Identification of weak non-canonical base pairs around riboswitch-ligand recognition sites by solid-state NMR exchange spectroscopy

Base pairs are fundamental building blocks of RNA structures, and their stability and open-close equilibrium constitutes the dynamic picture. Weak base pairs, which feature the characteristics of low stability and rapid base pair opening, often play a critical role in RNA functions. However, site-specific identification of weak base pairs in RNA is challenging. Here, we report a solid-state NMR (SSNMR)-based two-dimensional proton-detected water–RNA exchange spectroscopy (WaterREXSY) to address this challenge. The approach uses the chemical exchange between hydrogen-bonded imino protons within the base pair and excited water molecules to polarize the imino protons for SSNMR observation. This process takes advantages that the imino protons within weak pairs undergo fast exchange rates with water, enabling a quick build-up and efficient detection. This method is used to characterize the weak pair in the riboA71–adenine complex (i.e., the 71nt-aptamer domain of the add adenine riboswitch from Vibrio vulnificus). We identify U47•U51, a weak non-canonical base pair that constitutes the U47•U51•(adenine-U74) base tetrad around the ligand-binding pocket. This result suggests that the breakage of U47•U51 may be the early stage in the process of ligand release.