Structural comparison of fluorescent aptamers for apta-FRET. (A) Structure of the Mango-I aptamer (light gray, cartoon) bound to TO1-Biotin (orange stick and transparent spheres). GAA^A tetraloop-like junction (red), and helix (orange/gray) are proximally oriented to the binding pocket. (B) Mango-III core (light gray, cartoon) bound to TO1-Biotin (orange sticks and transparent spheres) coaxially stacked onto a helical-duplex junction (red) continuous with a variable helix (orange and gray). (C) Structure of Spinach (shown to represent Broccoli) bound to DFHBI (cyan sticks and transparent spheres). Coaxial helical junctions (red) are flanked by helical duplexes (cyan and gray). (D) Schematic representation of Broccoli (cyan)/Mango (orange) aptamers in a chimeric construct connected by an RNA duplex (gray).
