Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure

Colleen M. Connelly, Tomoyuki Numata, Robert E. Boer, Michelle H. Moon, Ranu S. Sinniah, Joseph J. Barchi, Adrian R. Ferré-D’Amaré and John S. Schneekloth ()
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Colleen M. Connelly: National Cancer Institute
Tomoyuki Numata: Lung and Blood Institute
Robert E. Boer: National Cancer Institute
Michelle H. Moon: National Cancer Institute
Ranu S. Sinniah: National Cancer Institute
Joseph J. Barchi: National Cancer Institute
Adrian R. Ferré-D’Amaré: Lung and Blood Institute
John S. Schneekloth: National Cancer Institute

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract Riboswitches are naturally occurring RNA aptamers that regulate gene expression by binding to specific small molecules. Riboswitches control the expression of essential bacterial genes and are important models for RNA-small molecule recognition. Here, we report the discovery of a class of synthetic small molecules that bind to PreQ1 riboswitch aptamers. These molecules bind specifically and reversibly to the aptamers with high affinity and induce a conformational change. Furthermore, the ligands modulate riboswitch activity through transcriptional termination despite no obvious chemical similarity to the cognate ligand. X-ray crystallographic studies reveal that the ligands share a binding site with the cognate ligand but make different contacts. Finally, alteration of the chemical structure of the ligand causes changes in the mode of RNA binding and affects regulatory function. Thus, target- and structure-based approaches can be used to identify and understand the mechanism of synthetic ligands that bind to and regulate complex, folded RNAs.

Date: 2019
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DOI: 10.1038/s41467-019-09493-3

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