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Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme

Nature Structural Biology volume 9, pages 928–933 (2002)Cite this article

Abstract

The formation of individual tertiary contacts of the Tetrahymena L-21 Sca I ribozyme has been monitored by hydroxyl radical footprinting and its global conformation by analytical ultracentrifugation as a function of monovalent ion concentration in the absence of divalent ions. Advanced methods of data analysis, which allow the hydroxyl radical reactivity of every nucleotide to be quantified, permit monitoring of each and every structural element of the RNA. Monovalent ion-mediated global compaction of the ribozyme is accompanied by the formation of native tertiary contacts; most native tertiary contacts are evident except several that are located near where divalent ions are observed in crystallographic structures. Non-native tertiary contacts are also observed at low but not high concentrations of monovalent ions. In light of recent studies that have shown that the presence of monovalent ions greatly accelerates the Mg2+-dependent folding of the Tetrahymena ribozyme, the present studies suggest that Na+ concentration changes not only the starting position of the RNA on its folding funnel but also pushes it deep into the well by forming native tertiary contacts and, thus, favoring fast and correct folding pathways.

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Figure 1: Summary of the data analysis procedures.
Figure 2: A false-color map of the changes in OH· reactivity for the Tetrahymena ribozyme observed as a function of Na+ concentration.
Figure 3: Structural mapping and classification of the OH· reactivity changes.
Figure 4: Examples of the Na+-dependent folding isotherms derived from the data summarized in the false-color map of Fig. 2.
Figure 5: Values of the Stokes radius and axial ratio (RH and a / b, respectively) derived from sedimentation velocity experiments conducted in CE buffer to which the indicated [NaCl] or [MgCl2] was added.

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Acknowledgements

We thank D. Herschlag and R. Russell for pre-publication discussion of their results. This work was supported by grants from the National Institute of General Medical Sciences and the Biomedical Technology Program of the Division of Research Resources.

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Authors and Affiliations

  1. Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, 10461, New York, USA

    Keiji Takamoto, Qin He & Mark R. Chance

  2. Center for Synchrotron Biosciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, 10461, New York, USA

    Keiji Takamoto, Qin He, Mark R. Chance & Michael Brenowitz

  3. Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, 10461, New York, USA

    Stephanie Morris, Mark R. Chance & Michael Brenowitz

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  1. Keiji Takamoto
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Correspondence to Michael Brenowitz.

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Takamoto, K., He, Q., Morris, S. et al. Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme. Nat Struct Mol Biol 9, 928–933 (2002). https://doi.org/10.1038/nsb871

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