Structural specificity of groove binding mechanism between imidazolium-based ionic liquids and DNA

IIn the present work, we implement a joint combination of advanced spectroscopic techniques such as synchrotron radiation-UV Resonance Raman spectroscopy (SR-UVRR) and molecular dynamics (MD) simulations for deepening insight into the sequence and structural specificity of the binding interactions between imidazolium-based ILs and both the phosphate groups and nucleobases in the minor and major grooves of double-stranded DNA. Our experimental and simulation findings consistently suggest the predominance of a groove binding mechanism between the imidazolium cations and dsDNA, with a preferential interaction established

between guanine residues and the imidazolium cations with shorter alkyl-chain length. This seems to be a common behavior observed for both short and large DNA molecules hydrated in imidazolium-based ILs.

SR-UVRR technique is able to differentiate contributions of single nucleobases interactions to the structural transformation of DNA duplexes during thermal pathway.