Label-free and ratiometric detection of nuclei acids based on graphene quantum dots utilizing cascade amplification by nicking endonuclease and catalytic G-quadruplex DNAzyme

Graphene quantum dots: synthesis, properties, and applications to the development of optical and electrochemical sensors for chemical sensing

GQDs exhibits exceptional electrochemical activity owing to their active edge sites that make them very attractive for biosensing applications. However, their use in the design of new biosensing devices for application to the detection and quantification of toxins, pathogens, and clinical biomarkers has so far not investigated in detail. In this regard, herein we provide a detailed review on various methodologies employed for the synthesis of GQDs, including bottom-up and top-down approaches, with a special focus on their applications in biosensing via fluorescence, photoluminescence, chemiluminescence, electrochemiluminescence, fluorescence resonance energy transfer, and electrochemical techniques. We believe that this review will shed light on the critical issues and widen the applications of GQDs for the design of biosensors with improved analytical response for future applications. HIGHLIGHTS: • Properties of GQDs play a critical role in biosensing applications. • Synthesis of GQDs using top-down and bottom-up approaches is discussed comprehensively. • Overview of advancements in GQD-based sensors over the last decade. • Methods for the design of selective and sensitive GQD-based sensors. • Challenges and opportunities for future GQD-based sensors.

Construction of DNA Biosensors for Mercury (II) Ion Detection Based on Enzyme-Driven Signal Amplification Strategy

Mercury ion (Hg²⁺) is a well-known toxic heavy metal ion. It is harmful for human health even at low concentrations in the environment. Therefore, it is very important to measure the level of Hg²⁺. Many methods, reviewed in several papers, have been established on DNA biosensors for detecting Hg²⁺. However, few reviews on the strategy of enzyme-driven signal amplification have been reported. In this paper, we reviewed this topic by dividing the enzymes into nucleases and DNAzymes according to their chemical nature. Initially, we introduce the nucleases including Exo III, Exo I, Nickase, DSN, and DNase I. In this section, the Exo III-driven signal amplification strategy was described in detail. Because Hg²⁺ can help ssDNA fold into dsDNA by T-Hg-T, and the substrate of Exo III is dsDNA, Exo III can be used to design Hg²⁺ biosensor very flexibly. Then, the DNAzyme-assisted signal amplification strategies were reviewed in three categories, including UO₂²⁺-specific DNAzymes, Cu²⁺-specific DNAzymes and Mg²⁺-specific DNAzymes. In this section, the Mg²⁺-specific DNAzyme was introduced in detail, because this DNAzyme has highly catalytic activity, and Mg²⁺ is very common ion which is not harmful to the environment. Finally, the challenges and future perspectives were discussed.

2'-O-Methyl molecular beacon: a promising molecular tool that permits elimination of sticky-end pairing and improvement of detection sensitivity

An innovative 2'-O-methyl molecular beacon (MB) has been designed and prepared with improved thermal stability and unique nuclease resistance. The employment of 2'-O-methyl MBs helps efficiently suppress the background signal, while DNase I is responsible for the signal amplification and elimination of sticky-end pairing. The coupled use of 2'-O-methyl MBs and DNase I makes it possible to develop an enzyme-aided strategy for amplified detection of DNA targets in a sensitive and specific fashion. The analysis requires only mix-and-measure steps that can be accomplished within half an hour. The detection sensitivity is theoretically determined as 27.4 pM, which is nearly 200-fold better than that of the classic MB-based assay. This proposed sensing system also shows desired selectivity. All these features are of great importance for the design and application of MBs in biological, chemical, and biomedical fields.

Applications of Graphene Quantum Dots in Biomedical Sensors

Due to the proliferative cancer rates, cardiovascular diseases, neurodegenerative disorders, autoimmune diseases and a plethora of infections across the globe, it is essential to introduce strategies that can rapidly and specifically detect the ultralow concentrations of relevant biomarkers, pathogens, toxins and pharmaceuticals in biological matrices. Considering these pathophysiologies, various research works have become necessary to fabricate biosensors for their early diagnosis and treatment, using nanomaterials like quantum dots (QDs). These nanomaterials effectively ameliorate the sensor performance with respect to their reproducibility, selectivity as well as sensitivity. In particular, graphene quantum dots (GQDs), which are ideally graphene fragments of nanometer size, constitute discrete features such as acting as attractive fluorophores and excellent electro-catalysts owing to their photo-stability, water-solubility, biocompatibility, non-toxicity and lucrativeness that make them favorable candidates for a wide range of novel biomedical applications. Herein, we reviewed about 300 biomedical studies reported over the last five years which entail the state of art as well as some pioneering ideas with respect to the prominent role of GQDs, especially in the development of optical, electrochemical and photoelectrochemical biosensors. Additionally, we outline the ideal properties of GQDs, their eclectic methods of synthesis, and the general principle behind several biosensing techniques.

Dual amplification in a fluorometric acetamiprid assay by using an aptamer, G-quadruplex/hemin DNAzyme, and graphene quantum dots functionalized with D-penicillamine and histidine

D-penicillamine and histidine-functionalized graphene quantum dot (DPA-GQD-His) was synthesized and applied in a fluorometric method for determination of acetamiprid using a G-quadruplex DNAzyme. At first DNA probe (probe 1) consists of a target-specific aptamer with two arms of DNA segments. Probe 1 was hybridized with DNA probe 2 composed of a single DNA sequence with two split G-rich DNA sequences. This leads to the formation of a triplex-to-G-quadruplex (TPGQ). Next, acetamiprid was hybridized with the aptamer in the TPGQ to release free DNA probe 2. The released probe 2, in the presence of of K⁺, undergoes a structural change into a stem-loop structure (by self-complementary hybridization and Hoogsteen hydrogen bonding) that bears a G-quadruplex structure. This is followed by conjugation with hemin to form the G-quadruplex/hemin DNAzyme. The DNAzyme catalyzes the oxidation of o-phenylenediamine by H₂O₂ to produce a yellow fluorescent product with excitation/emission maxima at 420/560 nm. The oxidation product interacts with DPA-GQD-His to achieve a rapid energy transfer between DPA-GQD-His and oxidation product. This increases the fluorescence of the oxidation product and quenches the fluorescence of DPA-GQD-His. DPA-GQD-His also improves the catalytic activity of DNAzyme towards oxidation of ophenylenediamine oxidization and enhances fluorometric response to acetamiprid. The assay works in the 1.0 fM to 1.0 nM acetamiprid concentration range and has a 0.38 fM detection limit. It was successfully applied to the determination of acetamiprid in tea. Graphical abstractThe study reported one double amplification strategy for ultrasensitive fluorescence detection of acetamiprid in tea with D-penicillamine and histidine-functionalized graphene quantum dots and G-quadruplex/heminDNAzyme. The analtyical method exhibits ultra high sensitivity, selectivity and rapidity of fluorescence response to acetamiprid.

Integrating Target-Responsive Hydrogels with Smartphone for On-Site ppb-Level Quantitation of Organophosphate Pesticides

Precise on-site profiling of organophosphate pesticides (OPs) is of significant importance for monitoring pollution and estimating poisoning. Herein, we designed a simple and convenient portable kit based on Ag⁺-responsive hydrogels for accurate detection of OPs. The newly developed hydrogels employed o-phenylenediamine (OPD) and silicon quantum dots (SiQDs) as indicator, which possessed ratiometric response. In this sensor, OPs as inhibitor of acetylcholinesterase prevented the generation of thiocholine, which blocked the formation of metal-polymer with Ag⁺, further triggered the oxidation of OPD to yield yellow 2,3-diaminophenazine (DAP) with fluorescence emission at 557 nm. The fluorescence intensity of SiQDs (444 nm) was quenched by DAP through inner filter effect (IFE) process, emerging a typical ratiometric response. Interestingly, the ratiometric signal of kit, which was recorded by smartphone's camera, can be transduced by ImageJ software into the hue parameter that was linearly proportional to the concentration of OPs. The simplicity of portable kit combined with smartphone operation, which possessed high sensitivity (detection limit <10 ng mL^-1) and rapid sample-to-answer detection time (45 min) in agricultural sample, indicating that the methodology offered a new sight for portable monitoring of food safety and human health.

Ratiometric fluorescent nanoprobes for visual detection: Design principles and recent advances - A review

Signal generation techniques for visual detection of analytes have received a great deal of attention in various sensing fields. These approaches are considered to be advantageous when instrumentation cannot be employed, such as for on-site assays, point-of-care tests, and he althcare diagnostics in resource-constrained areas. Amongst various visual detection approaches explored for non-invasive quantitative measurements, ratiometric fluorescence sensing has received particular attention as a potential method to overcome the limitations of intensity-based probes. This technique relies on changes in the intensity of two or more emission bands (induced by an analyte), resulting in an effective internal referencing which improves the sensitivity of the detection. The self-calibration, together with the unique optophysical properties of nanoparticles (NPs) have made the ratiometric fluorescent nanoprobes more sensitive and reliable, which in turn, can result in more precise visual detection of the analytes. Over the past few years, a vast number of ratiometric sensing probes using nanostructured fluorophores have been designed and reported for a wide variety of sensing, imaging, and biomedical applications. In this work, a review on the NP-based ratiometric fluorescent sensors has been presented to meticulously elucidate their development, advances and challenges. With a special emphasis on visual detection, the most important steps in the design of fluorescent ratiometric nanoprobes have been given and based on different classes of analytes, recent applications of fluorescent ratiometric nanoprobes have been summarized. The challenges for the future use of the technique investigated in this review have been also discussed.

An "off-on" fluorescent sensor for copper ion using graphene quantum dots based on oxidation of l-cysteine

A simple and highly efficient "off-on" fluorescent sensor based on grapheme quantum dots (GQDs) for Cu²⁺ was developed. In this sensing platform, the fluorescence of GQDs was quenched in the presence of 2,4-dinitrophenylcysteine (DNPC), which is the reaction product of 1-chloro-2,4-dinitrobenzene (CDNB) and l-cysteine, owing to the spectral overlap between the absorption of DNPC and the excitation of GQDs. In the presence of Cu²⁺, l-cysteine was catalytically oxidized to l-cystine by O₂, resulting in the reduction of DNPC. Thus, the fluorescence of GQDs was recovery. Based on this, the fluorescent detection of Cu²⁺ could be achieved. The proposed sensing strategy offered a selective identification of Cu²⁺ with a detection limit of 4.5 nM. Additionally, the practical application of this assay for Cu²⁺ determination in real water samples was also demonstrated.

Rapid cancer diagnosis by highly fluorescent carbon nanodots-based imaging

Carbon dots (Cdots) with bright green fluorescence were applied to the rapid and selective cell imaging for a variety of cell lines. Different labeling distributions of hepatoma cells (HepG2) and normal human liver cells (LO2) were achieved using Cdots as imaging agents. For HepG2 cells, the Cdots could rapidly permeate the cell membrane and diffuse into the cytoplasm and nucleus within 3 min, and retained their location in the targets for 24 h. However, the Cdots exhibited bright fluorescence only in the cytoplasm of LO2 cell lines. Moreover, the Cdots were almost non-cytotoxic and exhibited superior photostability over a wide range of pH. Therefore, these Cdots have great potential for rapid, luminous and selective bioimaging applications, and are expected to be used as a nucleus-staining agent in cancer diagnosis. Graphical abstract ᅟ.

Graphene quantum dots as nanoprobes for fluorescent detection of propofol in emulsions

We report a new fluorescent detection method for propofol based on graphene quantum dots (GQDs). Citric acid (CA) was selected as the carbon precursor, and fluorescent GQDs were prepared by carbonizing CA. The product, which efficiently quenched the fluorescence of GQDs, could be obtained through the oxidation of propofol in the presence of horseradish peroxidase and hydrogen peroxide. The fluorescence intensity ratio of GQDs (F/F ₀) was positively correlated with the concentration of propofol, which ranged within 5.34-89.07 mg l^-1, the limit of detection was 0.5 mg l^-1 and the limit of quantity was 5.34 mg l^-1. The developed fluorescence method reported in the present study is simple, sensitive, reproducible, and can serve in determining propofol contents in emulsions.

Graphitic C3N4 nanosheet and hemin/G-quadruplex DNAzyme-based label-free chemiluminescence aptasensing for biomarkers

Here we first reported that graphitic carbon nitride nanosheet (g-C₃N₄ NS) could effectively quench the chemiluminescence (CL) of luminol-hydrogen peroxide (H₂O₂) system. According to the new discovery, a label-free and homogeneous CL aptasensing platform was designed for sensitive detecting of biomarkers. In the absence of target, DNA probe containing hemin/G-quadruplex DNAzyme structure was adsorbed on the surface of g-C₃N₄ NS, causing the CL quenching of luminol through an electron transfer process. However, in the presence of the target, a DNA-DNA duplex was formed due to DNA hybridization reaction and target recognition effect, which could not be adsorbed onto the g-C₃N₄ NS surface because of its weak affinity. Thus, the electron transfer was blocked and the CL emission of luminol could be enhanced. The proposed CL aptasensor could detect carcinoembryonic antigen (CEA) with a detection limit of 63.0 pg/mL and it can also be used as a general detecting strategy for adenosinetriphosphate (ATP) detection. This aptasensing platform exhibited high sensitivity toward biomarkers and the probe need not be labeled, showing great promise for disease diagnosis.

Rapid and visual detection of aflatoxin B1 in foodstuffs using aptamer/G-quadruplex DNAzyme probe with low background noise

Contamination of foods by aflatoxin B1 (AFB1) is a common serious problem. To improve the efficiency of AFB1 detection, this study aims to develop a sensitive aptasensor for detection of AFB1 in food samples based on the catalytic effect of aptamer/G-quadruplex DNAzyme probe. The resulting reassembly of this probe in the presence of hemin and K⁺ catalyzes the generation of fluorescent 2,3-diaminophenazine (DAP) from o-phenylenediamine (OPD). Interestingly, we first found that the high background induced by the superfluous hemin can be effectively suppressed with the aid of sequential adsorption and magnetic separation by magnetic oxidized multiwall carbon nanotubes (Fe₃O₄@oMWCNTs). This aptasensor exhibits a high sensitivity toward AFB1 with a detection limit of 0.02 ng/mL. The assay also shows higher selectivity for AFB1 compared to other reported agents and can be employed to detect AFB1 in foodstuffs, which might find broad practical applications in other food contaminants determination.

Recent progress in two-dimensional inorganic quantum dots

This review critically summarizes recent progress in the categories, synthetic routes, properties, functionalization and applications of 2D materials-based quantum dots (QDs).

A Sensitive Electrochemical Aptasensor for Thrombin Detection Based on Electroactive Co-Based Metal-Organic Frameworks with Target-Triggering NESA Strategy

In this work, an improved target-triggering nicking enzyme signaling amplification (NESA) strategy as signal enhancer has been fabricated to obtain a sensitive electrochemical thrombin (TB) biosensor combined with PtPd NPs decorated electroactive Co-based metal-organic frameworks (Co-MOFs/PtPdNPs) as a redox mediator. Traditionally, in the NESA strategy, only one of the output double strands DNA is available in the next cycle. However, in this work, all of the output DNA involved in the improved NESA strategies could be further employed, resulting in high utilization of output DNA, which further enhanced signal amplification and sensitivity of the biosensor. In addition, the electroactive Co-MOFs were not only used as nanocarriers but also acted as signal labels, avoiding adding extra redox media. Simultaneously, in the presence of H₂O₂, PtPd NPs decorated on the Co-MOFs act the same as horseradish peroxidase to promote the oxidation of H₂O₂, further promoting the conversion of Co²⁺ to Co³⁺, leading to electrochemical signal amplification. With such design, the TB biosensor exhibited good sensitivity from 1 pM to 30 nM with a detection limit of 0.32 pM. This new NESA strategy with high utilization of output DNA can supply one efficient approach to improve signal amplification, which also open an avenue for sensitivity enhancement in detection of analytes.

On-site detection of stacked genetically modified soybean based on event-specific TM-LAMP and a DNAzyme-lateral flow biosensor

Stacked genetically modified organisms (GMO) are becoming popular for their enhanced production efficiency and improved functional properties, and on-site detection of stacked GMO is an urgent challenge to be solved. In this study, we developed a cascade system combining event-specific tag-labeled multiplex LAMP with a DNAzyme-lateral flow biosensor for reliable detection of stacked events (DP305423× GTS 40-3-2). Three primer sets, both event-specific and soybean species-specific, were newly designed for the tag-labeled multiplex LAMP system. A trident-like lateral flow biosensor displayed amplified products simultaneously without cross contamination, and DNAzyme enhancement improved the sensitivity effectively. After optimization, the limit of detection was approximately 0.1% (w/w) for stacked GM soybean, which is sensitive enough to detect genetically modified content up to a threshold value established by several countries for regulatory compliance. The entire detection process could be shortened to 120min without any large-scale instrumentation. This method may be useful for the in-field detection of DP305423× GTS 40-3-2 soybean on a single kernel basis and on-site screening tests of stacked GM soybean lines and individual parent GM soybean lines in highly processed foods.

Simple method for O-GlcNAc sensitive detection based on graphene quantum dots

Simple and sensitive method for O-GlcNAc detection in cell lysates based on graphene quantum dots combination; WGA was successfully developed.

A bio-chemical application of N-GQDs and g-C3N4 QDs sensitized TiO2 nanopillars for the quantitative detection of pcDNA3-HBV

Herein, TiO₂ nanopillars (NPs)/N-doped graphene quantum dots (N-GQDs)/g-C₃N₄ QDs heterojunction efficiently suppressed the photogenerated charges recombination and improved photo-to-current conversion efficiency. The introduced N-GQDs and g-C₃N₄ QDs could result in more effective separation of the photogenerated charges, and thus produce a further increase of the photocurrent. TiO₂ NPs/N-GQDs/g-C₃N₄ QDs were firstly applied as the photoactive materials for the fabrication of the biosensors, and the primers of pcDNA3-HBV were then adsorbed on the TiO₂ NPs/N-GQDs/g-C₃N₄ QDs modified electrode under the activation of EDC/NHS. With increase of the pcDNA3-HBV concentration, the photocurrent reduced once the double helix between the primers and pcDNA3-HBV formed. The developed photoelectrochemical (PEC) biosensor showed a sensitive response to pcDNA3-HBV in a linear range of 0.01 fmol/L to 20nmol/L with a detection limit of 0.005 fmol/L under the optimal conditions. The biosensor exhibited high sensitivity, good selectivity, good stability and reproducibility.

A upconversion luminescene biosensor based on dual-signal amplification for the detection of short DNA species of c-erbB-2 oncogene

High-sensitivity detection of trace amounts of c-erbB-2 oncogene was reported to be equal to or surpass the ability of CA 15-3 for early diagnosis and/or follow-up recurrent screening of breast cancer. Therefore, in the current study, by using upconversion nanoparticles (UCNPs), rare earth-doped NaYF4:Yb(3+)/Er(3+) as the luminescent labels, a upconversion luminescent (UCL) biosensor based on dual-signal amplification of exonuclease III (ExoIII)-assisted target cycles and long-range self-assembly DNA concatamers was developed for the detection of c-erbB-2 oncogene. The proposed biosensor exhibited ultrasensitive detection with limit as low as 40 aM, which may express the potential of being used in trace analysis of c-erbB-2 oncogene and early diagnosis of breast cancer.