title: A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
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.
authors: Department of Chemistry, University of Chicago, Chicago, Illinois, USA.
authors: Hao
authors: H
authors: Huang
authors: 1] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. [2].
authors: Nikolai B
authors: NB
authors: Suslov
authors: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
authors: Nan-Sheng
authors: NS
authors: Li
authors: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
authors: Sandip A
authors: SA
authors: Shelke
authors: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
authors: Molly E
authors: ME
authors: Evans
authors: Department of Chemistry, University of Chicago, Chicago, Illinois, USA.
authors: Yelena
authors: Y
authors: Koldobskaya
authors: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
authors: Phoebe A
authors: PA
authors: Rice
authors: 1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
authors: Joseph A
authors: JA
authors: Piccirilli
mesh_terms: D001483:Base Sequence; D001593:Benzyl Compounds / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000378:metabolism; D054856:G-Quadruplexes; D049452:Green Fluorescent Proteins; D006860:Hydrogen Bonding; D048288:Imidazolines / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D018749:RNA, Plant / Q000737:chemistry; D018724:Spinacia oleracea / Q000235:genetics
chemical_list: C560120:3,5-difluoro-4-hydroxybenzylidene imidazolinone; D001593:Benzyl Compounds; D005456:Fluorescent Dyes; D048288:Imidazolines; D018749:RNA, Plant; D049452:Green Fluorescent Proteins; D012313:RNA