The critical importance of RNA elements in gene regulation and the potential of targeting RNA with small molecules are increasingly appreciated, yet many questions remain unanswered in small molecule:RNA recognition. These questions include which RNA structures can best be differentiated by small molecules and how small molecules can be used as tools to probe RNA structure and function. We developed a method termed Pattern Recognition of RNA with Small Molecules (PRRSM) that evaluates the ability of small molecules to classify RNA structures under a variety of conditions and in turn uses these small molecule “receptors” to identify site-specific RNA structural changes. Using this method, we identified conditions under which aminoglycosides may be able to differentiate specific sequences of labeled RNA loops as well as conditions where canonical secondary structures are classified. PRRSM could then be used to accurately predict site-specifically labeled secondary structures in TAR RNA as well as the unbound and ligand bound conformations of riboswitch aptamer sequences.

Sensing patterns in RNA structure and recognition via small molecules

255th National Meeting (2018)

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