Unveiling the Structural Modifications of Cyanines to Target G‑Quadruplex DNA through Biophysical, Computational, and...

Six cyanine ligands differing in the polymethine linker and the substituents have been developed and investigated as binders for DNA. The interaction with DNA was assessed by fluorescence resonance energy transfer (FRET) melting, UV-vis, and fluorimetric assays and completed with computational experiments. The ligand containing a shorter linker of one carbon length shows no interaction, while increasing the linker length enhances the interaction toward G-quadruplex DNA structures. The largest binding is observed for the cyanines containing five carbon connectors, while the change of the electronic nature of the substituents has no significant effect on the binding to G4s. The binding modes show a preference for the cis conformation of the cyanines, which overlaps more efficiently with the G-quartet through π-π interactions. Whole-transcriptome RNA-seq analysis shows the global gene expression in HeLa cells treated with the strongest and most selective G4 ligand, C3. The changes produced by C3 represent a global response to a complex mechanism, which sheds light on the cellular activity of cyanines.