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Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures

Liu, Di and Geary, Cody and Chen, Gang and Shao, Yaming and Li, Mo and Mao, Chengde and Andersen, Ebbe S. and Piccirilli, Joseph A. and Rothemund, Paul W. K. and Weizmann, Yossi (2020) Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nature Chemistry, 12 (3). pp. 249-259. ISSN 1755-4330. https://resolver.caltech.edu/CaltechAUTHORS:20191016-120007639

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41557-019-0406-7DOIArticle
https://doi.org/10.26434/chemrxiv.7837610DOIDiscussion Paper
https://rdcu.be/b0zyTPublisherFree ReadCube access
ORCID:
AuthorORCID
Liu, Di0000-0002-0708-7466
Geary, Cody0000-0003-2083-4259
Mao, Chengde0000-0001-7516-8666
Andersen, Ebbe S.0000-0002-6236-8164
Piccirilli, Joseph A.0000-0002-0541-6270
Rothemund, Paul W. K.0000-0002-1653-3202
Weizmann, Yossi0000-0002-3467-990X
Additional Information:© The Author(s), under exclusive licence to Springer Nature Limited 2020. Received: 25 February 2019; Accepted: 6 December 2019; Published: 20 January 2020. 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. Author 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. 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. The authors declare no competing interests.
Funders:
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Carlsberg Research FoundationUNSPECIFIED
NSFDMR-1555361
NIHR01GM102489
European Research Council (ERC)683305
NSFCCF-1317694
NSFCMMI-1636364
Office of Naval Research (ONR)N00014-16-1-2159
Office of Naval Research (ONR)N00014-17-1-2610
Office of Naval Research (ONR)N00014-18-1-2649
Issue or Number:3
Record Number:CaltechAUTHORS:20191016-120007639
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191016-120007639
Official Citation: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
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:99301
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:16 Oct 2019 21:31
Last Modified:02 Mar 2020 15:55

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