Base-specific pre-melting and melting transitions of DNA in presence of ionic liquids probed by synchrotron-based UV resonance Raman scattering

Abstract

Hydrated ionic liquids (ILs) have been identified as solvent media able to enhance the structural stability of deoxyribonucleic acid (DNA). In this work, we investigate the molecular interaction between imidazolium-based ILs and DNA during its thermal unfolding pathway, by exploiting synchrotron-based UV Resonance Raman scattering (UVRR) experiments. This technique gives a selective focus on the thermal responses of specific nucleobases in the structure of DNA, providing the experimental sensitivity to both cooperative and local structural changes occurring along the complex unfolding process of DNA. UVRR measurements probe two distinct temperature-dependent phenomena occurring in the DNA double-helix, i.e. a non-cooperative pre-melting mainly involving adenine bases and a cooperative melting transition primarily localized on guanine tracts. The analysis of Raman spectra reveals that both the cation and anion of the ionic liquids strongly interact with the structure of DNA, thus affecting the melting process but not perturbing the pre-melting transition that precedes the complete separation of the strands of DNA. Overall these results suggest that the dominant interaction occurs between the imidazolium cation and the bases of guanine and thymine in the structure of DNA, in agreement with previous results of molecular dynamics simulations.