Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift

Kaiyi Huang; Qianqian Song; Mengyue Fang; Deqiang Yao; Xin Shen; Xiaochen Xu; Xianjun Chen; Linyong Zhu; Yi Yang; Aiming Ren

doi:10.1038/s41589-024-01633-1

journal article Open Access May 30, 2024

Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift

Kaiyi Huang Qianqian Song

Mengyue Fang Deqiang Yao Xin Shen

Xiaochen Xu Xianjun Chen

Linyong Zhu

Yi Yang

Aiming Ren

Nature Methods Vol. 20 No. 11 pp. 1453-1460 · Springer Science and Business Media LLC

View at Publisher Save 10.1038/s41589-024-01633-1

Abstract

AbstractRNA-based fluorogenic modules have revolutionized the spatiotemporal localization of RNA molecules. Recently, a fluorophore named 5-((Z)-4-((2-hydroxyethyl)(methyl)amino)benzylidene)-3-methyl-2-((E)-styryl)-3,5-dihydro-4H-imidazol-4-one (NBSI), emitting in red spectrum, and its cognate aptamer named Clivia were identified, exhibiting a large Stokes shift. To explore the underlying molecular basis of this unique RNA–fluorophore complex, we determined the tertiary structure of Clivia–NBSI. The overall structure uses a monomeric, non-G-quadruplex compact coaxial architecture, with NBSI sandwiched at the core junction. Structure-based fluorophore recognition pattern analysis, combined with fluorescence assays, enables the orthogonal use of Clivia–NBSI and other fluorogenic aptamers, paving the way for both dual-emission fluorescence and bioluminescence imaging of RNA molecules within living cells. Furthermore, on the basis of the structure-based substitution assay, we developed a multivalent Clivia fluorogenic aptamer containing multiple minimal NBSI-binding modules. This innovative design notably enhances the recognition sensitivity of fluorophores both in vitro and in vivo, shedding light on future efficient applications in various biomedical and research contexts.

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Metrics

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Citations

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References

Details

Published: May 30, 2024
Vol/Issue: 20(11)
Pages: 1453-1460
License: View

Authors

Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

Capital Medical University

A

Aiming Ren

Funding

National Natural Science Foundation of China Award: 32325029

Cite This Article

Kaiyi Huang, Qianqian Song, Mengyue Fang, et al. (2024). Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift. Nature Methods, 20(11), 1453-1460. https://doi.org/10.1038/s41589-024-01633-1

Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift

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