in aquaculture. However, human or animal exposure to MG causes carcinogenic, teratogenic and mutagenic effects. Herein, a novel fluorescent assay was designed for the detection of MG using manganese dioxide nanosheets (MnO₂ NS) as an energy acceptor to quench the fluorescence of branched poly(ethylenimine) carbon dots (BPEI-CDs) via Förster resonance energy transfer. When butyrylcholinesterase is introduced to form thiocholine in the presence of S-butyrylthiocholine iodide, MnO₂ NS can be recovered by thiocholine to Mn²⁺, resulting in restoration of the fluorescence of BPEI-CDs. Exploiting these changes in fluorescence intensity in the above system, a fluorescence probe was successfully developed for the quantitative detection of MG. Besides, this assay was applied to fish samples, verifying the high potential for practical application of the proposed sensor for the monitoring of MG in aquatic products.

Carbon dot composites for bioapplications: a review

Recent advancements in the synthesis of carbon dot composites and their applications in biomedical fields (bioimaging, drug delivery and biosensing) have been carefully summarized. The current challenges and future trends of CD composites in this field have also been discussed.

Quantification of ATP in cell by fluorescence spectroscopy based on generalized ratio quantitative analysis model

In this contribution, fluorescence spectroscopy based on G-quadruplex formation was developed for the quantification of ATP in cell. In the absence of ATP, thioflavin T (ThT) dye can combine with the G-rich ATP aptamer to form an ATP aptamer-ThT G-quandruplex complex, resulting in the enhancement of fluorescence intensity; otherwise, fluorescence intensity of the system will weaken with the addition of ATP, because ATP has a strong affinity with G-rich ATP aptamer and can replace ThT to form an ATP aptamer-ATP complex. A calibration model based on generalized ratio quantitative analysis model was employed to mitigate the influence of scatterers and background absorbers in cell suspensions. The proposed fluorescence method was applied to the quantitative analysis of ATP in two type of cell lines, and achieved satisfactory quantitative results with accuracy comparable to that of the reference method-ATP detection kit. The limit of detection and limit of quantification of the proposed method for ATP in cell were estimated to be 0.22 and 0.66 μM, respectively. This proposed fluorescence method is highly simple and rapid, and does not require the use of fluorescent labeling.

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.

A Review of Off-On Fluorescent Nanoprobes: Mechanisms, Properties, and Applications

With the development of nanomaterials, fluorescent nanoprobes have attracted enormous attention in the fields of chemical sensing, optical materials, and biological detection. In this paper, the advantages of "off-on" fluorescent nanoprobes in disease detection, such as high sensitivity and short response time, are attentively highlighted. The characteristics, sensing mechanisms, and classifications of disease-related target substances, along with applications of these nanoprobes in cancer diagnosis and therapy are summarized systematically. In addition, the prospects of "off-on" fluorescent nanoprobe in disease detection are predicted. In this review, we presented information from all the papers published in the last 5 years discussing "off-on" fluorescent nanoprobes. This review was written in the hopes of being useful to researchers who are interested in further developing fluorescent nanoprobes. The characteristics of these nanoprobes are explained systematically, and data references and supports for biological analysis, clinical drug improvement, and disease detection have been provided appropriately.

Fluorometric Aptasensor for Determination of Escherichia coli O157:H7 by FRET Effect between Aminated Carbon Quantum Dots and Graphene Oxide

A fluorometric aptasensor based on Escherichia coli O157:H7 (E. coli O157:H7) aptamer labeled aminated carbon quantum dots (NH₂-CQDs) and graphene oxide (GO) for the determination of E. coli O157:H7 was developed. In this research, carboxyl group (-COOH) terminated E. coli O157:H7 aptamer was steadily labeled to NH₂-CQDs by amidation reaction, and played the role of energy donor and was responsible for chemical recognition. Correspondingly, GO served as an energy acceptor. The introduction of NH₂-CQDs not only made the aptamer bond stably through covalent bond, but also significantly enhanced the fluorescence intensity compared with general CQDs. The NH₂-CQDs-aptamer is adsorbed on the surface of GO through π-π stacking and hydrophobic interaction. The fluorescence of NH₂-CQDs-aptamer was quenched via fluorescence resonance energy transfer (FRET) between NH₂-CQDs and GO. After adding E. coli O157:H7, the specific binding affinity between NH₂-CQDs-aptamer and E. coli O157:H7 lead to desorption of NH₂-CQDs-aptamer from GO, and recovery of the fluorescence intensity of NH₂-CQDs-aptamer. Under the optimal conditions, the increased fluorescence intensity showed a good linear relationship to concentrations of E. coli O157:H7 in the range 10² - 10⁷ cells/mL, with a detection limit of 89 cells/mL. Furthermore, the developed method was successfully applied to the determination of E. coli O157:H7 in commercial milk samples.

Ultra-sensitive detection of ATP in serum and lysates based on nitrogen-doped carbon dots

In this work, novel types of nitrogen-doped carbon dots (N-CDs) were prepared from citric acid and glycine (GLY) as precursors through a simple pyrolysis method. The GLY-CDs showed strong fluorescence with a fluorescence quantum yield as high as 33.34% and good water solubility. The fluorescence of GLY-CDs could be selectively quenched by iron(III) ion (Fe³⁺ ) resulting in the non-fluorescent complex. Due to the high affinity of Fe³⁺ to adenosine-5'-triphosphate (ATP), the fluorescence of the GLY-CDs in GLY-CDs-Fe³⁺ could be recovered by ATP. Thereby, quantitatively fluorescent turn-on detection of ATP could be achieved. The fluorescence recovery ratio was linearly proportional to the concentration of ATP with a detection limit as low as 15.0 nM, indicating the CDs have high sensitivity. The GLY-CDs were successfully employed in the detection of ATP in serum and cell lysates.

Fluorescence Determination of Peptidase Activity Based on the Quenching of a Fluorophore-Labelled Peptide by Graphene Oxide

In this study, a fluorescence detection strategy is reported for the peptidase activity assay, which is based on fluorescence resonance energy transfer (FRET) from a fluorophore-labelled peptide to graphene oxide (GO). By the hydrolysis of the peptide, the fluorophore-labelled peptide releases the fluorophore 5-carboxyfluorescein, which can avoid quenching from GO. Thus, the increased intensity of the obtained fluorescence signal in the assay is directly dependent on the peptidase activity. As a model case of the developed strategy, the activity determination of pancreatic elastase (PE) is performed. Under the optimal experimental conditions at an excitation wavelength of 494 nm, the activity of PE can be determined in the range from 0.003 to 0.10 U/mL, with a detection limit of 0.001 U/mL at the emission wavelength of 518 nm. This is ultra-sensitive for the determination of PE. The specificity of the method is demonstrated by the analysis of PE under complex conditions using fetal bovine serum as the substrate. Hence, the developed method might provide an intrinsically convenient, sensitive platform for the PE activity assay and related biochemical studies due to its homogeneous, and fluorescence-based detection strategy.

Multi-carbon dots and aptamer based signal amplification ratiometric fluorescence probe for protein tyrosine kinase 7 detection

Background

Protein tyrosine kinase 7 (PTK 7) is a membrane receptor, which can be found in various kinds of cancers. In view of this, detection of PTK 7 in the peripheral circulation would be an effective way for the early diagnosis of cancer.

Results

In this work, a multi-carbon dots and aptamer-based signal amplification ratiometric fluorescence probe was developed. The fluorescence of the aptamer-modified y-CDs and b-CDs were respectively chosen as the detection signal and interior label. The fluorescence of y-CDs was quenched by Fe₃O₄ and cDNA (complement to aptamer) compound without PTK 7, but recovered by the addition of PTK 7. Then, the free aptamer was cut by DNase I, which amplified the detection signal. The ratiometric fluorescence sensor for PTK 7 was established with the LOD of 0.016 ng mL⁻¹.

Conclusions

Summary, a multi-carbon dots and aptamer-based signal amplification ratiometric fluorescence probe was developed for the detection of protein tyrosine kinase 7. The developed probe was applied to PTK 7 detection in MCF-7 cells and human serum with satisfying results, thus indicating that this probe has huge potential in clinical practice.

Recent advances in the construction and analytical applications of carbon dots-based optical nanoassembly

Recently, more and more attention has been focused on the construction and analytical applications of optical nanoassembly through combining carbon dots (CDs) with various other functional nanomaterials. The rational design and manufacture of CDs-based optical nanoassembly will be critical to meeting the needs of analytical science. The last decade has witnessed the immense potential of CDs-based optical nanoassembly in multiple sensing applications owing to their controlled optical properties, adjustable surface chemistry and microscopic morphology. This feature article collects the recent advances in the research and development of CDs-based optical nanoassembly and their applications in analytical sensors, aiming to provide vital insights and suggestions to inspire their broad sensing applications.

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/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.

One-step and ultrasensitive ATP detection by using positively charged nano-gold@graphene oxide as a versatile nanocomposite

A versatile nanocomposite was simply prepared based upon the electrostatic adsorption of positively charged gold nanoparticles with negatively charged graphene oxide (nano-gold@GO), and utilized as a novel fluorescence quenching platform for ultrasensitive detection of adenosine triphosphate (ATP). In the designed system, DNA-stabilized Ag nanoclusters (DNA/AgNCs) were used as fluorescent probes, DNA duplex was formed in the presence of ATP, and they can electrostatically adsorb onto the surface of nano-gold@GO to quench the fluorescence signal. Upon the addition of exonuclease III (Exo III), the DNA duplex would be hydrolyzed into DNA fragments and resulted in the recovery of the fluorescence signals due to the diffusion of AgNCs away from nano-gold@GO. Based on these, sensitive detection of ATP was realized with a detection range of 5.0 pM-20 nM. Notably, a good recovery in the range of 94-104% was obtained when detecting ATP in human serum samples, indicating a promising application value in early disease diagnosis. Graphical abstract A functional positively charged nano-gold@graphene oxide was fabricated and utilized as an enhanced fluorescence quenching platform for the detection of ATP, coupled with exonuclease III-assisted signal amplification.

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

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

Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014-2019)

Fluorescence resonance energy transfer, one of the most powerful phenomena for elucidating molecular interactions, has been extensively utilized as a biosensing tool to provide accurate information at the nanoscale. Numerous aptamer- and nanomaterial-based FRET bioassays has been developed for detection of a large variety of molecules. Affinity probes are widely used in biosensors, in which aptamers have emerged as advantageous biorecognition elements, due to their chemical and structural stability. Similarly, optically active nanomaterials offer significant advantages over conventional organic dyes, such as superior photophysical properties, large surface-to-volume ratios, photostability, and longer shelf life. In this report (with 175 references), the use of aptamer-modified nanomaterials as FRET couples is reviewed: quantum dots, upconverting nanoparticles, graphene, reduced graphene oxide, gold nanoparticles, molybdenum disulfide, graphene quantum dots, carbon dots, and metal-organic frameworks. Tabulated summaries provide the reader with useful information on the current state of research in the field. Graphical abstract Schematic representation of a fluorescence resonance energy transfer-based aptamer nanoprobe in the absence and presence of a given target molecule (analyte). Structures are not drawn to their original scales.

A label-free fluorescent probe for the detection of adenosine 5'‑triphosphate via inhibiting the aggregation-induced emission enhancement of glutathione modified silver nanoclusters triggered by zinc ion

It is important to establish sensitive and simple analysis methods for adenosine 5'‑triphosphate (ATP). A label-free fluorescent probe for the determination of ATP was constructed based on glutathione modified silver nanoclusters (AgNCs/GSH). AgNCs/GSH showed aggregation-induced emission enhancement (AIEE) property in the organic solvent. The effects of metal ions on the fluorescence of AgNCs/GSH were also studied. Only zinc ion enhanced the fluorescence of AgNCs/GSH obviously. This was because Zn²⁺ coordinated with AgNCs/GSH to cause the aggregation of AgNCs/GSH, which was sufficiently proved by TEM. With the addition of ATP, Zn²⁺ bound with ATP through ZnOP bond and the binding between Zn²⁺ and AgNCs/GSH was inhibited. Hence the fluorescence of AgNCs/GSH was decreased with increasing the ATP concentration. The fluorescence response was linear in the ATP concentration range of 1-110 μM, and the detection limit was 0.8 μM. Then this method was successfully applied for determining ATP in the samples of human urine and rat serum, the recoveries were in the range of 97.6%-103%.

A fluorometric aptamer nanoprobe for alpha-fetoprotein by exploiting the FRET between 5-carboxyfluorescein and palladium nanoparticles

Alpha-fetoprotein (AFP) is a reliable clinical marker of hepatocellular carcinoma (HCC). A highly sensitive fluorometric aptamer nanoprobe is described for AFP detection. It is based on fluorescence resonance energy transfer (FRET) between AFP aptamer labelled with 5-carboxyfluorescein (FAM) and palladium nanoparticles (PdNPs). The PdNPs quench the green fluorescence of the FAM-AFP aptamer via interactions between nitrogen functional groups of the AFP aptamer and PdNPs. When AFP was introduced into the FAM-AFP aptamer-PdNPs FRET system, the AFP aptamer preferentially combines with AFP. This results in a conformational change and weakens the interaction between the aptamer and the PdNPs. Thus, the fluorescence of FAM recovers. The fluorescence recovery of FAM increases linearly in the 5.0-150 ng·mL^-1 AFP concentration range and has a 1.4 ng·mL^-1 detection limit. The assay was applied to the analysis of spiked diluted human serum. The recovery values ranged from 98.3 to 112.9%, with relative standard deviations of <1.1%. This biosensing strategy provides a reliable and ultrasensitive protocol for the quantification of biomarkers with relevant antigens and aptamers. Graphical abstract Schematic presentation of a fluorometric aptamer nanoprobe for AFP assay based on fluorescence resonance energy transfer (FRET) between AFP aptamer labelled with 5-carboxyfluorescein (FAM) and palladium nanoparticles (PdNPs).

A fluorometric displacement assay for adenosine triphosphate using layered cobalt(II) double hydroxide nanosheets

A turn-on fluorometric method is described for the determination of adenosine-5'-triphosphate (ATP). It is based on the displacement of a dye-labeled oligonucleotide from a cobalt(II) based layered double hydroxide (LDH). Due to the electrostatic and ligand exchange interaction, the FAM-labeled DNA is readily adsorbed on the LDH. This leads to complete and fast quenching of the green fluorescence of the label. However, on addition of ATP, the DNA is detached from the LDH because of the stronger affinity of ATP for LDH. This results in the restoration of the green fluorescence. The effect was used to design a sensitive assay that has a linear response in the 0.5-100 μM ATP concentration range and a 0.23 μM lower detection limit. It was applied to the determination of ATP in spiked serum samples. Graphical abstract Schematic presentation of a fluorometric ATP assay based on the displacement of a dye-labeled oligonucleotide from a layered double hydroxide (LDH).

A critical comparison of lanthanide based upconversion nanoparticles to fluorescent proteins, semiconductor quantum dots, and carbon dots for use in optical sensing and imaging

The right choice of a fluorescent probe is essential for successful luminescence imaging and sensing and especially concerning in vivo and in vitro applications, the development of new classes have gained more and more attention in the last years. One of the most promising class are upconversion nanoparticles (UCNPs)-inorganic nanocrystals capable to convert near-infrared light in high energy radiation. In this review we will compare UCNPs with other fluorescent probes in terms of (a) the optical properties of the probes, such as their brightness, photostability and excitation wavelength; (b) their chemical properties such as the dispersibility, stability under experimental or physiological conditions, availability of chemical modification strategies for labelling; and (c) the potential toxicity and biocompatibility of the probe. Thereby we want to provide a better understanding of the advantages and drawbacks of UCNPs and address future challenges in the design of the nanocrystals.

A bioinspired antifouling zwitterionic interface based on reduced graphene oxide carbon nanofibers: electrochemical aptasensing of adenosine triphosphate

An antifouling electrochemical aptasensor for ATP is described that has a zwitterionic self-assembled sensing interface on a glassy carbon electrode modified with a reduced graphene oxide carbon nanofiber (GO-CNF). The GO-CNF was first modified by self-polymerization of dopamine which provided a platform for simultaneously self-assembly of the ATP aptamer and cysteine. By using hexacyanoferrate as the electrochemical probe, in the presence of ATP, the aptamer strands fold around ATP molecules, thus leading to the variation of the electrochemical signal. The aptasensor has a linear response in the 0.1 pM to 5 nM ATP concentration range, and a 13 fM lower detection limit. The electrode is strongly resistant to nonspecific adsorption and biofouling. This enabled the detection of ATP even in spiked human plasma. Graphical abstract An antifouling electrochemical aptasensor employing reduced graphene oxide carbon nanofiber as conductive substrate and zwitterionic cysteine as antifouling material for adenosine triphosphate detection.

A colorimetric ATP assay based on the use of a magnesium(II)-dependent DNAzyme

A colorimetric assay for ATP is described that uses a strategy that combines the concept of split Mg(II)-dependent DNAzyme, split aptamer, and hybridization-induced aggregation of gold nanoparticles (AuNPs). Both ATP aptamer and Mg(II)-dependent DNAzyme are split into two fragments which are allocated to two well-designed DNA probes. The probes also possess mutually complementary stem sequences and spacer sequences. In the presence of ATP, the separated DNAzyme sequences in the two probes assemble via the synchronous recognition of ATP with two fragments of the aptamer. Then, the activated DNAzyme catalyzes multiple cycles of the cleavage of its substrate DNA sequence. The latter acts as a linker and induces the aggregation of two types of ssDNA-modified AuNP through the hybridization between the complementary sequences. Thus, the color of the AuNP solution remains red. However, in the absence of ATP, the detached aptamer cannot induce the assembly of DNAzyme to cleave the linker DNA. This results in the aggregation of AuNP and a concomitant color transition from red to purple. This ATP assay, performed at a wavelength of 530 nm, has a linear detection range that extends from 10 pM to 100 nM, with a detection limit of 5.3 pM. It was applied to the detection of ATP in human serum. Conceivably, the strategy has a wide scope in that it may be applied to the colorimetric detection of various other analytes through the split aptamer configuration. Graphical abstract Schematic presentation of colorimetric assay for adenosine triphosphate (ATP) based on the use of a split Mg(II)-dependent DNAzyme, a split aptamer, and by exploiting the hybridization-induced aggregation of gold nanoparticles that leads to a color change from red to purple.

A glassy carbon electrode modified with graphene oxide, poly(3,4-ethylenedioxythiophene), an antifouling peptide and an aptamer for ultrasensitive detection of adenosine triphosphate

An antifouling aptasensor is described for voltammetric determination of adenosine triphosphate (ATP). A glassy carbon electrode (GCE) was modified with a graphene oxide and poly(3,4-ethylenedioxythiophene) (GO-PEDOT) composite film by electrodeposition. Next, the zwitterionic peptide (EKEKEKE) was attached. It forms an antifouling layer on the modified GCE and serves as the support for subsequent aptamer immobilization. The resulting aptasensor typically is operated at a potential of 0.18 V (vs. SCE) using hexacyanoferrate as the electrochemical probe. It has a linear response in the 0.1 pM to 1.0 μM ATP concentration range, a 0.03 pM detection limit and a sensitivity of 2674.7 μA·μM^-1·cm^-2. It has outstanding selectivity, satisfactory reproducibility and desired stability. It was used to quantify ATP in ATP-spiked 10% serum solutions. Graphical abstract Schematic presentation of the construction of the aptamer based electrode for voltammetric determination of ATP.

A split aptamer-labeled ratiometric fluorescent biosensor for specific detection of adenosine in human urine

A dual-emission ratiometric fluorometric aptasensor is presented for highly specific detection of adenosine. An adenosine binding aptamer (ABA) was split into two halves (termed as ABA1 and ABA2). ABA1 was covalently bound to blue-emitting carbon dots (with excitation/emission maxima at 365/440 nm) as responsive fluorophore (referred to as ABA1-CDs). ABA2 was linked to red-emitting silica-coated CdTe quantum dots (with excitation/emission maxima at 365/613 nm) acting as internal reference and referred to as ABA2-QDs@SiO₂. Upon addition of graphene oxide, the fluorescence of ABA1-CDs is quenched. After subsequent addition of ABA2-QDs@SiO₂ and different amounts of adenosine, the blue fluorescence is recovered and causes a color change from red to royal blue. The method represents a ratiometric turn-on assay for visual, colorimetric and fluorometric determination of adenosine. The limit of detection is as low as 2.4 nM in case of ratiometric fluorometry. The method was successfully applied to the determination of adenosine in (spiked) human urine. Recoveries range from 98.8% to 102%. Graphical abstract Adenosine binding aptamer1-carbon dots (ABA1-CDs) can absorb on graphene oxide (GO) via π stacking. This causes fluorescence to be quenched by fluorescence resonance energy transfer (FRET). After addition of ABA2-silica-coated quantum dots (ABA2-QDs@SiO₂) and adenosine, binding of adenosine to two pieces of aptamers forms a complex (ABA1-CD/adenosine/ABA2-QD@SiO₂) which dissociates from GO. As a result, fluorescence is recovered.

Signal amplification by strand displacement in a carbon dot based fluorometric assay for ATP

A fluorometric ATP assay is described that makes use of carbon dots and graphene oxide along with toehold-mediated strand displacement reaction. In the absence of target, the fluorescence of carbon dots (with excitation/emission maxima at 360/447 nm) is strong and in the "on" state, because the signal probe hybridizes with the aptamer strand and cannot combine with graphene oxide. In the presence of ATP, it will bind to the aptamer and induce a strand displacement reaction. Consequently, the signal probe is released, the sensing strategy will change into the "off" state with the addition of graphene oxide. This aptasensor exhibits selective and sensitive response to ATP and has a 3.3 nM detection limit. Graphical abstract Schematic of signal amplification by strand displacement in a carbon dot based fluorometric assay for ATP. This strategy exhibits high sensitivity and selectivity with a detection limit as low as 3.3 nM.

A terbium-based metal-organic framework@gold nanoparticle system as a fluorometric probe for aptamer based determination of adenosine triphosphate

This study reports on a method for fluorometric aptasensing of adenosine triphosphate (ATP). It is based on the interaction of dispersed (red) and agglomerated (blue) gold nanoparticles (AuNPs) with a water-dispered terbium(III) based metal-organic framework (Tb-MOF). The dispersed AuNPs quench the emissions of the Tb-MOF, while the aggregated AuNPs have little effect. Under the condition of high salt concentration, the free aptamer against ATP does not stabilize the AuNPs against aggregation. This causes a color change from red to blue and weak quenching of the fluorescence of the Tb-MOF (with peaks at 489 nm and 544 nm after excitation at 290 nm). On addition of ATP, it will be bound by its aptamer to form a complex that is adsorbed on the AuNPs. This protects the AuNPs from salt-induced aggregation and the color (with a peak at 525 nm) remains red. The two fluorescence bands of the Tb-MOF are therefore suppressed by fluorescence resonance energy transfer (FRET) between Tb-MOF and the dispersed AuNPs. Fluorescence drops linearly in the 50 nM to 10 μM ATP concentration range, and the detection limit is 23 nM. ATP analogs such as guanosine triphosphate, uridine triphosphate, cytidine triphosphate, adenosine monophosphate and cyclic adenosine monophosphate have no obvious interference. The method was successfully applied to the determination of ATP in (spiked) human plasma samples and gave satisfactory recoveries. Graphical abstract Schematic of a terbium-based metal-organic framework@gold nanoparticle system as a fluorometric probe for aptamer based determination of adenosine triphosphate. The dispersed gold nanoparticles (AuNPs) quench the fluorescence of the terbium-based metal-organic framework (Tb-MOF), while the aggregated AuNPs have little effect. In the presence of adenosine triphosphate (ATP), the aptamer-ATP complexes provide greater protection towards AuNPs than aptamer alone under high salt condition. Based on this, a novel Tb-MOF@AuNP platform is established for ATP detection.

Nanosensing of ATP by fluorescence recovery after surface energy transfer between rhodamine B and curcubit[7]uril-capped gold nanoparticles

The authors describe a method for functionalization of gold nanoparticles (AuNPs) with the supramolecular host molecule, curcubit[7]uril (CB[7]) which can bind rhodamine B (RhB). The fluorescence of RhB is quenched by the AuNPs via surface energy transfer. On addition of ATP, a dimeric RhB-ATP complex is formed and RhB is pushed out of CB[7]. Hence, fluorescence increases by a factor of 8. This fluorescence recovery effect has been utilized to develop a new detection scheme for ATP. The assay, measured at fluorescence excitation and emission wavelengths of 500 nm and 574 nm respectively, works in the 0.5-10 μM concentration range and has a 100 nM detection limit. The method is not interfered by UTP, GTP, CTP, TTP, ascorbic acid and glutathione. Graphical abstract Schematic of a method for determination of ATP in the 500 nM to 10 μM concentration range by using fluorescence recovery after surface energy transfer (SET) between rhodamine B (RhB) and gold nanoparticles capped with curcubit[7]uril (CB[7]).