Structure and thermodynamics of a UGG motif interacting with Ba²⁺ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)–G(syn) pair

Secondary and tertiary structure models of the AUGUGGCAU duplex. (A) The UGG/UGG motif (gray) forms two U·G pairs and one noncanonical G–G pair. (B) Cartoon representation of the RNA-Ba(2) model with bound Ba²⁺ ions (green balls) in the major groove of the helix. The 2F_o–F_c electron density map (gray) is contoured at the 1σ level. (C) Cartoon representation of the unliganded model with sulfate (dark blue sticks) and acetate ions (pink sticks) located in the major and minor grooves of the helix. (D) A superposition of RNA-Ba(2) (orange) and unliganded structures (yellow).