Tuning a riboswitch response through structural extension of a pseudoknot Academic Article uri icon


MeSH Major

  • Nucleic Acid Conformation
  • RNA
  • Riboswitch


  • Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA function in the cell and are particularly central to riboswitch-mediated control of gene expression. Here, using single-molecule fluorescence energy transfer imaging, we explore the folding dynamics of the preQ1 class II riboswitch, an upstream mRNA element that regulates downstream encoded modification enzymes of queuosine biosynthesis. For reasons that are not presently understood, the classical pseudoknot fold of this system harbors an extra stem-loop structure within its 3'-terminal region immediately upstream of the Shine-Dalgarno sequence that contributes to formation of the ligand-bound state. By imaging ligand-dependent preQ1 riboswitch folding from multiple structural perspectives, we reveal that the extra stem-loop strongly influences pseudoknot dynamics in a manner that decreases its propensity to spontaneously fold and increases its responsiveness to ligand binding. We conclude that the extra stem-loop sensitizes this RNA to broaden the dynamic range of the ON/OFF regulatory switch.

publication date

  • August 27, 2013



  • Academic Article



  • eng

PubMed Central ID

  • PMC3761628

Digital Object Identifier (DOI)

  • 10.1073/pnas.1304585110

PubMed ID

  • 23940363

Additional Document Info

start page

  • E3256

end page

  • 64


  • 110


  • 35