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Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures

Nature Chemistry volume 12, pages 249–259 (2020)Cite this article

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Abstract

In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy—homooligomerization—allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson–Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.

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Fig. 1: The bKL motif.
Fig. 2: Effects of beam and strut lengths on ladders made from tiles with beams of equal length.
Fig. 3: Controlling in-plane curvature using tiles of unequal beam lengths.
Fig. 4: Two strategies to construct multi-railed ladders.
Fig. 5: Tetrameric RNA nanocage.
Fig. 6: Cellular production of RNA tiles.
Fig. 7: Integration of RNA bKLs into RNA origami tiles, and design of a DNA bKL.

Data availability

The data supporting the findings of this study are principally within the figures and the associated Supplementary Information. Additional data are available from the authors upon request.

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Acknowledgements

D.L. acknowledges the HHMI International Student Research Fellowship. C.W.G. acknowledges a fellowship from the Carlsberg Research Foundation. This work was supported by NSF CAREER Award (DMR-1555361) to Y.W., NIH grant (R01GM102489) to J.A.P., ERC grant (683305) to E.S.A. and NSF grants (CCF-1317694 and CMMI-1636364) and ONR grants (N00014-16-1-2159, N00014-17-1-2610 and N00014-18-1-2649) to P.W.K.R. Cryo-EM experiments were conducted with the Structural Biology Facility at Northwestern University, and we thank J. Remis for assistance. We thank N.-s. Li for synthesizing DFHBI. We thank P. Yin for sharing unpublished results based on bKL and helpful discussions.

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  1. Gang Chen

    Present address: Department of Chemistry, University of Central Florida, Orlando, FL, USA

Authors and Affiliations

  1. Department of Chemistry, University of Chicago, Chicago, IL, USA

    Di Liu, Gang Chen, Joseph A. Piccirilli & Yossi Weizmann

  2. Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark

    Cody W. Geary & Ebbe S. Andersen

  3. Departments of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA

    Cody W. Geary & Paul W. K. Rothemund

  4. Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA

    Yaming Shao & Joseph A. Piccirilli

  5. Department of Chemistry, Purdue University, West Lafayette, IN, USA

    Mo Li & Chengde Mao

  6. Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel

    Yossi Weizmann

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Contributions

D.L. and Y.W. conceived the project. D.L., C.W.G., G.C., Y.S. and M.L. performed the research. C.M., E.S.A., J.A.P., P.W.K.R. and Y.W. supervised the project. D.L., C.W.G., P.W.K.R. and Y.W. wrote the manuscript. All authors analysed the data and commented on the manuscript.

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Liu, D., Geary, C.W., Chen, G. et al. Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat. Chem. 12, 249–259 (2020). https://doi.org/10.1038/s41557-019-0406-7

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