8HZD

A new fluorescent RNA aptamer bound with N618

8HZD の概要

• エントリーDOI: 10.2210/pdb8hzd/pdb
• 分子名称: RNA (36-MER), MAGNESIUM ION, 4-[(~{E})-2-[(4~{Z})-4-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]methylidene]-1-methyl-5-oxidanylidene-imidazol-2-yl]ethenyl]benzenecarbonitrile, ... (5 entities in total)
• 機能のキーワード: fluorescent rna aptamer, rna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 24220.82

構造登録者

Song, Q.Q.,Ren, A.M. (登録日: 2023-01-09, 公開日: 2024-06-19, 最終更新日: 2024-11-13)

主引用文献

Huang, K.,Song, Q.,Fang, M.,Yao, D.,Shen, X.,Xu, X.,Chen, X.,Zhu, L.,Yang, Y.,Ren, A.
Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift.
Nat.Chem.Biol., 20:1453-1460, 2024

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.

PubMed: 38816645
DOI: 10.1038/s41589-024-01633-1

実験手法

X-RAY DIFFRACTION (1.87 Å)