Sequential metabolic probes illuminate nuclear DNA for discrimination of cancerous and normal cells

Elucidating the timing and spatial distribution of DNA synthesis within cancer cells is vital for cancer diagnosis and targeted therapy. However, current probes for staining nucleic acids rely on electrostatic interactions and hydrogen bonds with the nucleic acid, resulting in "static" DNA staining and the inability to distinguish cell types. Here, we present a proof-of-concept study of sequential metabolic probes, for the first time allowing for cancer-cell-specific illumination of DNA. This breakthrough is achieved by the combination of a "dual-locked" nucleoside analog VdU-Lys, and a new tetrazine-based bioorthogonal probe. Specifically, 5-vinyl-2'-deoxyuridine (VdU) release is only conducted in programmatically triggered histone deacetylases (HDACs) and cathepsin L (CTSL) as "sequential keys", enabling the modification of vinyl groups into the nuclear DNA of cancerous cells rather than normal cells. Subsequently, tetrazine-based Et-PT-Tz could in situ light-up DNA containing VdUs with significant fluorescence illumination (120-fold enhancement) through rapid bioorthogonal reaction. We demonstrated the compatibility of our probe in cancer-specific sensing of DNA with a high signal-to-noise ratio ranging from in vitro multiple cell lines to whole-organism scale. This approach would serve as a benchmark for the development of cell-specific metabolic reporters for DNA labelling, to characterize DNA metabolism in various types of cell lines.