Elucidating the stabilization mechanism of a K⁺-depleted c-MYC DNA G-quadruplex in hydrophobic imidazolium-based ionic liquids using spectroscopy coupled with molecular dynamics simulations

Stabilizing native nucleic acid structures is critical for developing nucleic acid-based therapeutics, which have enormous potential in biomedicine for disease prevention, disease treatment and diagnostics. Imidazolium chloride ionic liquids (ImCl ILs) can increase the thermal stability of G-Quadruplex DNA structures. Generally, G-Quadruplex DNA requires K⁺ (or sometimes Na⁺) to stabilize their structures via coordination of the guanine bases. In this work we investigated the ability of ImCl ILs to stabilize G-Quadruplex DNA without K⁺ present. Temperature-dependent CD spectroscopy showed that the ImCl ILs that can form micelles in aqueous solution ([OMIM]Cl and [DMIM]Cl) increase the thermal stability of G-Quadruplex DNA without K⁺, while the ImCl ILs that do not form micelles ([EMIM]Cl, [BMIM]Cl, and [HMIM]Cl) do not stabilize the structure. Notably, [OMIM]Cl and [DMIM]Cl only stabilize G-Quadruplex DNA at concentrations above their CMC values; at concentrations equal to their CMC values these ILs actually destabilize the structure. MD simulations were performed to elucidate the mechanism of thermal stabilization. Simulations are consistent with experimental results as [DMIM]Cl micelles keep the G-Quadruplex structure stable without K⁺ present. These results show how ILs can encapsulate and stabilize DNA, which can help guide the development of new strategies for stabilizing DNA and RNA structures at room temperature.