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Small angle X-ray scattering reveals a compact intermediate in RNA folding

Nature Structural Biology volume 7, pages 367–370 (2000)Cite this article

Abstract

We have used small angle X-ray scattering (SAXS) to monitor changes in the overall size and shape of the Tetrahymena ribozyme as it folds. The native ribozyme, formed in the presence of Mg2+, is much more compact and globular than the ensemble of unfolded conformations. Time-resolved measurements show that most of the compaction occurs at least 20-fold faster than the overall folding to the native state, suggesting that a compact intermediate or family of intermediates is formed early and then rearranges in the slow steps that limit the overall folding rate. These results lead to a kinetic folding model in which an initial ‘electrostatic collapse’ of the RNA is followed by slower rearrangements of elements that are initially mispositioned.

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Figure 1: The Tetrahymena ribozyme.
Figure 2: Limiting models for the rate of compaction of the ribozyme relative to overall folding.
Figure 3: Tertiary folding of the ribozyme detected by SAXS.
Figure 4: Compaction of the ribozyme is much faster than overall folding to the native state.

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Acknowledgements

We thank H. Tsurata for help on beamline 4-2 and K. Hodgson for his support. This research was supported by an NIH grant to D.H. The US Department of Energy and the National Institutes of Health support SSRL. R.R. was supported by an NIH postdoctoral fellowship.

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Authors and Affiliations

  1. Department of Biochemistry, Stanford University, Stanford, 94305, California, USA

    Rick Russell & Daniel Herschlag

  2. Department of Chemistry, Stanford University, Stanford, 94305, California, USA

    Ian S. Millett & Daniel Herschlag

  3. Department of Applied Physics, Stanford University, Stanford, 92343, California, USA

    Sebastian Doniach

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  1. Rick Russell
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  2. Ian S. Millett
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  4. Daniel Herschlag
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Correspondence to Daniel Herschlag.

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Russell, R., Millett, I., Doniach, S. et al. Small angle X-ray scattering reveals a compact intermediate in RNA folding . Nat Struct Mol Biol 7, 367–370 (2000). https://doi.org/10.1038/75132

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