We demonstrate for the first time the utilization of fluorogenic RNA aptamers for label-free uracil-DNA glycosylase (UDG) assay. Through rationally engineering the transcription machine with dU substitution, this assay requires only a single probe to simultaneously sense and amplify the UDG signal, achieving a low detection limit of 6.3 × 10 U mL. Moreover, it can be applied for screening UDG inhibitors and measuring endogenous UDG activity in different cells.
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http://dx.doi.org/10.1039/d2cc03628b | DOI Listing |
Biosens Bioelectron
December 2024
Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China. Electronic address:
J Am Chem Soc
December 2024
Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States.
Genetically encoded fluorescent protein and fluorogenic RNA sensors are indispensable tools for imaging biomolecules in cells. To expand the toolboxes and improve the generalizability and stability of this type of sensor, we report herein a genetically encoded fluorogenic DNA aptamer (GEFDA) sensor by linking a fluorogenic DNA aptamer for dimethylindole red with an ATP aptamer. The design enhances red fluorescence by 4-fold at 650 nm in the presence of ATP.
View Article and Find Full Text PDFChemMedChem
December 2024
Universite de Dijon, Institut de Chimie Moleculaire, ICMUB CNRS UMR6302, 9, avenue Alain Savary, 21078, Dijon, FRANCE.
Fluorescence detection of DNA and RNA G-quadruplexes (G4s) is a very efficient strategy to assess not only the existence and prevalence of cellular G4s but also their relevance as targets for therapeutic interventions. Among the fluorophores used to this end, turn-on probes are the most interesting since their fluorescence is triggered only upon interaction with their G4 targets, which ensures a high sensitivity and selectivity of detection. We reported on a series of twice-as-smart G4 probes, which are both smart G4 ligands (whose structure is reorganized upon interaction with G4s) and smart fluorescent probes (whose fluorescence is turned on upon interaction with G4s).
View Article and Find Full Text PDFProc Natl Acad Sci U S A
December 2024
Institute of Molecular Medicine, Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai 200127, China.
Artificially functional RNAs, such as fluorogenic RNA aptamer (FRApt)-based biosensing tag, represent significant advancements in various biological applications but are limited by the lack of insight into dynamic structure ensembles and universal design concepts. Through the development of an artificial RNA structure ensemble, we rationally established an RNA reconstitution model, "SSPepper-Apt," to generate a universal fluorogenic RNA biosensing tag. By utilizing various target-recognizing RNA motifs, SSPepper-Apt enables the modular generation of sensing tags for low-background, highly selective imaging of metabolites, peptides, and proteins in living cells.
View Article and Find Full Text PDFInt J Mol Sci
November 2024
Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
Japanese encephalitis virus (JEV) NS2B-NS3 is a protein complex composed of NS3 proteases and an NS2B co-factor. The N-terminal protease domain (180 residues) of NS3 (NS3(pro)) interacts directly with a central 40-amino acid hydrophilic domain of NS2B (NS2B(H)) to form an active serine protease. In this study, the recombinant NS2B(H)-NS3(pro) proteases were prepared in and used to compare the enzymatic activity between genotype I (GI) and III (GIII) NS2B-NS3 proteases.
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