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bioRxiv · 10.1101/2025.02.07.637188

Size switchable DNA origami structure enabled by dynamic crossovers

Li, X.·Gao, R.·Wang, X.·Wu, W.·Liu, H.·Zhang, T.
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Abstract

DNA nanostructures are formed by many DNA double helices connected via crossovers. If multiple DNA double helices are connected by crossovers at different base positions (different rotational angles), these DNA double helices are stacked together to obtain desired two- or three-dimensional DNA structures. Here we inserted i-motif or hairpin motifs in crossover regions of one layer DNA origami structure and employed dynamic DNA element to implement size-switchablity between expansion and contraction. By changing pH or adding complementary strands to regulate interspacings between DNA double helixes, multiple crossover replacements realize the dynamic size changes between 68 nm and 150 nm as characterized by atomic force microscopy. We further demonstrated dynamic sizes changes enabled or inhibited FRET (fluorescence resonance energy transfer) signals between Cy3 and Cy5 and the controlled distances between protein molecules. The results reveal the feasibility of fabricating size-switchable DNA origami nanostructures via crossover redesign, demonstrating their potential in nano-engineering, proximity enabled chemical reacitons, as well as for biomedical applications.

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Li, X., Gao, R., Wang, X., Wu, W., Liu, H., Zhang, T.. 2025-02-08. Size switchable DNA origami structure enabled by dynamic crossovers. https://doi.org/10.1101/2025.02.07.637188

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