文献类型：期刊文献

英文题名：Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift

作者：Huang, Kaiyi[1,2];Song, Qianqian[2];Fang, Mengyue[3,4];Yao, Deqiang[5];Shen, Xin[2];Xu, Xiaochen[2];Chen, Xianjun[3,4];Zhu, Linyong[3,6];Yang, Yi[3,4];Ren, Aiming[1,2]

机构：[1]Zhejiang Univ, Affiliated Hosp 2, Sch Med, Dept Cardiol, Hangzhou, Peoples R China;[2]Zhejiang Univ, Life Sci Inst, Hangzhou, Peoples R China;[3]East China Univ Sci & Technol, Optogenet & Synthet Biol Interdisciplinary Res Ctr, Shanghai Frontiers Sci Ctr Optogenet Tech Cell Met, State Key Lab Bioreactor Engn, Shanghai, Peoples R China;[4]East China Univ Sci & Technol, Sch Pharm, Shanghai, Peoples R China;[5]Shanghai Jiao Tong Univ, Renji Hosp, Inst Aging & Tissue Regenerat, Sch Med, Shanghai, Peoples R China;[6]Shanghai Jiao Tong Univ, Sch Biomed Engn, Shanghai, Peoples R China

年份：2024

卷号：20

期号：11

起止页码：1453

外文期刊名：NATURE CHEMICAL BIOLOGY

收录：;WOS:【SCI-EXPANDED(收录号:WOS:001235493400001)】；

基金：We thank the staff of the BL17U1, BL17B, BL18U1 and BL19U1 beamlines at the National Center for Protein Sciences Shanghai (NCPSS) at SSRF. We thank H. Wu of the Life Sciences Institute (LSI), Zhejiang University for her help with the preparation of some crystallization solutions. We acknowledge the technical assistance from the LSI core facility. This research was supported by grants from the Natural Science Foundation of China (32325029, 32022039, 91940302 and 91640104 to A.R., 32121005, 92357308, 32150028 and 21937004 to Y.Y. and 21907029 and 21877037 to L.Z.), the National Key Research and Development Project of China (2023YFC2604300 and 2021YFC2300300 to A.R., 2022YFC3400100 to Y.Y. and 2019YFA0904800 to Y.Y. and L.Z.).

语种：英文

摘要：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. Huang et al. report the tertiary structure of a small monomeric fluorogenic RNA aptamer named Clivia, characterized by a large Stokes shift, revealing the fluorescence activation mechanism and enabling a multivalent design to enhance the fluorescence output at specific dye concentrations.