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.

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

“…As mentioned above, since the Raman band dGI of sDNA is mainly attributable to normal in-plane modes of the purine ring of guanine, the intensity of this signal is very sensitive to base-stacking interactions involving the guanine residues [18,24,[27][28][29][30]34,35]. Figure 3a-c display the temperature-dependent intensity of the dGI Raman band of sDNA measured in an aqueous buffer solution and in hydrated ChCl:U.…”

“…The prominent signal dGI~1485 cm −1 in the spectrum of the sDNA is mainly attributed to the combination of the N7 = C8 and C8-N9 ring stretching and C8-H in-plane deformation of the dG purine group [22,[25][26][27] as well as to the C6 = O stretching [28]. The contribution to the band at~1485 cm −1 from the Raman signal of adenine can be considered negligible at the excitation wavelength of 250 nm due to the proximity of the 255 nm electronic transition of guanine [18,19,25]. The intensity and the frequency position of the dGI band in DNA are very sensitive markers of the base-stacking interactions and hydrogen bonds (H-bonds) involving the guanine residues [29][30][31].…”

“…This reliably allows us to analyze in detail the spectral modifications of the Raman bands associated with sDNA in the presence of DES. The different spectra in Figure 2 show that the Raman features of the sDNA at ~1336, 1485, and 1637 cm −1 are sensitive to temperature throughout the range 300-375 K, with the most pronounced spectral changes above 350 K. These heat-induced intensity and frequency modifications of the Raman bands of sDNA indicate that such vibrations can be adopted as markers of structural perturbations in sDNA, such as H-bond breaking, base The different spectra in Figure 2 show that the Raman features of the sDNA at~1336, 1485, and 1637 cm −1 are sensitive to temperature throughout the range 300-375 K, with the most pronounced spectral changes above 350 K. These heat-induced intensity and frequency modifications of the Raman bands of sDNA indicate that such vibrations can be adopted as markers of structural perturbations in sDNA, such as H-bond breaking, base unstacking, and the bases' conformational changes occurring in the double-stranded structure of DNA following an increment in temperature [8,18,19,30,33].…”

“…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].…”

“…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]. These studies revealed the important role played by guanine bases in the DNA groove that are preferentially involved in interactions with the imidazolium cations of ILs [19,21].…”