Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Temperature dependence of vibrational spectra provides important information about the geometry and stability of nucleic acid segments. Even in cases of simple structural transitions between the folded and unfolded states, three types of spectral changes may occur - the actual structural transition, the influence of temperature change on the oligonucleotide in the folded state, and that in the unfolded state. In this work, the temperature dependences of UV resonance Raman spectroscopy (RRS) spectra excited at 244 and 257 nm were measured on two dodecadeoxynucleotides, duplex and hairpin. In both cases, the total base composition was the same, containing (in the folded state) a double-strand section of guanine-cytosine (GC) pairs and a central section of adenine-thymine (AT) pairs forming a flexible part of the double helix in the duplex or the loop in the hairpin. Principal component analysis (PCA) showed that UV RRS spectrum, unlike non-resonance RS, can reliably distinguish between the three types of temperature changes. Spectral images of the changes confirmed the B-form double helix of GC sections in both the duplex and hairpin and different base positions in AT base sections. Additionally, minimal stacking interactions between the bases in the loop and other types of interactions of adenine with the bases of the stem in the hairpin were shown, and the main effects of heating in the folded state on the GC sections manifested weakening of stacking interactions. The results demonstrate UV RRS potential for studies of non-canonical nucleic acid structures, providing properly analyzed and executed measurements of temperature dependence.