Characterizing RNA 3D 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 3D structural features remains incomplete. To address this, we systematically analyzed DMS reactivity across a library of 7500 RNA constructs containing two-way junctions with known 3D structures. DMS reactivity exists on a continuum over four orders of magnitude, with ∼10% overlap between WC and non-WC nucleotides. Non-WC bases with WC-like protection exhibit increased hydrogen bonding and decreased solvent accessibility, whereas reactive WC pairs tend to flank junctions, correlating with weaker base stacking and greater junction dynamics. Reactivity in noncanonical pairs correlates with specific atomic distances, allowing discrimination among base-pair conformations. These underlying reactivity-distance correlations are independently reproduced under in vivo-like probing conditions (37°C, 2 min). Using a single reactivity-derived distance constraint in Rosetta Full-Atom Refinement (FARFAR) recovers native A-G base-pair conformations and lowers root-mean-square deviation to high-resolution structures. These results establish that DMS reactivity provides predictive geometric information for RNA 3D modeling.