Riboswitch conformations revealed by small-angle X-ray scattering.
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 Mg(2+)-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.
Lipfert
Jan
J
Department of Physics, Stanford University, Stanford, CA 94305, USA.
Herschlag
Daniel
D
Doniach
Sebastian
S
D052157:Aptamers, Nucleotide / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D053838:Scattering, Small Angle; D014158:Transcription, Genetic; D014961:X-Ray Diffraction / Q000379:methods*
D052157:Aptamers, Nucleotide; D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid