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Highly selective fluorescence sensor for hydrogen sulfide based on the Cu(II)-dependent DNAzyme
摘要： Hydrogen sul?de (H2S) is a highly toxic gas, which poses a serious threat to human health and safety. It is necessary to develop some simple and highly selective and sensitive approach for the detection of hydrogen sul?de. In this study, a highly selective and sensitive ?uorescence sensor for H2S detection has been developed on the basis of Cu(II)-dependent DNAzyme. The catalytic DNA strand (Cu-enzyme) was labeled with a quencher (black hole quencher, BHQ1) at the 5′-termini and its corresponding DNA substrate strand (Cu-substrate) was labeled with a 6-carboxy?uorescein (FAM ?uorophore) at the 3′-end and an additional quencher was attached on the 5′-end. Cu-enzyme and Cu-substrate could hybridize with each other to form a triplex structure ?rstly and the FAM emission was quenched by the labeled quenchers. The present of Cu(II) could catalyze the oxidative cleavage of the Cu-substrate and hence caused the releasing of the quencher from the FAM ?uorophore and the enhanced ?uorescence of the system. However, in the presence of H2S, Cu(II) reacted with H2S to form CuS ?rstly, hindering the cleavage and the ?uorescence enhancement. The decrease of ?uorescence intensity had a linear relationship with the concentration of H2S in the range between 0.5 and 25 μM with a detection limit of 0.2 μM (S/N = 3). The proposed method innovatively used ?uorescent labeling technology and DNAzyme sensing to detect gaseous hydrogen sul?de, and it has been successfully applied to detect the contamination of hydrogen sul?de gas in the refuse collectors with a simple puri?cation procedure.
关键词： Hydrogen sul?de,Cu(II)-dependent DNAzyme,Fluorescence sensor
更新于2025-09-23 15:21:01
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Global Folding of a Na+-Specific DNAzyme Studied by FRET
摘要： Recently a few RNA-cleaving DNAzymes have been isolated with excellent specificity for Na+, and some of them contain a Na+ binding aptamer. This metal recognition mechanism is different from most previously reported DNAzymes. Previous studies using 2-aminopurine (2AP) as a probe have indicated interesting local folding by Na+. In this work, fluorescence resonance energy transfer (FRET) was used to probe the global folding of the Ce13d DNAzyme, one of the Na+-specific DNAzymes. FRET pairs were at different locations yielding a total of five constructs to probe its three-way junction structure with a large loop. With end-labelled DNAzymes, the global structure appears quite rigid with little folding by adding up to 200 mM monovalent metal ions, although some minor differences were observed between Li+, Na+ and K+. This lack of large conformational change is also consistent with CD spectroscopy data. The loop was then labelled with an internal TMR fluorophore at the G14 position, and its cleavage activity was partially retained. A clear Na+-dependent folding was observed with spectral crossover. From a biosensing standpoint, global folding based sensors are unlikely to work due to the overall rigid structure of the DNAzyme. Therefore, the best way using this DNAzyme to discriminate Na+ from K+ is based on cleavage activity, followed by probing local folding, while global folding is the least effective for metal discrimination.
关键词： Na+,aptamer,FRET,global folding,DNAzyme
更新于2025-09-23 15:21:01
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Controlled assembly of AIEgens based on a super-quadruplex scaffold for detection of plasma membrane proteins
摘要： Quantification of plasma membrane proteins (PMPs) is crucial for understanding the fundamentals of cellular signaling systems and their related diseases. In this work, a super-quadruplex scaffold was designed to regulate assembly of oligonucleotide-grafted AIEgens for detection of PMPs. The nonfluorescence oligonucleotide-grafted AIEgen (Oligo-AIEgen) was firstly synthesized by attaching the AIEgen to 3′-terminus of the oligonucleotide through click chemistry. Meanwhile, the tetramolecular hairpin-conjugated super-quadruplex (THP-G4) as cleavage element and signal enhancement scaffold composited of three elements: a substrate sequence of DNAzyme in the loop region, partial hybridization region in the stem, and six guanine nucleotides to form G-quadruplex. Once the DNAzyme was anchored on the specific PMPs through aptamer-protein recognition, the substrate sequence on the loop of THP-G4 was cleaved by DNAzyme with the aid of cofactor MnII, resulting in the conformation switch of THP-G4 to the activated G-quadruplex scaffold. The latter could assemble Oligo-AIEgens to generate aggregation-induced emission (AIE) enhancement, resulting in a simple and sensitive strategy for detection of membrane proteins. Moreover, the DNAzyme continuously cut the next THP-G4 to achieve recycling amplification. Under the optimized conditions, this AIE-based strategy exhibited good linear relationship with the logarithm of MUC1 concentration from 0.01 to 10 μg mL-1 with the limit of detection down to 4.3 ng mL-1. The G4-assembled AIEgens provides a universal platform for detecting various biomolecules and a proof-of concept for AIE biosensing.
关键词： Biosensors,Fluorescence,DNAzyme,Aggregation-induced emission,DNA quadruplexes,Plasma membrane protein
更新于2025-09-16 10:30:52
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A rotary plasmonic nanoclock
摘要： One of the fundamental challenges in nanophotonics is to gain full control over nanoscale optical elements. The precise spatiotemporal arrangement determines their interactions and collective behavior. To this end, DNA nanotechnology is employed as an unprecedented tool to create nanophotonic devices with excellent spatial addressability and temporal programmability. However, most of the current DNA-assembled nanophotonic devices can only reconfigure among random or very few defined states. Here, we demonstrate a DNA-assembled rotary plasmonic nanoclock. In this system, a rotor gold nanorod can carry out directional and reversible 360° rotation with respect to a stator gold nanorod, transitioning among 16 well-defined configurations powered by DNA fuels. The full-turn rotation process is monitored by optical spectroscopy in real time. We further demonstrate autonomous rotation of the plasmonic nanoclock powered by DNAzyme-RNA interactions. Such assembly approaches pave a viable route towards advanced nanophotonic systems entirely from the bottom-up.
关键词： DNA nanotechnology,nanophotonics,DNAzyme-RNA interactions,plasmonic nanoclock,gold nanorod
更新于2025-09-11 14:15:04
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Temporal and reversible control of a DNAzyme by orthogonal photoswitching
摘要： The reversible switching of catalytic systems capable of performing complex DNA computing operations using the temporal control of light is described. Two distinct photoresponsive molecules have been separately incorporated into a split horseradish peroxidase mimicking DNAzyme. We show that its catalytic function can be turned on and off reversibly upon irradiation with specific wavelengths of light. The system responded orthogonally not only to a sophisticated selection of irradiation wavelengths but depended also on different durations of irradiation. Furthermore, the DNAzyme exhibits reversible switching and retains this ability throughout multiple switching cycles. We apply the DNAzyme to act as a light-controlled 4:2 multiplexer. Photoswitchable DNAzyme-based catalysts as introduced here have potential use for controlling complex logical operations and for future applications in DNA nanodevices.
关键词： orthogonal control,nanotechnology,DNAzyme,DNA computing,photoswitching
更新于2025-09-10 09:29:36
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Aptamers Improving Fluorescence Anisotropy and Fluorescence Polarization Assays for Small Molecules
摘要： Nucleic acid affinity probes, such as aptamers, have been combined with fluorescence anisotropy (FA) / fluorescence polarization (FP) technology for the development of a diverse range of assays. Formation of a complex between a small fluorescent molecule and its binding partner usually increases the overall size of the fluorescent molecule and decreases its rate of rotation, resulting in increases in fluorescence anisotropy/polarization. Structure-switching of the fluorescently labeled aptamers arising from target binding can also affect molecular volume, local rotation of the fluorophore, and/or fluorescence lifetime, causing changes in anisotropy/polarization. Incorporation of the unique adsorptive properties of single-stranded nucleic acid aptamers on nanomaterials, hybridization of aptamers with complementary sequences, and the amplifiable ability of nucleic acid aptamers have broadened the applications of fluorescence anisotropy assays and enhanced their sensitivity. This review focuses on aptamer-based fluorescence anisotropy assays for the detection of small molecules, such as therapeutic drugs, environmental contaminants, natural toxins, and metabolites.
关键词： aptamer,adenosine triphosphate (ATP),nanomaterials,anisotropy,cocaine,nucleic acids,toxins,DNAzyme,polarization,aflatoxin B1,ochratoxin A (OTA),tyrosinamide
更新于2025-09-10 09:29:36
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A Novel Fluorescence Switch for MicroRNA Imaging in Living Cells based on DNAzyme Amplification Strategy.
摘要： MicroRNAs (miRNAs) play important roles in the regulation of target gene expression and cell development. Therefore, developing of accurate and visual detection methods for miRNAs is important for early diagnosis of cancer. In this study, we established a visual detection method for miRNA 155 based on DNAzyme amplification strategy in living cells. MnO2 nanosheets were employed to deliver Locked DNAzyme and Substrate DNA into cells. AuNPs-Probe were taken up by cells autonomously. Then, MnO2 nanosheets were reduced to Mn2+ by glutathione (GSH) in cells and DNA modules were released. MiRNA 155 took away Locker DNA by strand displacement reaction to activate the DNAzyme. Then the DNAzyme cleaved substrate DNA and released single-stranded DNA named Key DNA. Key DNA opened the hairpin DNA that modified on gold nanoparticles (AuNPs) and turn on the fluorescence of cy5. One target miRNA led to plenty of released Key DNA when lots of substrate DNA were added. Thus, the visual detection of miRNA 155 in living cells would be initiated. Under confocal laser microscopy, the fluorescence was obviously observed in tumor cells but not in normal cells. The method has a linear range from 0.1 nM to 10 nM and a low detection limit of 44 pM in vitro detection.
关键词： DNA walker,microRNA,AuNPs,Fluorescence imaging,MnO2,DNAzyme,Signal amplification
更新于2025-09-09 09:28:46
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Versatile Catalytic Deoxyribozyme Vehicles for Multimodal Imaging-Guided Efficient Gene Regulation and Photothermal Therapy
摘要： Catalytic deoxyribozyme has great potential for gene regulation, but poor efficiency of the cleavage of mRNA and lack of versatile DNAzyme vehicles remain big challenges for potent gene therapy. By rational designing a diverse vehicle of polydopamine-Mn2+ nanoparticles (MnPDA), we demonstrate that MnPDA has integrated functions as an effective DNAzyme delivery vector, self-generation source of DNAzyme cofactor for catalytic mRNA cleavage, inherent therapeutic photothermal agent, as well as contrast agents for photoacoustic and magnetic resonance imaging. Specifically, the DNAzyme-MnPDA nanosystem protects catalytic deoxyribozyme from degradation and enhances cellular uptake efficiency. In the presence of intracellular glutathione, the nanoparticles are able to in-situ generate free Mn2+ as a cofactor of DNAzyme to effectively trigger catalytic cleavage of mRNA for gene silencing. In addition, the nanosystem shows high photothermal conversion efficiency and excellent stability against photothermal processing and degradation in complex environments. Unlike previous DNAzyme delivery vehicles, this vehicle exhibits diverse functionalities for potent gene regulation, allowing multimodal imaging-guided synergetic gene regulation and photothermal therapy both in vitro and in vivo.
关键词： deoxyribozyme,multimodal imaging,photothermal therapy,DNAzyme,gene therapy
更新于2025-09-04 15:30:14