Conformational stability of DNA in hydrated ionic liquid by synchrotron-based UV resonance raman

Abstract

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.

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

“…Fig. 6(a) point outs a red-shift upon the increment of temperature of the dG-I mode that has been attributed to the formation of stronger hydrogen bonding of solvent with the guanine N7 site, occurring in the denatured structure of DNA [40,57]. We note that the presence of [BMIM]MeSO 4 and [BMIM]TfO induces a slight blue-shift in the position of band dG-I with respect to the case of pristine DNA.…”

“…We note that the presence of [BMIM]MeSO 4 and [BMIM]TfO induces a slight blue-shift in the position of band dG-I with respect to the case of pristine DNA. This effect has been likewise ascribed to i) the formation of H-bond interaction on N7 atom of guanine with CH groups of [BMIM] and ii) the reduction of H-bond interaction between water molecules and N7 site due to the presence of cations of IL [57,58]. The overall effect is consistent with the partial "dehydration" of DNA by ILs, predicted also by theoretical simulations [20,22], that tend to hamper the diffusion of water molecules across the nucleobases in DNA.…”

Effect of Hydrated Deep Eutectic Solvents on the Thermal Stability of DNA

“…These facts thus prompted us to use reline as a natural "first choice" for this brand-new investigation on DES-DNA interaction. As recently reported [18][19][20][21], the synchrotron radiation UV resonance raman (SR-UVRR) spectroscopy gives promising results in the selective probing of the local order-disorder or conformational transitions in large nucleic acid molecules. We have shown the technique to provide the molecular sensitivity needed to monitor subtle changes in base geometry and local intra-and intermolecular interactions of DNA dissolved in aqueous solutions of ionic liquids [18,19,21].…”

228‐nm quadrupled quasi‐three‐level Nd:GdVO4 laser for ultraviolet resonance Raman spectroscopy of explosives and biological molecules

“…Most recently, a few researchers utilized a synchrotron generated tunable DUV light source for UVRR. [12,13] Our group at the University of Pittsburgh pioneered the development and application of multiple DUV lasers for UVRR spectroscopy. During the early 1980s, Asher and coworkers developed UVRR spectrometers that utilized the frequency doubled and mixed output of dye lasers pumped by the second or third harmonics of Nd: YAG lasers.…”

“…Most recently, a few researchers utilized a synchrotron generated tunable DUV light source for UVRR. [ 12,13 ]…”