Characterizing 3D RNA structural features from DMS reactivity

Dimethyl sulfate (DMS) chemical mapping probes RNA structure, where low reactivity is generally interpreted as Watson-Crick (WC) base pairs and high reactivity as unpaired nucleotides. Studies examining DMS reactivity of RNAs with known 3D structures have identified nucleotides that deviate from this interpretation with distinct solvent accessibility and hydrogen bonding patterns. Understanding the frequency of these outliers and their recurring structural 3D features remains incomplete. To address this knowledge gap, we systematically analyzed DMS reactivity patterns across a library of 7,500 RNA constructs containing two-way junctions with known 3D structures. We observe DMS reactivity exists on a continuum over four orders of magnitude with approximately 10% overlap in reactivity between WC and non-WC nucleotides. We find that non-WC bases with WC-like DMS protection exhibit increased hydrogen bonding and decreased solvent accessibility, whereas WC pairs exhibiting greater DMS reactivity tend to flank junctions, correlating with weaker base stacking and greater junction dynamics. Furthermore, we discover that DMS reactivity values in non-canonical pairs correlate with atomic distances and base pair geometry, enabling discrimination between different 3D conformations. These DMS reactivity patterns indicate that DMS reactivity provides atomic-scale information about RNA 3D conformations, which can be used to model RNA structures and dynamics.