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

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.

SUBMITTER: Connelly CM

PROVIDER: S-EPMC6445138 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Synthetic ligands for PreQ<sub>1</sub> riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.

Connelly Colleen M CM Numata Tomoyuki T Boer Robert E RE Moon Michelle H MH Sinniah Ranu S RS Barchi Joseph J JJ Ferré-D'Amaré Adrian R AR Schneekloth John S JS

Nature communications 20190402 1

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 PreQ<sub>1</sub> riboswitch aptamers. These molecules bind specifically and reversibly to the aptamers with high affinity and induce a conformational change. Furthermore, ...[more]

PMID: 30940810

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Dataset Information

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

Publications

Synthetic ligands for PreQ<sub>1</sub> riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.

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