Fig. 1: Overall structure of the Beetroot fluorescence turn-on aptamer in complex with DFAME.

a Chemical structures of the fluorophores DFHBI (1), DFHO (2), DFAME (3), and ThT (4). b Cartoon representation of the Beetroot-DFAME homodimeric complex. Arrows indicate 5′ to 3′ chain direction, and purple spheres represent K⁺. The bound DFAME molecules are shown in ball-and-stick representation with translucent spheres. c, Orthogonal view of b. d Secondary structure representation of Beetroot color-coded as in c. Lines with embedded arrowheads and Leontis-Westhof symbols⁴¹ denote connectivity and base pairs, respectively. e Cartoon representation of the homodimeric fluorogenic aptamer Corn-DFHO complex¹⁷ (PDB: 5BJO). f Sequence alignment of the aptamers Beetroot and Corn, both numbered according to the Beetroot register. Nucleotides conserved in sequence are boxed in gray, while structural elements are denoted by rectangles colored as in c and e. Nucleotides that form the four quartets of each RNA are numbered in color. g Graphical G-quartet schematics (ref. ¹¹) for Beetroot and h Corn, in Beetroot numbering. Each row represents the nucleotides of a quartet tier, and columns indicate nucleotide stacks. Upper-case, lower-case, bold, and Italic letters denote anti, syn, 2′-endo and 3′-endo nucleotides, respectively; upside-down letters denote strand polarity inversion with respect to the 5′-most nucleotide in the scheme. Lines connecting nucleotides are loops and bulges, with the number of nucleotides indicated within a circle.