A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore

Journal Article · Thu Aug 21 04:00:00 EDT 2014 · Nat. Chem. Biol.

DOI:https://doi.org/10.1038/nchembio.1561· OSTI ID:1148592

Huang, Hao; Suslov, Nikolai B.; Li, Nan-Sheng; Shelke, Sandip A.; Evans, Molly E.; Koldobskaya, Yelena; Rice, Phoebe A.; Piccirilli, Joseph A. ^[1]

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1. UC

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.

• Research Organization: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)
• Sponsoring Organization: NIHNIGMS
• OSTI ID: 1148592
• Journal Information: Nat. Chem. Biol., Journal Name: Nat. Chem. Biol. Journal Issue: 08, 2014 Vol. 10
• Country of Publication: United States
• Language: ENGLISH