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Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering

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Riboswitches

Part of the book series: Methods in Molecular Biology ((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.

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Acknowledgments

We thank Yu Bai, Rhiju Das, Nathan Boyd, Adelene Y.-L. Sim, Mona Ali, Vincent B. Chu, Rebecca Fenn, Sönke Seifert, and the members of the Herschlag group for useful discussions and for help with data collection and sample preparation. This research was supported by the National Institutes of Health Grant PO1 GM0066275. Use of the Advanced Photon Source was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

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  1. Department of Physics, Stanford University, Stanford, CA 94305, USA

    Jan Lipfert, Daniel Herschlag & Sebastian Doniach

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  1. Jan Lipfert
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  2. Daniel Herschlag
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  3. Sebastian Doniach
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Correspondence to Sebastian Doniach .

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

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    Lipfert, J., Herschlag, D., Doniach, S. (2009). Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering. In: Serganov, A. (eds) Riboswitches. Methods in Molecular Biology, vol 540. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-558-9_11

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    • DOI: https://doi.org/10.1007/978-1-59745-558-9_11

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