Target-triggered hairpin-free chain-branching growth of DNA dendrimers for contrast-enhanced imaging in living cells by avoiding signal dispersion

Integration of Hybridization Chain Reaction and Protein-Binding Amplification for Long-Term Imaging of Intracellular mRNA: Avoiding Signal Fluctuation

Amplified nanoprobes based on hybridization chain reaction (HCR) have been widely developed for the detection of intracellular low abundance mRNA. However, the formed chain-like assembly decorated with fluorophore would be degraded rapidly by endogenous enzyme, resulting in failure of the long-term fluorescence imaging. To address this issue, herein, a composite signal-amplifying strategy that integrates HCR into protein-binding signal amplification (HPSA) was communicated for the in situ imaging of mRNA by avoiding signal fluctuation. Different from conventional HCR-based nanoprobes (HCR-nanoprobe), the HCR was used as the signal-triggered mode and the amplifying signal generated from in situ fluorophore-protein binding in cells, which can maintain high stability of the signal for a long time. As a proof-of-principle, a nanobeacon based on HPSA (HPSA-nanobeacon) was constructed to detect TK1 mRNA. Taking advantage of the double signal-amplifying mode, the endogenous TK1 mRNA was sensitively detected and the fluorescence signal was maintained for more than 8 h in HepG2 cells. The attempt in this work provides a new option to the current signal-amplifying strategy for sensing nucleic acid targets with high stability, significantly enhancing the acquisition of intracellular molecular information.

A magnetic nanozyme platform for bacterial colorimetric detection and chemodynamic/photothermal synergistic antibacterial therapy

Rapid, convenient, and sensitive detection of bacteria and development of novel antibacterial materials are conducive to accurate treatment of bacterial infection and reducing the generation of drug-resistant bacteria caused by overuse of antibiotics. A dual-function magnetic nanozyme, Fc-MBL@rGO@Fe3O4, has been constructed with broad-spectrum bacterial affinity and good peroxidase-like activity. Detection signal amplification was realized in the presence of 3,3',5,5'-tetramethylbenzidine (TMB) with a detection limit of 26 CFU/mL. In addition, the excellent photothermal properties of Fc-MBL@rGO@Fe3O4 could realize synergistic chemodynamic/photothermal antibacterial therapy. Furthermore, the good bacterial affinity of Fc-MBL@rGO@Fe3O4 enhances the accurate and rapid attack of hydroxyl radical (·OH) on the bacterial membrane and achieves efficient sterilization (100%) at low concentration (40 µg/mL) and mild temperature (47℃). Notably, Fc-MBL@rGO@Fe3O4 has a broad spectrum of antibacterial activity against Gram-negative, Gram-positive, and drug-resistant bacteria. The magnetic nanoplatform integrating detection-sterilization not only meets the need for highly sensitive and accurate detection in different scenarios, but can realize low power density NIR-II light-responsive chemodynamic/photothermal antibacterial therapy, which has broad application prospects.

Endogenously Gated DNA Walking Machine for Prescreened MicroRNA Detection in Extracellular Vesicles

Tumor-derived extracellular vesicle (T-EV) microRNAs have been investigated as promising biomarkers in clinical diagnosis as well as disease progression monitoring. However, the expression profiles of microRNA in different tissues vary widely, the precise monitoring of microRNA levels in EVs originating from diseased tissues is susceptible to background interference, thus remains a challenge. Conventional assays require extensive processing, such as EV isolation and even sample lysis, which is both slow and laborious, and the cumbersome pretreatment could spoil the downstream analysis. To address this issue, we developed a generalizable strategy for T-EVs-selective activation and therefore specific amplified microRNA imaging. The conditional signal amplification is established by integrating a traditional DNA walker system with endogenously activated motif to achieve sensitized microRNA imaging in T-EVs. The preorganized endogenous activation with additional sensing criteria narrowed the scope against the complex specimens, and the amplified sensing with reduced off-target signals was supposed to be sensitive to monitor the tiny changes of microRNA expression during the disease course, which holds great potential for accurate diagnosis and prognosis.

Bismuth, Nitrogen-Codoped Carbon Dots as a Dual-Read Optical Sensing Platform for Highly Sensitive, Ultrarapid, Ratiometric Detection of Doxorubicin

Doxorubicin (DOX) is a potent anticancer drug, but it has side effects on normal tissues, particularly myocardial cells. Therefore, it is crucial to detect the DOX concentration in body fluids for effective clinical treatment. In this work, N,Bi-codoped CDs (Bi,N-CDs) were synthesized through a one-step hydrothermal method to carbonize the raw materials of 2,4-dinitroaniline and bismuth nitrate. The resulting Bi,N-CDs showed a reduced emission at 490 nm and an enhanced emission at 590 nm in the presence of DOX. The ratio of fluorescence (FL) intensity (F590/F490) was found to be a reliable indicator of DOX concentration, ranging from 0.05 to 30 μM and 40-200 μM, with detection limits (LOD) of 34 and 24 nM, respectively. A ratiometric fluorescence nanoprobe was established for highly selective and sensitive detection of DOX using a specific electrostatic interaction and inner filter effect between Bi,N-CDs and DOX. Meanwhile, Bi,N-CDs exhibited a distinct color change ranging from yellow to orange-red when exposed to DOX, allowing for a colorimetric method to measure DOX levels in the range of 0.05-30 μM, with a detection limit of 169 nM. The probe was triumphantly used to monitor DOX in actual samples via a dual-mode optical sensing strategy. This study contributes to the development of heteroatom-doped CDs and expands their potential applications for detecting biological samples.

A single-domain green fluorescent protein catenane

Natural proteins exhibit rich structural diversity based on the folds of an invariably linear chain. Macromolecular catenanes that cooperatively fold into a single domain do not belong to the current protein universe, and their design and synthesis open new territories in chemistry. Here, we report the design, synthesis, and properties of a single-domain green fluorescent protein catenane via rewiring the connectivity of GFP's secondary motifs. The synthesis could be achieved in two steps via a pseudorotaxane intermediate or directly via expression in cellulo. Various proteins-of-interest may be inserted at the loop regions to give fusion protein catenanes where the two subunits exhibit enhanced thermal resilience, thermal stability, and mechanical stability due to strong conformational coupling. The strategy can be applied to other proteins with similar fold, giving rise to a family of single-domain fluorescent proteins. The results imply that there may be multiple protein topological variants with desirable functional traits beyond their corresponding linear protein counterparts, which are now made accessible and fully open for exploration.

Synthesis of tetrahedron DNA nanostructures for detecting the activation of cell signal transduction via their specific binding to transcriptional factors

A technique for detecting the activation of cell signal transduction is particularly important for disease diagnosis and therapy. Transcriptional factor (TF) activities that could indicate the status of cell signal transduction are a favorable target for cell signal detection. Tetrahedron DNA nanostructures (TDNs) which contain specific binding sequences of TFs were designed and synthesized in this research, and their effects on detecting cell signal transduction were evaluated. We found that FAM-labeled TDNs with the indicated TF binding sequences could specifically bind to activated TFs of hypoxia signaling or TGF-β signaling. Signaling pathway activities detected via TDNs could be exhibited by various methods including fluorescence imaging, flow cytometry and fluorescence spectrometer analysis. The reliability of this new technique is in line with the classical dual luciferase reporter assay system. This work develops a novel and effective tool to examine the activation of intracellular signaling pathways via nanotechnology. In addition, good stability and programmability of TDNs ensure their widespread application in various signaling pathways.

A colorimetric smartphone-based platform for pesticides detection using Fe-N/C single-atom nanozyme as oxidase mimetics

In this study, a novel highly sensitive colorimetric platform has been designed for malathion assay based on Fe-N/C SAzyme. The as-synthesized SAzyme can directly oxidize 3,3´,5,5´-tetramethylbenzidine (TMB) to generate blue colored oxidized TMB. L-ascorbic acid-2-phosphate (AA2P), a substrate of acid phosphatase (ACP), could be hydrolyzed to AA, thereafter inhibit the oxidization reaction of TMB, leading to a conspicuous blue color fading. With the addition of malathion hindered the ACP activity and limited the AA production, resulting in the recovery of the catalytic activity of single-atom nanozyme. Under optimized operational conditions, a novel colorimetric assay has been designed for malathion detection with LOD of 0.42 nM. Besides, quantification of malathion in environmental and food samples was achieved based on the proposed strategy. In addition, the successfully integrated paper/smartphone sensor provided sensitive, and rapid, reliable detection of malathion with a LOD of 1 nM.

A novel fluorescence method for detection of phosphate anions based on porphyrin metalation

In this work, a novel fluorescence method for the detection of phosphate anions (PO₄^3-) was developed based on porphyrin metalation. Through catalysis by G-quadruplex (G4), Cu²⁺ could insert into the porphyrins to quench their fluorescence. G4 simultaneously improved the fluorescence of the porphyrins but not that of Cu²⁺-porphyrin. In the absence of PO₄^3-, the porphyrins were metallized by Cu²⁺, and no fluorescence was observed. In the presence of PO₄^3-, PO₄^3- could coordinate with Cu²⁺ to prevent porphyrin metalation. Free porphyrin could bind with G4 to emit strong fluorescence. By comparing four common porphyrins, we found that G4 had the greatest effect on increasing the fluorescence intensity of N-methylmesoporphyrin IX (NMM). Thus, NMM/G4 was chosen for the design of a biosensor. Under optimal experimental conditions, this method showed high sensitivity and satisfactory selectivity for PO₄^3- with a detection limit of 44 nM in a linear range of 0.01-1.0 μM. The recovery experiments showed recovery rates of 93.75-106.00%, suggesting a great potential for measuring PO₄^3- in real samples.

β-Cyclodextrin Polymer-Based Host-Guest Interaction and Fluorescence Enhancement of Pyrene for Sensitive Isocarbophos Detection

The extensive use of organophosphorus pesticides in agriculture poses a high risk to human health and has boosted the demands for developing sensitive monitoring methods. Herein, we developed a facile and sensitive method for isocarbophos detection based on the remarkable fluorescence enhancement of pyrene during host-guest interaction of β-cyclodextrin polymer (β-CDP) and pyrene. The 3'-pyrene-labeled isocarbophos aptamer could be cleaved by exonuclease I to obtain free pyrene that was tagged on mononucleotides, which could enter the hydrophobic cavity of β-CDP, resulting in a prominent fluorescence enhancement. While the target isocarbophos was added, aptamer could undergo a conformational change into a hairpin complex, which prevented the cleavage and host-guest interaction because of the steric hindrance, leading to a weak fluorescence. The isocarbophos has been sensitively and selectively analyzed by detecting the system fluorescence intensity with a detection limit as low as 1.2 μg/L. In addition, we have verified the ability of our proposed method in real sample detection from fruit extract.

Hybridization chain reaction circuit-based electrochemiluminescent biosensor for SARS-cov-2 RdRp gene assay

In this work, we designed an ECL ratiometric biosensor with a three-stranded Y-type DNA (Y-DNA) probe and induced a hybridization chain reaction (HCR) for the highly sensitive detection of SARS-CoV-2 nucleic acid. The important component of this system is the self-assembled Y-Shaped probe based on three nucleic acids. Y1, Y2, and Y3 can be linked by complementary base pairing to Hairpin1 (H1), Hairpin2 (H2), and Ru modified DNA (Ru1), respectively. H1 and H2 can trigger the HCR reaction when activated by the SARS-CoV-2 RdRp gene and the 5′ end of Ru1. The 5′ end of Ru1 is modified with the Ru complex, which can produce a strong electrochemiluminescence luminescence signal at 620 nm under an applied voltage. Through the amplification of Y-DNA-induced HCR reaction, Ru1 on the electrode surface gradually increased, the ECL signal at 460 nm was gradually quenched, and the signal at 620 nm was steadily generated. The SARS-CoV-2 RdRp gene can be quantified according to the degree of decrease of ECL signal at 460 nm and the increase of ECL signal at 620 nm. Combining the two signal amplification strategies, this ratiometric ECL biosensor can accurately and efficiently detect the target gene with a detection limit of 59 aM.