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A collapsed non-native RNA folding state

Nature Structural Biology volume 7, pages 362–366 (2000)Cite this article

Abstract

At physiological Mg2+ concentrations, the catalytic core of the bI5 group I intron does not fold into its native structure. In contrast, as judged by the global size, this RNA undergoes structural collapse at Mg2+ concentrations much lower than required to drive folding of the RNA completely to the native state. The bI5 RNA therefore exists in equilibrium between expanded and collapsed non-native states. The activation energy of RNA folding from the collapsed state to the native state is negligible and the reaction is not accelerated by the addition of urea. This collapsed state is thus distinct from the kinetic traps observed during folding of other large RNAs. The collapsed non-native state forms readily in the case of bI5 RNA and may exist generically prior to assembly of other ribonucleoprotein holoenzymes, such as the ribosome.

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Figure 1: Secondary structure of bI5core RNA, its solvent inaccessible interior, and the Mg2+ dependence of native tertiary folding.
Figure 2: Collapse of bI5core RNA analyzed by native gel electrophoresis and size exclusion chromatography.
Figure 3: Conformation of the bI5core RNA at equilibrium as a function of MgCl2.
Figure 4: Simplified schemes for determining the rate constant for reaction of the native (N) RNA (kc), and for folding of the RNA from non-native states (kfold).
Figure 5: Nature of the rate limiting step for bI5 RNA catalysis and folding determined from the activation enthalpy and urea dependence.

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Acknowledgements

This work was supported by grants from the Searle Scholars Program of the Chicago Community Trust and by the NIH to K.M.W. Plasmids pGJ122A38 and pGJ122B38 used to produce the 174 bp dsRNA were the gift of P.J. Hagerman. We thank members of the Weeks laboratory for helpful discussion and T. Hall for advice on size exclusion chromatography.

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  1. Karen L. Buchmueller, Amy E. Webb, D. Ashley Richardson and Kevin M. Weeks: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry, University of North Carolina, Chapel Hill, 27599-3290, North Carolina, USA

    Karen L. Buchmueller, Amy E. Webb, D. Ashley Richardson & Kevin M. Weeks

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  1. Karen L. Buchmueller
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  2. Amy E. Webb
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Correspondence to Kevin M. Weeks.

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Buchmueller, K., Webb, A., Richardson, D. et al. A collapsed non-native RNA folding state. Nat Struct Mol Biol 7, 362–366 (2000). https://doi.org/10.1038/75125

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