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Using environment-sensitive tetramethylated thiophene-BODIPY fluorophores in DNA probes for studying effector-induced conformational changes of protein-DNA complexes.
RSC Chem Biol
January 2025
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo n. 2 Prague 6 Czechia
The LutR protein represses the transcription of genes encoding enzymes for the utilization of l-lactate in through binding to a specific DNA region. In this study, we employed oligonucleotide probes modified by viscosity-sensitive tetramethylated thiophene-BODIPY fluorophores to investigate the impact of selected metabolites on the LutR-DNA complex. Our goal was to identify the effector molecule whose binding alters the protein-DNA affinity, thereby enabling gene transcription.
View Article and Find Full Text PDFEnhancing single-cell transcriptomics using interposed anchor oligonucleotide sequences.
Commun Biol
January 2025
Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Single-cell transcriptomics, which utilises barcodes and unique molecular identifiers (UMIs) for polyA+ mRNA capture, is compromised by oligonucleotide synthesis errors. To address this, we modified the oligonucleotide capture design and integrated an interposed anchor between the barcode and the UMI. This design significantly reduces the need to discard reads due to synthesis inaccuracies.
View Article and Find Full Text PDFDNA Dendron Tagging as a Universal Way to Deliver Proteins to Cells.
J Am Chem Soc
January 2025
Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
The use of proteins as intracellular probes and therapeutic tools is often limited by poor intracellular delivery. One approach to enabling intracellular protein delivery is to transform proteins into spherical nucleic acid (proSNA) nanoconstructs, with surfaces chemically modified with a dense shell of radially oriented DNA that can engage with cell-surface receptors that facilitate endocytosis. However, proteins often have a limited number of available reactive surface residues for DNA conjugation such that the extent of DNA loading and cellular uptake is restricted.
View Article and Find Full Text PDFBifunctional cascaded single-atom nanozymes for enhanced photodynamic immunotherapy through dual-depressing PD-L1 and regulating hypoxia.
Biomaterials
January 2025
Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin, 300072, China. Electronic address:
As a promising anti-tumor modality, photodynamic immunotherapy (PDIT) has been applied for the treatment of many solid tumors. However, tumor hypoxic condition and immunosuppressive microenvironment severely limit the treatment outcome of PDIT. Here, we have designed a hairpin tetrahedral DNA nanostructure (H-TDN)-modified bifunctional cascaded Pt single-atom nanozyme (PCFP@H-TDN) with encapsulation of the photosensitizer.
View Article and Find Full Text PDFElectrochemical aptasensor based on zirconium/copper oxides embedded in mesoporous carbon derived from bimetallic metal-organic framework for ultrasensitive detection of miR-21.
Mikrochim Acta
January 2025
Electroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran.
A novel electrochemical aptasensor based on bimetallic zirconium and copper oxides embedded within mesoporous carbon (denoted as ZrOCuO@mC) was constructed to detect miRNA. The porous ZrOCuO@mC was created through the pyrolysis of bimetallic zirconium/copper-based metal-organic framework (ZrCu-MOF). The substantial surface area and high porosity of ZrOCuO@mC nanocomposite along with its robust affinity toward aptamer strands, facilitated the effective anchoring of aptamer strands on the ZrOCuO@mC-modified electrode surface.
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