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bioRxiv · 10.1101/2025.07.21.665968

SHAPE-based chemical probes for studying preQ1-RNA interactions in living bacteria

Reyes Franceschi, J.·Cardenas, E. L.·Klein, B. J. C.·Weidmann, C. A.·Garner, A. L.
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Abstract

Interrogating RNA-small molecule interactions inside cells is critical for advancing RNA-targeted drug discovery. In particular, chemical probing technologies that both identify small molecule-bound RNAs and define their binding sites in the complex cellular environment will be key for establishing the on-target activity necessary for successful hit-to-lead campaigns. Using the small molecule metabolite preQ1 and its cognate riboswitch RNA as a model, herein we describe a chemical probing strategy for filling this technological gap. Building on well-established RNA acylation chemistry employed by in vivo click selective 2'-hydroxyl acylation analyzed by primer extension (icSHAPE) probes, we developed an icSHAPE-based preQ1 probe that retains biological activity in a preQ1 riboswitch reporter assay and successfully enriches the preQ1 riboswitch from living bacterial cells. Further, we map the preQ1 binding site on probe-modified riboswitch RNA by mutational profiling (MaP). As the need for rapid profiling of on- and off-target small molecule interactions continues to grow, this chemical probing strategy offers a method to interrogate cellular RNA-small molecule interactions and support the future development of RNA-targeted therapeutics.

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Reyes Franceschi, J., Cardenas, E. L., Klein, B. J. C., Weidmann, C. A., Garner, A. L.. 2025-07-21. SHAPE-based chemical probes for studying preQ1-RNA interactions in living bacteria. https://doi.org/10.1101/2025.07.21.665968

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