Tunable G-Quadruplex Ligands: Azobenzene Derivatives for Light-Controlled DNA Modulation

During transcription, replication, and DNA repair, DNA unwinds to reveal guanine-rich sequences that form stable G-quadruplexes. In cancer cells, increased transcription and replication promote G4 formation, making them attractive therapeutic targets. G4 s block DNA and RNA polymerases, inducing replication stress and causing toxic single- and double-strand breaks. Small-molecule ligands can stabilize G4 structures, prolonging their effects and exacerbating replication stress. However, most G4 ligands operate through a one-way mechanism that remains permanent over time. A more versatile approach involves systems that can switch between active and inactive states on demand using external stimuli, such as light. This study aims to deepen knowledge of the current state of the design of photoactive G4-ligand through the synthesis of azobenzene-based compounds that vary in substitution patterns, size of the substituent, electronic effects, and molecular structure. Using orthogonal biophysical methods and quantum-chemical calculations, we evaluate how these factors affect the compounds' ability to bind and stabilize G4 structures. Importantly, our results demonstrate that the interaction mode of the trans isomer with G4 influences its ability to modulate G4 properties bidirectionally. These findings provide insights for designing photoactive G4 ligands with tunable on-off functionality, paving the way for precise control of G4 structures in biological systems.