Fingerprinting tertiary structural communication in RNAs with complex folds

Single molecule correlated chemical probing (smCCP) is an experimentally concise and high-throughput strategy to measure complex, higher-order structural interactions in RNA. smCCP identifies through-space structural communication, including base-pairing and higher-order interactions, as observations of nucleotides that become modified together in a correlated way. These correlated reactivites can be complex and, to date, through-space communication specifically reflective of tertiary structure (RING correlations) can be difficult to isolate from other internucleotide correlations detected in smCCP experiments. Here we use smCCP to characterize the structure ensemble of the SAM-III riboswitch and, with an improved filtering strategy, identify a structural communication fingerprint selective for states with tertiary structure, concurrent with cognate ligand binding. These RING filters isolate through-space tertiary interactions when subsequently applied to diverse RNAs with complex structures. These studies pave the way for using the profoundly simple smCCP experiment to detect tertiary structure motifs in complex RNAs.Bachelor of Art