Riboswitches pp 141-159 | Cite as

Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 540)

Summary

Riboswitches are functional RNA molecules that control gene expression through conformational changes in response to small-molecule ligand binding. In addition, riboswitch 3D structure, like that of other RNA molecules, is dependent on cation–RNA interactions as the RNA backbone is highly negatively charged. Here, we show how small-angle X-ray scattering (SAXS) can be used to probe RNA conformations as a function of ligand and ion concentration. In a recent study of a glycine-binding tandem aptamer from Vibrio cholerae, we have used SAXS data and thermodynamic modeling to investigate how Mg2+-dependent folding and glycine binding are energetically coupled. In addition, we have employed ab initio shape reconstruction algorithms to obtain low-resolution models of the riboswitch structure from SAXS data under different solution conditions.

Key words

RNA Riboswitches Small-angle X-ray scattering RNA folding RNA aptamers 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jan Lipfert
    • 1
  • Daniel Herschlag
    • 1
  • Sebastian Doniach
    • 1
  1. 1.Department of PhysicsStanford UniversityUSA

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