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

Abstract

The self-complementary triplet 5′UGG3′/5′UGG3′ is a particular structural motif containing a noncanonical G–G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba²⁺ ions. Crystallographic research has shown that two Ba²⁺ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba²⁺, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidated the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba²⁺ cations and point to possible applications of this metal-binding propensity.