Angle-controllable RNA tiles for programable array assembly and RNA sensing

Qi Yang, Xu Chang, Jung Yeon Lee, Henry Wisniewski, You Zhou, Ashley D. Bernstein, Edward M. Bonder, Jason T. Kaelber, Teresa Wu, Giulia Pedrielli and Fei Zhang ()
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Qi Yang: Rutgers University
Xu Chang: Rutgers University
Jung Yeon Lee: Rutgers University
Henry Wisniewski: Rutgers University
You Zhou: Arizona State University
Ashley D. Bernstein: Rutgers University
Edward M. Bonder: Rutgers University
Jason T. Kaelber: Rutgers University
Teresa Wu: Arizona State University
Giulia Pedrielli: Arizona State University
Fei Zhang: Rutgers University

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Programmed self-assembly of RNA nanostructures presents a strategic approach to developing biomaterials with tailored properties and functionalities. Despite advancements, the variety, complexity, and programmability of de novo engineered RNA nanostructures remain limited. Here, we introduce a category of artificially designed RNA tiles by integrating antiparallel crossovers and T-junctions, featuring a controllable angle of either 65o or 90o. A total of 22 distinct tiles are explored, significantly expanding the collection of artificially designed multi-stranded RNA tiles. We investigate the design strategies that affect array assembly including T-loop configuration, sticky end pairing, structural diversification, and variations in annealing methods. Additionally, one single-stranded TC-RNA tile is designed and folded co-transcriptionally, suggesting promising applications in synthetic biology and molecular engineering. Furthermore, we demonstrate the integration of split broccoli RNA aptamers into the multi-stranded monomer tiles, enabling fluorescence activation along linear arrays for programmable RNA sensing. The facile incorporation with RNA functional nanostructures highlights the vast potential of these RNA tiles in constructing more sophisticated nanostructures for diverse biomaterial applications.

Date: 2025
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DOI: 10.1038/s41467-025-58938-5

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