8U60
Structure of Mango II variant2 aptamer bound to T01-6A
Summary for 8U60
| Entry DOI | 10.2210/pdb8u60/pdb |
| Descriptor | RNA Mango II variant 2 aptamer, POTASSIUM ION, 2-[(~{E})-[6-(4-methoxyphenyl)-1-methyl-quinolin-4-ylidene]methyl]-3-methyl-1,3-benzothiazole, ... (4 entities in total) |
| Functional Keywords | rna, aptamer, fluorescence, turn-on, fluorogenic, fluorophore, g-quartet, g-quadruplex |
| Biological source | synthetic construct |
| Total number of polymer chains | 3 |
| Total formula weight | 37443.50 |
| Authors | Passalacqua, L.F.M.,Ferre-D'Amare, A.R. (deposition date: 2023-09-13, release date: 2024-03-27, Last modification date: 2025-10-08) |
| Primary citation | Lu, X.,Passalacqua, L.F.M.,Nodwell, M.,Kong, K.Y.S.,Caballero-Garcia, G.,Dolgosheina, E.V.,Ferre-D'Amare, A.R.,Britton, R.,Unrau, P.J. Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD. Nucleic Acids Res., 52:8039-8051, 2024 Cited by PubMed Abstract: Fluorogenic RNA aptamer tags with high affinity enable RNA purification and imaging. The G-quadruplex (G4) based Mango (M) series of aptamers were selected to bind a thiazole orange based (TO1-Biotin) ligand. Using a chemical biology and reselection approach, we have produced a MII.2 aptamer-ligand complex with a remarkable set of properties: Its unprecedented KD of 45 pM, formaldehyde resistance (8% v/v), temperature stability and ligand photo-recycling properties are all unusual to find simultaneously within a small RNA tag. Crystal structures demonstrate how MII.2, which differs from MII by a single A23U mutation, and modification of the TO1-Biotin ligand to TO1-6A-Biotin achieves these results. MII binds TO1-Biotin heterogeneously via a G4 surface that is surrounded by a stadium of five adenosines. Breaking this pseudo-rotational symmetry results in a highly cooperative and homogeneous ligand binding pocket: A22 of the G4 stadium stacks on the G4 binding surface while the TO1-6A-Biotin ligand completely fills the remaining three quadrants of the G4 ligand binding face. Similar optimization attempts with MIII.1, which already binds TO1-Biotin in a homogeneous manner, did not produce such marked improvements. We use the novel features of the MII.2 complex to demonstrate a powerful optically-based RNA purification system. PubMed: 38945550DOI: 10.1093/nar/gkae493 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.3 Å) |
Structure validation
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