Volume 540 of the series Methods in Molecular Biology pp 141-159


Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering

  • Jan LipfertAffiliated withDepartment of Physics, Stanford University
  • , Daniel HerschlagAffiliated withDepartment of Physics, Stanford University
  • , Sebastian DoniachAffiliated withDepartment of Physics, Stanford University Email author 

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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