Molecule of the Month: Fluorescent RNA Aptamers
RNA aptamers are being engineered to track molecules inside living cells
Exploring the Structure
Spinach Fluorescent RNA Aptamer
The Spinach aptamer surrounds its fluorophore, forming a rigid pocket that enhances the fluorescence of the molecule. One face of the fluorophore is packed against a G-quadruplex (colored pink), and the other face is covered by a nucleotide base triplet (colored magenta). An additional guanine (white) interacts with the edge of the fluorophore and positions it in the pocket. To explore this structure in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- To see the packing of spinach aptamers in the crystal lattice, choose 3D View: Structure at the main RCSB site and choose the options for Unit Cell or Supercell in the Assembly menu.
- Most of these aptamers have a G-quadruplex that packs against the fluorophore—as you’re exploring these structures, try to follow how the RNA chain folds to position the four guanines in the proper orientation.
January 2019, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2019_1