8FHZ

Structure of Lettuce aptamer bound to DFHO

8FHZ の概要

• エントリーDOI: 10.2210/pdb8fhz/pdb
• 分子名称: Lettuce DNA aptamer, POTASSIUM ION, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: dna, 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: 1
• 化学式量合計: 16999.19

構造登録者

Passalacqua, L.F.M.,Ferre-D'Amare, A.R. (登録日: 2022-12-15, 公開日: 2023-05-10, 最終更新日: 2023-10-25)

主引用文献

Passalacqua, L.F.M.,Banco, M.T.,Moon, J.D.,Li, X.,Jaffrey, S.R.,Ferre-D'Amare, A.R.
Intricate 3D architecture of a DNA mimic of GFP.
Nature, 618:1078-1084, 2023

PubMed Abstract: Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates conditional fluorophores derived from GFP. To extend previous structural studies of fluorogenic RNAs, GFP and other fluorescent proteins to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.

PubMed: 37344591
DOI: 10.1038/s41586-023-06229-8

実験手法

X-RAY DIFFRACTION (2.6 Å)