Fig. 2.

Loop–loop interactions. a Cartoon representation of loop L1 and loop L3. For clarity, fluorophore OTB-SO₃ is omitted. b A41 forms the hub of the A15A41G39 base triple, ligand-stacking platform. Shown are hydrogen-bonding interactions between A41 and adjacent nucleotides. c Hydrogen-bonding interactions in the UAU base triple that supports the A15A41G39 stacking platform from below. d, e A13 and G12 (shown in green) interactions with neighboring nucleotides via stacking and hydrogen-bonding. Red spheres represent water molecules, and blue dashed lines denote inferred water-mediated hydrogen bonds. f Water-mediated hydrogen-bonding networks stabilize the loop L3 conformation, facilitating a sharp backbone bend at A40. Red spheres represent water molecules and dashed green lines denote hydrogen bonds