DNA branched junctions induced the enhanced fluorescence recovery of FAM-labeled probes on rGO for detecting Pb2

A novel fluorescent strategy for Golgi protein 73 determination based on aptamer/nitrogen-doped graphene quantum dots/molybdenum disulfide @ reduced graphene oxide nanosheets

The effective detection of biomarkers associated with hepatocellular carcinoma (HCC) is of great importance. Golgi protein 73 (GP73), a serum biomarker of HCC, has better diagnostic value than Alpha-fetoprotein (AFP) has been reported. In this paper, highly accurate fluorescence sensing platform for detecting GP73 was constructed based on fluorescence resonance energy transfer (FRET), in which nitrogen-doped graphene quantum dots (NGQDs) labelling with GP73 aptamer (GP73_Apt) was used as fluorescence probe, and molybdenum disulfide @ reduced graphene oxide (MoS₂@RGO) nanosheets was used as fluorescent receptors. MoS₂@RGO nanosheets can quench the fluorescence of NGQDs-GP73_Apt owing to FRET mechanisms. In the presence of GP73, the NGQDs-GP73_Apt specifically bound with GP73 to from the deployable structures, making NGQDs-GP73_Apt far away from MoS₂@RGO nanosheets, blocking the FRET process, resulting in fluorescence recovery of NGQDs-GP73_Apt. Under optimal conditions, the recovery intensity of fluorescence in the detection system is linearly related to the concentration of GP73 in the range of 5 ng/mL - 100 ng/mL and the limit of detection is 4.54 ng/mL (S/N = 3). Moreover, detection of GP73 was performed in human serum samples with good recovery (97.21-100.83%). This platform provides a feasible method for the early diagnosis of HCC, and can be easily extended to the detection of other biomarkers.

A ratiometric fluorescence platform for lead ion detection via RNA cleavage-inhibited self-assembly of three-arm branched junction

Heavy metal pollution can pose a threat to food safety and human health, and accurate quantification of heavy metal ions is a vital requirement. Emerging DNA nanostructures-based biosensors offer attractive tools toward ultra-sensitive or rapid analysis of heavy metal ions. However, the problems including complex design, severe reaction conditions and undesirable reliability are inevitable obstacle in advancing their extension and application. Herein, a ratiometric fluorescent platform was established for monitoring lead ion (Pb²⁺) in food based on dual Förster resonance energy transfer (FRET) and RNA cleavage-inhibited self-assembly of three-arm branched junction (TBJ). GR-5 DNAzyme was employed for Pb²⁺ recognition, and enzyme-free amplification technique catalytic hairpin assembly (CHA) served to form FRET probes-carried TBJ. The substrate strand (S) of DNAzyme triggered the generation of CHA-TBJ, and Pb²⁺-responsive cleavage of S hindered the assembly of CHA-TBJ, causing opposite changes in the FRET states of FAM/BHQ1 and ROX/BHQ2 pairs. The fluorescence responses were recorded through synchronous fluorescence spectrometry to indicate Pb²⁺ concentration, allowing sensitive and reliable identification of Pb²⁺ in the linear range of 0.05-5 ng mL^-1 with the detection limit of 0.03 ng mL^-1. The Pb²⁺ detection can be achieved under conventional reaction conditions, simple mixing procedures and one-step measurement operation. The approach can afford excellent specificity for Pb²⁺ against competing metal ions, and can be applied to analyze Pb²⁺ in tea samples with satisfactory results. This facile fluorescence platform shows a capable method for Pb²⁺ detection, and provides new avenue in the development of ratiometric approaches and DNAzyme strategies for monitoring heavy metal pollution, facilitating the transformation of DNAzyme-based biosensors for food safety control.

Signal-on fluorescent sensing strategy for Pb2+ detection based on 8-17 DNAzyme-mediated molecular beacon-type catalytic hairpin assembly circuit

Based on a Pb²⁺-specific 8-17 DNAzyme-induced catalytic hairpin assembly (CHA), a simple signal-on fluorescence strategy for lead ion detection was established. 8-17 DNAzyme was used as the recognition element of Pb²⁺, which catalyzed the cleavage of the RNA base embedded in the DNA substrate strand, while releasing part of the substrate strand (S') as CHA initiator. And two hairpin probes (H1 and H2-FQ) were designed according to the sequence of S' for CHA, in which H2-FQ was labeled with the fluorophore FAM and quencher BHQ-1 as fluorescent "molecular switch" based on fluorescence resonance energy transfer (FRET). In the presence of Pb²⁺, the CHA reaction was triggered to form a large number of H1-H2 complexes, enabling enzyme-free isothermal amplification and a signal-on fluorescence strategy. In the concentration range of 0.5-1000 nM, the fluorescence signal increases with the increase of Pb²⁺ concentration. The quantitative detection limit of Pb²⁺ by this method is 0.5 nM, which has better detection performance compared with the FQ-labeled 8-17 DNAzyme method. The established biosensor exhibits good specificity and can be effectively used for the detection of Pb²⁺ in real samples of river water and grass carp. Through ingenious nucleic acid sequence design, DNAzyme and CHA reactions are integrated to realize the enzyme-free isothermal amplifications and sensitive detection of Pb²⁺, which holds potential versatility in food supervision and environmental monitoring.

A fluorescence aptasensor based on GSH@GQDs and RGO for the detection of Glypican-3

Glypican-3 (GPC3), a heparin sulfate proteoglycan, is a potential diagnostic and therapeutic target for hepatocellular carcinoma. In this paper, a novel fluorescent aptasensor for GPC3 detection is constructed via glutathione@graphene quantum dots-labeled GPC3 aptamer (GSH@GQDs-GPC3_Apt) as a fluorescence probe. First, GSH@GQDs is screened out with higher fluorescence intensity, which emits bright blue fluorescence under ultraviolet light. Then, the fluorescence-labeled GSH@GQDs-GPC3_Apt probe is formed by the combination of amination GPC3_Apt and GSH@GQDs using EDC/NHS coupled reaction. Under hydrogen bond and π-π interaction/stacking, the fluorescence of GSH@GQDs-GPC3_Apt could be quenched by reductive graphene oxide (RGO) with the help of the photoinduced electron transfer and the fluorescence resonance energy transfer mechanism. In the presence of GPC3, the GSH@GQDs-GPC3_Apt specifically recognizes and binds to GPC3, giving rise to the change of secondary structure of GPC3_Apt to form the GPC3/GPC3_Apt-GSH@GQDs complex, which would lead to the disintegration of the GSH@GQDs-GPC3_Apt-RGO compound. Therefore, the energy transfer process is blocked and the fluorescence intensity is restored, enabling a highly sensitive response to GPC3. When the concentration of GPC3 is from 5.0 ng/mL to 150.0 ng/mL, the fluorescence recovery rate is well linearly related to GPC3 concentration with the limit of detection of 2.395 ng/mL (S/N = 3). This strategy shows recoveries from 98.31% to 101.89% in human serum samples and provides simple, fast and cheap analysis of GPC3, which suggests that it has great potential applications in clinical diagnosis for hepatocellular carcinoma.

A fluorescence turn-on CDs-AgNPs composites for highly sensitive and selective detection of Hg2

In this paper, a simple and effective fluorescence turn-on approach for highly sensitive and selective monitoring Hg²⁺ ions was designed by using carbon dots (CDs) and silver nanoparticles (AgNPs). It reveals that the fluorescence of CDs solution can be quenched in the presence of AgNPs through inner filter effect (IFE) and the quenched CDs-AgNPs system is turned on after addition of Hg²⁺ ions, which is due to higher affinity of Hg²⁺ and AgNPs than that of CDs and AgNPs, thus resulting the disappearance of AgNPs from the CDs-AgNPs composites and leading to the fluorescence turn-on of CDs. The developed fluorescence turn-on approach exhibited high selectivity and sensitivity for detection of Hg²⁺. Under the optimum experimental conditions, good linearity was achieved over the range of 100-160 μM and the limit of detection (LOD) was estimated to be 2.22×10^-8 M for Hg²⁺. The recoveries of Hg²⁺ spiked in real samples ranged from 98.4% to 101.6%. Results of this study suggest that the fluorescence turn-on approach can be used to the detection of Hg²⁺ in real water samples.

DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate

Numerical computation is a focus of DNA computing, and matrix operations are among the most basic and frequently used operations in numerical computation. As an important computing tool, matrix operations are often used to deal with intensive computing tasks. During calculation, the speed and accuracy of matrix operations directly affect the performance of the entire computing system. Therefore, it is important to find a way to perform matrix calculations that can ensure the speed of calculations and improve the accuracy. This paper proposes a DNA matrix operation method based on the mechanism of the DNAzyme binding to auxiliary strands to cleave the substrate. In this mechanism, the DNAzyme binding substrate requires the connection of two auxiliary strands. Without any of the two auxiliary strands, the DNAzyme does not cleave the substrate. Based on this mechanism, the multiplication operation of two matrices is realized; the two types of auxiliary strands are used as elements of the two matrices, to participate in the operation, and then are combined with the DNAzyme to cut the substrate and output the result of the matrix operation. This research provides a new method of matrix operations and provides ideas for more complex computing systems.

TiO2 Nano-test tubes as a solid visual platform for sensitive Pb2+ ion detection based on a fluorescence resonance energy transfer (FRET) process

A cost-effective, facile, and sensitive fluorescence sensing strategy for Pb²⁺ ion detection has been developed based on the fluorescence resonance energy transfer (FRET) between carbon quantum dots (CQDs) and Au nanoparticles (NPs). Glutathione (GSH)-synthesized CQDs acted as both the fluorescence donor and the sorbent to extract Pb²⁺ ions from the solution via Pb-GSH complexes. Pb²⁺ ions on CQDs reacted with -SH groups on AuNPs to generate sandwich-type Au-PdS-CQDs, leading to a dramatic decrease in the fluorescence of the CQDs. To expand the potential applications of this strategy, we constructed a sensing strategy using self-organized TiO₂ nanotube arrays (TiNTs). The high aspect ratio and transparency for light emitted from the CQDs enabled the TiNTs to serve as a sensitive solid visual platform for the highly selective detection of Pb²⁺ ions with a detection limit as low as 4.1 × 10^-8 mg mL^-1. More importantly, the long observation length combined with a small volume enabled a sample acquisition volume of only 2.1 × 10^-3 μL, which is smaller than the traditional fluorescence analysis in solution and on commercially available test paper, thus endowing this visual platform with the potential for use in single-cell diagnostics.

Review of recent progress on DNA-based biosensors for Pb2+ detection

Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb²⁺ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb²⁺ has become a rapidly growing topic in the analytical community. Pb²⁺ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb²⁺ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb²⁺ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb²⁺ sensing. In this article, these Pb²⁺ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.