Synthetic ligands for PreQ 1 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, John S. Schneekloth

Research output: Contribution to journalArticle

2 Citations (Scopus)

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 PreQ 1 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.

Original languageEnglish
Article number1501
JournalNature communications
Volume10
Issue number1
DOIs
Publication statusPublished - Dec 1 2019

Fingerprint

Riboswitch
RNA
Ligands
ligands
Molecules
molecules
Nucleotide Aptamers
Bacterial Genes
gene expression
Essential Genes
Gene expression
genes
affinity
7-(aminomethyl)-7-deazaguanine
Genes
Binding Sites
X-Rays
Gene Expression
X rays
causes

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Synthetic ligands for PreQ 1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure . / Connelly, Colleen M.; Numata, Tomoyuki; Boer, Robert E.; Moon, Michelle H.; Sinniah, Ranu S.; Barchi, Joseph J.; Ferré-D’Amaré, Adrian R.; Schneekloth, John S.

In: Nature communications, Vol. 10, No. 1, 1501, 01.12.2019.

Research output: Contribution to journalArticle

Connelly, CM, Numata, T, Boer, RE, Moon, MH, Sinniah, RS, Barchi, JJ, Ferré-D’Amaré, AR & Schneekloth, JS 2019, ' Synthetic ligands for PreQ 1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure ', Nature communications, vol. 10, no. 1, 1501. https://doi.org/10.1038/s41467-019-09493-3
Connelly, Colleen M. ; Numata, Tomoyuki ; Boer, Robert E. ; Moon, Michelle H. ; Sinniah, Ranu S. ; Barchi, Joseph J. ; Ferré-D’Amaré, Adrian R. ; Schneekloth, John S. / Synthetic ligands for PreQ 1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure In: Nature communications. 2019 ; Vol. 10, No. 1.
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AU - Sinniah, Ranu S.

AU - Barchi, Joseph J.

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