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A universal mode of helix packing in RNA

Nature Structural Biology volume 8, pages 339–343 (2001)Cite this article

Abstract

RNA molecules fold into specific three-dimensional shapes to perform structural and catalytic functions. Large RNAs can form compact globular structures, but the chemical basis for close helical packing within these molecules has been unclear. Analysis of transfer, catalysis, in vitro-selected and ribosomal RNAs reveal that helical packing predominantly involves the interaction of single-stranded adenosines with a helix minor groove. Using the Tetrahymena thermophila group I ribozyme, we show here that the near-perfect shape complementarity between the adenine base and the minor groove allows for optimal van der Waals contacts, extensive hydrogen bonding and hydrophobic surface burial, creating a highly energetically favorable interaction. Adenosine is recognized in a chemically similar fashion by a combination of protein and RNA components in the ribonucleoprotein core of the signal recognition particle. These results provide a thermodynamic explanation for the noted abundance of conserved adenosines within the unpaired regions of RNA secondary structures.

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Figure 1: Type I and Type II base triples.
Figure 2: Energetics of Type I and Type II interactions.
Figure 3: Comparison of Type I/II base triples from different RNAs.

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Acknowledgements

We thank P. Nissen, J. Ippolito and T. Steitz for helpful discussions. This work was supported by the NIH and the David and Lucile Packard Foundation. E.A.D. was supported in part by NIH training grant. R.T.B was supported by a Jane Coffin Childs postdoctoral fellowship.

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Authors and Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06520, Connecticut, USA

    Elizabeth A. Doherty, Robert T. Batey, Benoît Masquida & Jennifer A. Doudna

  2. Howard Hughes Medical Institute, Yale University, New Haven, 06520, Connecticut, USA

    Robert T. Batey, Benoît Masquida & Jennifer A. Doudna

Authors
  1. Elizabeth A. Doherty
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  2. Robert T. Batey
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  4. Jennifer A. Doudna
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Correspondence to Jennifer A. Doudna.

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Doherty, E., Batey, R., Masquida, B. et al. A universal mode of helix packing in RNA. Nat Struct Mol Biol 8, 339–343 (2001). https://doi.org/10.1038/86221

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