The Deprotonation Sites of Gas Phase Uridine and Pseudouridine: Implications for mRNA Vaccines

The replacement of uridine (U) with pseudouridine (ψ) in mRNA vaccines reduces immune inflammation as a result of the molecular recognition of mRNA by one of the Toll-like Receptors (TLR7). This process, which makes the practical application of mRNA vaccines possible, is modulated at the molecular level by the protons shared between the carboxylate group of amino acid residues in TLR7 and the deprotonation sites on U or ψ that determine the charged state in which these molecules exist under physiological conditions. In the gas phase, U is deprotonated at the N3 site, while ψ is deprotonated at the N1 site. This difference originates from the distinct chemical environments of the respective nucleobase moieties rather than the ribose sugar group and can provide the stepping stone toward a molecular level insight into the recognition process in the complex biological environment.