8U60

Structure of Mango II variant2 aptamer bound to T01-6A

8U60 の概要

• エントリーDOI: 10.2210/pdb8u60/pdb
• 分子名称: 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)
• 機能のキーワード: rna, aptamer, fluorescence, turn-on, fluorogenic, fluorophore, g-quartet, g-quadruplex
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 37443.50

構造登録者

Passalacqua, L.F.M.,Ferre-D'Amare, A.R. (登録日: 2023-09-13, 公開日: 2024-03-27, 最終更新日: 2025-10-08)

主引用文献

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

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: 38945550
DOI: 10.1093/nar/gkae493

実験手法

X-RAY DIFFRACTION (3.3 Å)