Revealing hidden protonated conformational states in RNA dynamic ensembles.

ABSTRACT: Identifying protonated states within RNA ensembles, quantifying their pKas, and elucidating the kinetic mechanisms by which they form is essential for understanding protonation-coupled biochemical reactions and how RNAs sense and adapt to pH fluctuations. However, detecting protonated states is challenging when they are short-lived and lowly populated. Here, using pH-dependent NMR chemical exchange, kinetic solvent isotope effects, and mutation, we show that a low-populated (0.4% at pH 6.4) conformational state of HIV-1 TAR RNA is coupled to protonation of a C⁺-C mismatch. Despite an intrinsic pKa of ~7.1, the energetic penalty to form this alternative conformation depressed the apparent pKa to ∼4.0, below the pH range typically probed experimentally. Substituting C-C with a G-C base pair

SUBMITTER: Geng A 

PROVIDER: S-EPMC12714568 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature