Alexidine, identified as a Z-DNA inducer by the NanoZ screening platform, acts as a transcriptional regulator

To address this gap, we developed NanoZ, a two-step screening platform designed to identify Z-DNA–inducing molecules. The first step, a DNA condensation assay, detects ligand-induced DNA condensation using gold nanoparticles functionalized with Z-DNA–forming sequences, providing a rapid optical readout through localized surface plasmon resonance.

The second step, a biophysical validation pipeline, employs circular dichroism, 2-aminopurine fluorescence, and NMR spectroscopy to confirm Z-DNA formation. Using this workflow, we screened 2,000 compounds from the Natural Product and Prestwick Chemical Libraries, identifying 18 positive hits in the condensation assay and selecting Alexidine dihydrochloride as a Z-DNA inducer. Alexidine efficiently promoted the B-to-Z transition and DNA condensation in vitro, and markedly increased Z-DNA formation in cells, as confirmed by immunofluorescence and ChIP-seq.