Mechanistic\nInsights into the c‑MYC G‑Quadruplex\nand Berberine Binding inside an Aqueous Two-Phase System Mimicking\nBiomolecular Condensates

We\ninvestigated the binding between the c-MYC G-quadruplex\n(GQ)\nand berberine chloride (BCl) in an aqueous two-phase system (ATPS)\nwith 12.3 wt % polyethylene glycol and 5.6 wt % dextran, mimicking\nthe highly crowded intracellular biomolecular condensates formed via\nliquid–liquid phase separation. We found that in the ATPS,\ncomplex formation is significantly altered, leading to an increase\nin affinity and a change in the stoichiometry of the complex with\nrespect to neat buffer conditions. Thermodynamic studies reveal that\nbinding becomes more thermodynamically favorable in the ATPS due to\nentropic effects, as the strong excluded volume effect inside ATPS\ndroplets reduces the entropic penalty associated with binding. Finally,\nthe binding affinity of BCl for the c-MYC GQ is higher than those\nfor other DNA structures, indicating potential specific interactions.\nOverall, these findings will be helpful in the design of potential\ndrugs targeting the c-MYC GQ structures in cancer-related biocondensates.