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Nat Chem Biol. 2014 Aug;10(8):686-91. doi: 10.1038/nchembio.1561. Epub 2014 Jun 22.

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

Author information

1
Department of Chemistry, University of Chicago, Chicago, Illinois, USA.
2
1] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. [2].
3
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
4
1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.

Abstract

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.

PMID:
24952597
PMCID:
PMC4104137
DOI:
10.1038/nchembio.1561
[Indexed for MEDLINE]
Free PMC Article

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