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Nucleic Acids Research 2006 34(5):1381-1392; doi:10.1093/nar/gkl008
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Published online 6 March 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Controlling RNA self-assembly to form filaments

Lorena Nasalean1,2, Stéphanie Baudrey3, Neocles B. Leontis1,2 and Luc Jaeger3,*

1Department of Chemistry, Bowling Green State University OH 43402, USA 2Center for Biomolecular Sciences, Bowling Green State University OH 43402, USA 3Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, Material Research Laboratory, University of California Santa Barbara, CA 93106-9510, USA

*To whom correspondence should be addressed. Tel: +1 805 893 3628; Fax: +1 805 893 4210; Email: jaeger{at}chem.ucsb.edu

Received February 2, 2006. Revised February 10, 2006. Accepted February 10, 2006.

Fundamental control over supra-molecular self-assembly for organization of matter on the nano-scale is a major objective of nanoscience and nanotechnology. ‘RNA tectonics’ is the design of modular RNA units, called tectoRNAs, that can be programmed to self-assemble into novel nano- and meso-scopic architectures of desired size and shape. We report the three-dimensional design of tectoRNAs incorporating modular 4-way junction (4WJ) motifs, hairpin loops and their cognate loop–receptors to create extended, programmable interaction interfaces. Specific and directional RNA–RNA interactions at these interfaces enable conformational, topological and orientational control of tectoRNA self-assembly. The interacting motifs are precisely positioned within the helical arms of the 4WJ to program assembly from only one helical stacking conformation of the 4WJ. TectoRNAs programmed to assemble with orientational compensation produce micrometer-scale RNA filaments through supra-molecular equilibrium polymerization. As visualized by transmission electron microscopy, these RNA filaments resemble actin filaments from the protein world. This work emphasizes the potential of RNA as a scaffold for designing and engineering new controllable biomaterials mimicking modern cytoskeletal proteins.

Correspondence may also be addressed to Neocles B. Leontis. Tel: +1 419 372 8663; Fax: +1 419 372 9809; Email: leontis{at}bgnet.bgsu.edu

Present address: Stéphanie Baudrey, Institut de Biologie Moléculaire et Cellulaire, 15 rue Descartes, F-67084 Strasbourg, France


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