Structural and Thermodynamic Consequences of Base Pairs Containing Pseudouridine and N1‐methylpseudouridine in RNA Duplexes

Abstract Pseudouridine (Ψ) is one of the most common post‐transcriptional modifications in RNA and has been known to play a significant role in several crucial biological processes. The N1‐methyl derivative of pseudouridine, that is, N1‐methylpseudouridine has also been reported to be important for the stability and function of RNA. The critical contribution of N1‐methylpseudouridine in the efficiency of the COVID‐19 mRNA vaccines requires a better understanding of the role of these modifications in the structure, stability, and function of RNA. We have previously studied the structural and thermodynamic properties of RNA duplexes with an internal Ψ‐A pair and reported the stabilizing effect of Ψ over U. In the present study, we have extended our work to understand the properties of RNA duplexes with an internal m 1 Ψ‐A pair. Additionally, we theoretically demonstrate the effect of substituting internal U‐G, U‐U, and U‐C mismatches with the Ψ‐G, Ψ‐U, and Ψ‐C mismatches and also with the m 1 Ψ‐G, m 1 Ψ‐U, and m 1 Ψ‐C mismatches, respectively, within dsRNA. Our results indicate the context‐dependent stabilization of base stacking interactions by N1‐methylpseudouridine compared to uridine and pseudouridine, presumably resulting from the increased molecular polarizability due to the presence of the methyl group.