7oax | pdb_00007oax

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

spinqualitylabelsall models 7oax, resolution 2.24Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7oax is a 4 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.24Å Ligands: CL, GOL, GTP, K, MG, SPM, V5Z Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 pi-pi 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. Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.,Mieczkowski M, Steinmetzger C, Bessi I, Lenz AK, Schmiedel A, Holzapfel M, Lambert C, Pena V, Hobartner C Nat Commun. 2021 Jun 10;12(1):3549. doi: 10.1038/s41467-021-23932-0. PMID:34112799 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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