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The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U•U base pairs

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Abstract

The crystal structure of the RNA fragment, 5′-r(UUCGCG)-3′, has been determined at 1.4 Å resolution by a combination of single isomorphous replacement and molecular search methods. The 3′-terminal CGCG portion of the hexamer engages in Watson–Crick hydrogen bonding while the S′-terminal UU-overhang forms novel Hoogsteen-like UU self-base pairs with the overhang of an adjacent duplex. The U·U pairs display a single conventional hydrogen bond between O4 (U1) and N3 (U8) and a CH–O hydrogen bond between C5-H (U1) and O4(U8), through the Hoogsteen face of the pyrimidine base U1. This unusual arrangement of one of the bases results in a trans U·U pair on antiparallel strands in contrast to the usual cis base pairs. The structure emphasizes the pronounced polymorphism of U·U pairs and has implications for folding of RNA molecules.

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Authors and Affiliations

  1. The Ohio State University Laboratory of Biological Macromolecular Structure, Department of Chemistry, 1060 Carmack Road, Columbus, Ohio, 43210, USA

    Markus C. Wahl & Muttaiya Sundaralingam

  2. The Ohio State University Laboratory of Biological Macromolecular Structure, Department of Biochemistry, 1060 Carmack Road, Columbus, Ohio, 43210, USA

    Sambhorao T. Rao & Muttaiya Sundaralingam

Authors
  1. Markus C. Wahl
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  2. Sambhorao T. Rao
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  3. Muttaiya Sundaralingam
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Wahl, M., Rao, S. & Sundaralingam, M. The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U•U base pairs. Nat Struct Mol Biol 3, 24–31 (1996). https://doi.org/10.1038/nsb0196-24

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  • DOI: https://doi.org/10.1038/nsb0196-24

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