Investigation of simple BODIPY dyes as G-quadruplex recognizing ligands

An important class of fluorescent dyes used in studying interactions and visualization of vital biomolecules are compounds with a skeleton origin 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, known as BODIPY. The objects of the presented study are the simple, polar and hydrophobic 3,7-dimethyl-substituted-core BODIPY dyes with the unmodified or modified phenyl aromatic ring at the meso position. Their optical properties as well as binding interactions with different DNA forms (i-motif, parallel G4, antiparallel G4, hybrid G4, dsDNA and ssDNA) were investigated by biophysical methods. The BODIPY derivatives interact more preferably with tetraplexes than other DNA forms. Especially, ligand 1 and 3 exibit tendency to destabilize parallel c-MYC G-quadruplex. The experiments with peroxidase-mimicking DNAzymes manifest that the main interaction between these BODIPY ligands and parallel G-quadruplex occurs via end-stacking mode. Moreover, their biological activity was evaluated by MTT assay.