Download MendeleyStructural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift.
Huang, K., Song, Q., Fang, M., Yao, D., Shen, X., Xu, X., Chen, X., Zhu, L., Yang, Y., Ren, A.(2024) Nat Chem Biol
- PubMed: 38816645
- DOI: https://doi.org/10.1038/s41589-024-01633-1
- Primary Citation of Related Structures:
8HZD, 8HZE, 8HZF, 8HZJ, 8HZK, 8HZL, 8HZM - PubMed Abstract:
RNA-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.
Organizational Affiliation:
Department of Cardiology, The Second Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China.
