Superposition of the 10 NMR structures of lowest energy for each independently folded RNA segment studied in this work. DenvBS represents the bottom helix and forms a well-defined double helix with an unstructured 5′-tail (G1–U5, in cyan) and a U-rich bulge; DenvTSL represents the top stem–loop and forms a short helix interrupted by an internal loop, capped by a partially flexible loop; DenvSLAsh represents the three-way junction and forms an L-shaped structure, where the top and side stem helices stack coaxially, and the bottom helix is roughly perpendicular to the coaxial stack; this last image was generated by superposing only the two stacked helices to emphasize the coaxial stack and partial flexibility at the three-way junction.
