Riboswitches: emerging themes in RNA structure and function

Annu Rev Biophys. 2008;37:117-33. doi: 10.1146/annurev.biophys.37.032807.130000.


Riboswitches are RNAs capable of binding cellular metabolites using a diverse array of secondary and tertiary structures to modulate gene expression. The recent determination of the three-dimensional structures of parts of six different riboswitches illuminates common features that allow riboswitches to be grouped into one of two types. Type I riboswitches, as exemplified by the purine riboswitch, are characterized by a single, localized binding pocket supported by a largely pre-established global fold. This arrangement limits ligand-induced conformational changes in the RNA to a small region. In contrast, Type II riboswitches, such as the thiamine pyrophosphate riboswitch, contain binding pockets split into at least two spatially distinct sites. As a result, binding induces both local changes to the binding pocket and global architecture. Similar organizational themes are found in other noncoding RNAs, making it possible to begin to build a hierarchical classification of RNA structure based on the spatial organization of their active sites and associated secondary structural elements.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Gene Expression / physiology*
  • Gene Expression Regulation / physiology*
  • Models, Chemical*
  • Models, Genetic*
  • Models, Molecular*
  • RNA* / chemistry
  • RNA* / physiology
  • RNA* / ultrastructure
  • RNA-Binding Proteins* / chemistry
  • RNA-Binding Proteins* / physiology
  • RNA-Binding Proteins* / ultrastructure
  • Structure-Activity Relationship


  • RNA-Binding Proteins
  • RNA