investigation of DNA minor groove binding bibenzimidazoles in the context of UV phototherapy.

The versatility of DNA minor groove binding bibenzimidazoles extends to applications in cancer therapy, beyond their typical use as DNA stains. In the context of UV phototherapy, a series of halogenated analogues designated -, -, and -iodoHoechst have been investigated. Phototoxicity involves dehalogenation of the ligands following exposure to UV light, resulting in the formation of a carbon-centred radical. While the cytotoxic mechanisms have been well established, the nature and severity of DNA damage induced by the -, -, and -iodoHoechst isomers requires clarification. Our aims were to measure and compare the binding constants of iodoHoechst analogues, and to determine the proximity of the carbon-centred radicals formed following photodehalogenation to the C1', C4', and C5' DNA carbons. We performed molecular docking studies, as well as classical molecular dynamics simulations to investigate the interactions of Hoechst ligands with DNA including a well-defined B-DNA dodecamer containing the high affinity AATT minor groove binding site. Docking highlighted the binding of Hoechst analogues to AATT regions in oligonucleotides, nucleosomes, and origami DNA helical bundles. Further, MD simulations demonstrated the stability of Hoechst ligands in the AATT-containing minor groove over microsecond trajectories. Our findings reiterate that the efficiency of dehalogenation , rather than the proximity of the carbon-centred radicals to the DNA backbone, is responsible for the extreme phototoxicity of the - isomer compared to the - and -iodoHoechst isomers. More generally, our analyses are in line with the potential utility of -iodoHoechst in DNA-targeted phototherapy, particularly if combined with a cell-specific delivery system.