To probe the binding of TMPyP4 to c-MYC G-quadruplex with in water and in imidazolium-based ionic liquids using spectroscopy coupled with molecular dynamics simulations

•The 22mer c-MYC parallel-stranded DNA G-quadruplex (Pu22) structure is stable in the four imidazolium-based ILs with increasing hydrophobic chains.•OMIM-Cl increases the melting temperature of the G-quadruplex from ∼ 80 °C to ∼ 90 °C.•TMPyP4 binds G-quadruplex in 2:1 ratio.•The four IL decreases TMPyP4 binding to Pu22 in a cation-dependent manner.•TMPyP4 primarily binds to the top G-quadruplex layer.•The four ILs prevent TMPyP4 ligand binding via hydrophobic and electrostatic interactions. TMPyP4 is known to stabilize c-MYC Pu22 G-quadruplexes and decrease c-MYC oncogene expression. Ionic liquids (ILs) were demonstrated to modulate G-quadruplex stability, serving as attractive alternatives in nucleic acid storage for biomedical applications. However, no high-resolution structure of TMPyP4 complexed with Pu22 has been solved. Additionally, the effect of imidazolium-based ILs on G-quadruplex structure is unknown. Finally, the effect of ILs on ligand binding to G-quadruplexes has not been investigated. Using spectroscopy coupled with molecular dynamics (MD) simulations in this study, we elucidate the detailed binding interactions and effects of ligand TMPyP4 and four imidazolium-based ILs with increasing hydrophobic chains on the structure of a 22mer c-MYC parallel-stranded DNA G-quadruplex (Pu22) and the effect of these ILs on TMPyP4 binding to Pu22. UV–Vis and CD spectroscopy revealed 1) OMIM-Cl increases the melting temperature of the G-quadruplex from ∼ 80 °C to ∼ 90 °C. 2) TMPyP4 binds G-quadruplex in 2:1 ratio, 3) the four IL decreases TMPyP4 binding to Pu22 in a cation-dependent manner. MD simulations suggest that 1) TMPyP4 primarily binds to the top G-quadruplex layer, 2) the four ILs prevent TMPyP4 ligand binding via hydrophobic and electrostatic interactions. This study supports ILs could increase the thermal stability of G-quadruplex structure.