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Crystal structure of an 82-nucleotide RNA–DNA complex formed by the 10-23 DNA enzyme

Nature Structural Biology volume 6, pages 151–156 (1999)Cite this article

Abstract

The structure of a large nucleic acid complex formed by the 10–23 DNA enzyme bound to an RNA substrate was determined by X–ray diffraction at 3.0 Å resolution. The 82–nucleotide complex contains two strands of DNA and two strands of RNA that form five double–helical domains. The spatial arrangement of these helices is maintained by two four–way junctions that exhibit extensive base–stacking interactions and sharp turns of the phosphodiester backbone stabilized by metal ions coordinated to nucleotides at these junctions. Although it is unlikely that the structure corresponds to the catalytically active conformation of the enzyme, it represents a novel nucleic acid fold with implications for the Holliday junction structure.

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Figure 1: Structure of the 82–nucleotide RNA–DNA complex.
Figure 2: Stereo view of the RNA–DNA complex showing all nucleotides.
Figure 3: The structure of the four–way junction.
Figure 4: Stereo figure showing the experimental, solvent flattened MIR electron density map at 3.

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Acknowledgements

The authors would like to thank E. Stura for crystallization advice, W. Chazin, D.E. McRee, S. Santoro and J. Williamson for helpful discussions, N. Kresge for help with data collection, and the staff at Stanford Synchrotron Radiation Laboratory for their generous assistance. NMR experiments were conducted at the TSRI Biomolecular NMR Laboratory with the assistance of W. Chazin. This work was funded by The Skaggs Institute for Chemical Biology (G.F.J.) and an NIH grant to C.D.S.

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Authors and Affiliations

  1. Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Jacek Nowakowski & Gerald F. Joyce

  2. Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Jacek Nowakowski, Peter J. Shim, G. Sridhar Prasad, C. David Stout & Gerald F. Joyce

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  1. Jacek Nowakowski
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Correspondence to C. David Stout or Gerald F. Joyce.

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Nowakowski, J., Shim, P., Prasad, G. et al. Crystal structure of an 82-nucleotide RNA–DNA complex formed by the 10-23 DNA enzyme. Nat Struct Mol Biol 6, 151–156 (1999). https://doi.org/10.1038/5839

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