Cooperativity in RNA chemical probing experiments modulates RNA 2D structural ensembles

Small molecule chemical probes that covalently bond atoms of flexible nucleotides are widely employed in RNA structure determination. Atomistic molecular dynamic (MD) simulations recently revealed that the binding of RNA by chemical probes is influenced by cooperative effects, leading to measured reactivities that depend on the concentration of the chemical probe. In this work, we used selective 2 hydroxyl acylation analyzed by primer extension (SHAPE) and dimethyl sulfate (DMS) chemical probing experiments to explore whether RNA structures are modulated by chemical probe binding events. We find that as the concentration of a chemical probe increases, modified nucleotides locally modulate the RNA structure, resulting in the increase or decrease of chemical probe reactivity in surrounding nucleotides. This cooperative effect is dependent on both chemical probe concentration and size. We find that these cooperative effects can be used to link structurally related nucleotides and that the cooperative effects result in strikingly different 2D structure predictions as probe concentrations are varied.