Visualizing single base RNA mutations in living cells through DNA nanostructure mediated amplification

Ma, X.-Y.; Mutailifu, M.; Lin, Y.; Qiu, J.-H.; Wang, J.-J.; Wu, Z.; Gan, Y.-Z.; Zhu, L.; Hu, L.; Li, Q.; Luo, J.-M.; Li, D.-X.; Zhang, Z.

doi:10.64898/2026.02.14.705875

bioRxiv · 10.64898/2026.02.14.705875

Visualizing single base RNA mutations in living cells through DNA nanostructure mediated amplification

Ma, X.-Y.·Mutailifu, M.·Lin, Y.·Qiu, J.-H.·Wang, J.-J.·Wu, Z.·Gan, Y.-Z.·Zhu, L.·Hu, L.·Li, Q.·Luo, J.-M.·Li, D.-X.·Zhang, Z.

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Abstract

Capturing RNA dynamics in living cells would provide critical insights into transcriptional control and cellular adaptation, but remains technically formidable -- particularly at single-base precision. Here, we introduce a DNA tetrahedron based three-dimensional catalytic hairpin assembly (3D@CHA) nanoplatform that couples target recognition with catalytic activation in a spatially organized framework. Three cascaded hairpins (H-AN, H1, and H2) then enable localized and efficient signal amplification. Without external carriers or transfection, the platform exhibits robust biocompatibility, distinguishing highly homologous insulin I (Ins1) and insulin II (Ins2) mRNAs in living cells and tracking their redistribution and intercellular transfer during metabolic changes. Introducing a single-base mismatch site into H1 and coupling it with a Forster resonance energy transfer (FRET) readout yielded a KRAS-3D@CHA probe capable of detecting KRASG12D mutations at the RNA level with single-base resolution. This platform establishes a programmable framework for precise RNA imaging and mutation discrimination, opening new avenues for RNA-level diagnostics and precision oncology.

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Ma, X.-Y., Mutailifu, M., Lin, Y., Qiu, J.-H., Wang, J.-J., Wu, Z., Gan, Y.-Z., Zhu, L., Hu, L., Li, Q., Luo, J.-M., Li, D.-X., Zhang, Z.. 2026-02-15. Visualizing single base RNA mutations in living cells through DNA nanostructure mediated amplification. https://doi.org/10.64898/2026.02.14.705875

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