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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Benzyl Compounds / chemistry
  • Benzyl Compounds / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • Fluorescence
  • Fluorescent Dyes / metabolism
  • G-Quadruplexes*
  • Green Fluorescent Proteins
  • Hydrogen Bonding
  • Imidazolines / chemistry
  • Imidazolines / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • RNA, Plant / chemistry
  • Spinacia oleracea / genetics


  • 3,5-difluoro-4-hydroxybenzylidene imidazolinone
  • Benzyl Compounds
  • Fluorescent Dyes
  • Imidazolines
  • RNA, Plant
  • Green Fluorescent Proteins
  • RNA

Associated data

  • PDB/4KZD
  • PDB/4KZE
  • PDB/4Q9Q
  • PDB/4Q9R