Enzymatic probing analysis of an engineered riboswitch reveals multiple off conformations

Norihito Muranaka, Vandana Sharma, Yohei Yokobayashi

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


We investigated the gene regulatory mechanism of a previously engineered riboswitch +thiMN 15#19 that turns on gene expression in response to thiamine pyrophosphate (TPP). In vitro enzymatic probing was performed to identify the secondary structures of the OFF conformations predicted by Mfold. Interestingly, enzymatic probing data of the riboswitch and its variants indicated that the riboswitch in its OFF state adopts two distinct structures. Moreover, further in vivo experiments suggested that both OFF structures contribute to the riboswitch function. A deeper understanding of how riboswitches function at the molecular level should enhance our ability to design synthetic riboswitches with new or improved characteristics.

Original languageEnglish (US)
Pages (from-to)696-705
Number of pages10
JournalNucleosides, Nucleotides and Nucleic Acids
Issue number9
StatePublished - Sep 2011


  • Gene regulation
  • riboswitch
  • RNA aptamers
  • RNA conformation

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Molecular Medicine


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