A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Publication Type:Journal Article
Source:Nat Chem Biol, Volume 10, Issue 8, p.686-91 (2014)
Keywords:Base Sequence, Benzyl Compounds, Binding Sites, Crystallography, X-Ray, Fluorescence, Fluorescent Dyes, G-Quadruplexes, Green Fluorescent Proteins, Hydrogen Bonding, Imidazolines, Molecular Sequence Data, Nucleic Acid Conformation, RNA, RNA, Plant, Spinacia oleracea
<p>Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers. </p>