Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA.

Jeffrey E Ehrhardt, Kevin M Weeks

Journal of the American Chemical Society 2020 Nov 04

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Capturing the folding dynamics of large, functionally important RNAs has relied primarily on global measurements of structure or on per-nucleotide chemical probing. These approaches infer, but do not directly measure, through-space structural interactions. Here we introduce trimethyloxonium (TMO) as a chemical probe for RNA. TMO alkylates RNA at high levels in seconds, and thereby enables time-resolved, single-molecule, through-space probing of RNA folding using the RING-MaP correlated chemical probing framework. Time-resolved correlations in the RNase P RNA-a functional RNA with a complex structure stabilized by multiple noncanonical interactions-revealed that a long-range tertiary interaction guides native RNA</a> folding for both secondary and tertiary structure. This unanticipated nonhierarchical folding mechanism was directly validated by examining the consequences of concise disruption of the through-space interaction. Single-molecule, time-resolved RNA structure probing with TMO is poised to reveal a wide range of dynamic RNA folding processes and principles of RNA folding.

Citation

Jeffrey E Ehrhardt, Kevin M Weeks. Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA. Journal of the American Chemical Society. 2020 Nov 04;142(44):18735-18740