Summary information and primary citation
- PDB-id
-
8fi0;
SNAP-derived features in text and
JSON formats
- Class
- DNA
- Method
- X-ray (3.0 Å)
- Summary
- Structure of lettuce aptamer bound to dfame
- Reference
-
Passalacqua LFM, Banco MT, Moon JD, Li X, Jaffrey SR,
Ferre-D'Amare AR (2023): "Intricate
3D architecture of a DNA mimic of GFP."
Nature, 618, 1078-1084. doi:
10.1038/s41586-023-06229-8.
- Abstract
- Numerous studies have shown how RNA molecules can adopt
elaborate three-dimensional (3D)
architectures<sub>1-3</sub>. 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<sub>4</sub> conditional fluorophores
derived from GFP. To extend previous structural
studies<sub>5,6</sub> of fluorogenic RNAs, GFP
and other fluorescent proteins<sub>7</sub> 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<sub>8</sub>
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.
