Intricate 3D architecture of a DNA mimic of GFP

Passalacqua, L. F. M.; Banco, M. T.; Moon, J. D.; Li, X.; Jaffrey, S. R.; and Ferré-D’Amaré, A. R.* 

Nature,2023

https://www.nature.com/articles/s41586-023-06229-8

Abstract

While numerous studies have shown how RNA molecules can adopt elaborate three-dimensional architectures1-4, whether DNA can self-assemble into complex three-dimensional (3D) folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA that binds and activates5 conditional fluorophores derived from green fluorescent protein (GFP). To extend to DNA previous structural studies6-9 of fluorogenic RNAs as well as GFP and other fluorescent proteins10, we have characterized Lettuce-fluorophore complexes by X-ray crystallography and cryo-electron microscopy. These reveal that the 53-nucleotide DNA adopts a novel four-way junction (4WJ) fold. Instead of the canonical L- or H-shaped structures commonly seen11 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that by packing co-linearly, form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding –including by unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA– and coordination of monovalent and divalent cations, and is overall more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without employing RNA-like tertiary interactions, and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.