Although Deoxyribonucleic acid (DNA) is considered substantially stable in aqueous solution, slow hydrolysis can damage its double-helix structure and cause denaturation when it is stored for several months. Therefore, the design of aqueous solvents that are able to stabilize and maintain DNA conformation is a challenging issue. Ionic liquids (ILs) appear as ideal water co-solvents for DNA biotechnology due to their unique properties. We have investigated the thermal stability of DNA in 1-butyl-3-methylimidazolium aqueous solutions by synchrotron-based UV Resonance Raman (UVRR) spectroscopy with the aim to clarify the role played by concentration of IL in stabilizing the DNA natural conformation. The synchrotron-based UV source for UVRR measurements allows us to enhance specific vibrational signals associated to nitrogenous bases of DNA, through an appropriate tuning of the excitation wavelength. Such approach permits to probe the rearrangements in the local environment around specific nucleotides as a function of thermal conditions.