7OAW

Crystal structure of the Chili RNA aptamer in complex with DMHBI+

Summary for 7OAW

• Entry DOI: 10.2210/pdb7oaw/pdb
• Related: 7OA3
• Descriptor: Chili RNA Aptamer, GUANOSINE-5'-TRIPHOSPHATE, POTASSIUM ION, ... (7 entities in total)
• Functional Keywords: rna aptamer, aptamer, chili, fluorogenic rna, rna
• Biological source: synthetic construct
• Total number of polymer chains: 4
• Total formula weight: 72162.19

Authors

Mieczkowski, M.,Pena, V.,Hoebartner, C. (deposition date: 2021-04-20, release date: 2021-06-16, Last modification date: 2024-01-31)

Primary citation

Mieczkowski, M.,Steinmetzger, C.,Bessi, I.,Lenz, A.K.,Schmiedel, A.,Holzapfel, M.,Lambert, C.,Pena, V.,Hobartner, C.
Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.
Nat Commun, 12:3549-3549, 2021

PubMed Abstract: Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO and DMHBI ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.

PubMed: 34112799
DOI: 10.1038/s41467-021-23932-0

Experimental method

X-RAY DIFFRACTION (2.95 Å)