8HZK

A new fluorescent RNA aptamer bound with N, iridium hexammine soak

Summary for 8HZK

• Entry DOI: 10.2210/pdb8hzk/pdb
• Descriptor: RNA (36-MER), IRIDIUM HEXAMMINE ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: fluorescent rna aptamer, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 28491.19

Authors

Huang, K.Y.,Ren, A.M. (deposition date: 2023-01-09, release date: 2024-06-19, Last modification date: 2024-11-13)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2 Å)