pH-Dependent UV resonance raman spectra of cytosine and Uracil

Cytosine is a nucleobase found in both DNA and RNA, while uracil is found only in RNA. Uracil has abstractable protons at N₃ and N₁. Cytosine has only one abstractable proton at N1 but can also accept a proton at N₃. The pK_a values of these protons are well-known, but the effect of the change in protonation on the rest of the molecule is not well understood and is very important in base stacking, base pairing, and protein-nucleic acid interactions. In this paper, UV resonance Raman (UVRR) spectroscopy is used to probe the structures of both cytosine and uracil at varying pH to determine the structural changes that take place. The results show that cytosine has increased electronic delocalization when moving to either basic or acidic environments, whereas uracil shows no significant change in acidic environment but increases its electronic delocalization in basic environment.