The organization of biological materials into versatile three-dimensional assemblies could be used to build multifunctional therapeutic scaffolds for use in nanomedicine. Here, we report a strategy to design three-dimensional nanoscale scaffolds that can be self-assembled from RNA with precise control over their shape, size and composition. These cubic nanoscaffolds are only ∼13 nm in diameter and are composed of short oligonucleotides, making them amenable to chemical synthesis, point modifications and further functionalization. Nanocube assembly is verified by gel assays, dynamic light scattering and cryogenic electron microscopy. Formation of functional RNA nanocubes is also demonstrated by incorporation of a light-up fluorescent RNA aptamer that is optimally active only upon full RNA assembly. Moreover, we show that the RNA nanoscaffolds can self-assemble in isothermal conditions (37 °C) during in vitro transcription, which opens a route towards the construction of sensors, programmable packaging and cargo delivery systems for biomedical applications.
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The authors thank V. A. Piunova for assistance with DLS, K. Kahn for helping with Kd curve analysis, and C. Potter and B. Carragher for their invaluable scientific input regarding cryo-EM and single-particle reconstruction. Cryo-EM imaging was performed at National Resources for Automated Molecular Microscopy, which is supported by the National Institutes of Health (NIH) through the National Center for Research Resources P41 program (RR17573). This research was supported (in part) by the Intramural Research Program of the NIH, the National Cancer Institute, the Center for Cancer Research (B.A.S.) and by NIH R01 GM079604 (L.J.). This project has been funded in whole or in part with federal funds from the National Cancer Institute, NIH, under contract HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does any mention of trade names, commercial products or organizations imply endorsement by the US government. K.A. and L.J. wish to dedicate this work to Sts. Cyril and Methodius.
The authors declare no competing financial interests.
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Afonin, K., Bindewald, E., Yaghoubian, A. et al. In vitro assembly of cubic RNA-based scaffolds designed in silico. Nature Nanotech 5, 676–682 (2010). https://doi.org/10.1038/nnano.2010.160
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