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Synthetic RNA–protein complex shaped like an equilateral triangle

Nature Nanotechnology volume 6, pages 116–120 (2011)Cite this article

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Abstract

Synthetic nanostructures consisting of biomacromolecules such as nucleic acids have been constructed using bottom-up approaches1,2. In particular, Watson–Crick base pairing has been used to construct a variety of two- and three-dimensional DNA nanostructures3,4,5,6,7,8,9,10. Here, we show that RNA and the ribosomal protein L7Ae can form a nanostructure shaped like an equilateral triangle that consists of three proteins bound to an RNA scaffold. The construction of the complex relies on the proteins binding to kink-turn (K-turn) motifs in the RNA11,12,13, which allows the RNA to bend by ∼60° at three positions to form a triangle. Functional RNA–protein complexes constructed with this approach could have applications in nanomedicine14,15 and synthetic biology14,16,17,18.

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Figure 1: Molecular design of the triangular RNP (Tri-RNP).
Figure 2: Interaction between the RNA and the protein.
Figure 3: AFM imaging of Tri-RNP-1.
Figure 4: Comparison of the dimensions of Tri-RNP-1 and Tri-RNP-2.

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Acknowledgements

The authors thank R. Furushima, M. Sekiya and Y. Kodama (Japan Science and Technology Agency) for analysis and purification of Tri-RNPs, Y. Fujita (Kyoto University) and M. Takinoue (The University of Tokyo) for discussions, and A. Huttenhofer (Innsbruck Medical University) and T.S. Rozhdestvensky (University of Muenster) for providing the L7Ae plasmid. This work was supported by the JST International Cooperative Research Project. Part of the work was supported by the New Energy and Industrial Technology Development Organization (09A02021a).

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Authors and Affiliations

  1. Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, 606-8502, Kyoto, Japan

    Hirohisa Ohno, Tetsuhiro Kobayashi, Rinko Kabata, Takuma Iwasa & Tan Inoue

  2. International Cooperative Research Project (ICORP), Japan Science and Technology Agency (JST), 5 Sanban-cho, Chiyoda-ku, 102-0075, Tokyo, Japan

    Kei Endo, Tan Inoue & Hirohide Saito

  3. Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida-konoecho, Sakyo-ku, 606-8501, Kyoto, Japan

    Shige H. Yoshimura & Kunio Takeyasu

  4. The Hakubi Center, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, 606-8502, Kyoto, Japan

    Hirohide Saito

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  1. Hirohisa Ohno
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Contributions

H.O., T.K., T.I. and H.S. designed the project. H.O., T.I., S.H.Y. and H.S. performed AFM. H.O., R.K. and K.E. performed RNP biochemical assays. H.O., S.H.Y., K.T., T.I. and H.S. evaluated the experimental results. H.O., T.I. and H.S. wrote the manuscript.

Corresponding authors

Correspondence to Tan Inoue or Hirohide Saito.

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The authors declare no competing financial interests.

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Ohno, H., Kobayashi, T., Kabata, R. et al. Synthetic RNA–protein complex shaped like an equilateral triangle. Nature Nanotech 6, 116–120 (2011). https://doi.org/10.1038/nnano.2010.268

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