8VXZSummary for 8VXZ
| Entry DOI | 10.2210/pdb8vxz/pdb |
| Descriptor | Chains: A,B,C, POTASSIUM ION, 3-[2-(benzylamino)-2-oxoethyl]-2-[(E)-(1-methylquinolin-4(1H)-ylidene)methyl]-1,3-benzothiazol-3-ium, ... (4 entities in total) |
| Functional Keywords | rna, aptamer, fluorescence, turn-on, fluorogenic, fluorophore, g-quartet, g-quadruplex, small-molecule microarrays |
| Biological source | synthetic construct |
| Total number of polymer chains | 3 |
| Total formula weight | 37437.30 |
| Authors | Passalacqua, L.F.M.,Ferre-D'Amare, A.R.,Schneekloth, J.S. (deposition date: 2024-02-06, release date: 2025-02-19, Last modification date: 2025-10-08) |
| Primary citation | Yang, M.,Prestwood, P.R.,Passalacqua, L.F.M.,Balaratnam, S.,Fullenkamp, C.R.,Arney, J.W.,Weeks, K.M.,Ferre-D'Amare, A.,Schneekloth Jr., J.S. Structure-informed design of an ultrabright RNA-activated fluorophore. Nat.Chem., 17:1188-1195, 2025 Cited by PubMed Abstract: RNA-based fluorogenic aptamers, such as Mango, are uniquely powerful tools for imaging RNA that activate the fluorescence of a weakly or non-fluorescent small molecule when bound. A central challenge has been to develop brighter, more specific and high-affinity aptamer-ligand systems for cellular imaging. Here we report an ultrabright fluorophore for the Mango II system discovered using a structure-informed, fragment-based small-molecule microarray approach. This dye-termed SALAD1 (structure-informed, array-enabled LigAnD 1)-exhibits subnanomolar aptamer affinity and 3.5-fold brighter fluorescence than Mango II-TO1-biotin pair, a widely used fluorogenic system. Performance was improved by modulating RNA-dye molecular recognition without altering the fluorophore's π-system. High-resolution X-ray structures reveal the binding mode for SALAD1, which exhibits improved pocket occupancy, a more defined binding pose and a unique bonding interaction with potassium. SALAD1 is cell-permeable and facilitates improved in-cell confocal RNA imaging. This work introduces an additional RNA-activated fluorophore demonstrating how fragment-based ligand discovery can be used to create high-performance ligands for RNA targets. PubMed: 40437193DOI: 10.1038/s41557-025-01832-w PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3 Å) |
Structure validation
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