How does Mg²⁺ modulate the RNA folding mechanism — a case study of G:C W:W Trans base pair

Abstract

Reverse Watson-Crick G:C base pairs (G:C W:W Trans) occur frequently in different functional RNAs. It is one of the few base pairs whose gas phase optimized isolated geometry is inconsistent with the corresponding experimental geometry. Several earlier studies indicate that accumulation of positive charge near N7 of guanine, through posttranscriptional modification, direct protonation or coordination with Mg²⁺, can stabilize the experimental geometry. Interestingly, recent studies reveal significant variation in the position of putatively bound Mg²⁺. This, in conjunction with recently raised doubts regarding some of the Mg²⁺ assignments near the imino nitrogen of guanine, is suggestive of the existence of multiple Mg²⁺ binding modes for this base pair. Our detailed investigation of Mg²⁺ bound G:C W:W Trans pairs, occurring in high resolution RNA crystal structures, show that they occur in 14 different contexts, 8 out of which display Mg²⁺ binding at the Hoogsteen edge of guanine. Further examination of occurrences in these 8 contexts led to the characterization of three different Mg²⁺ binding modes, (i) direct binding via N7 coordination, (ii) direct binding via O6 coordination and (iii) binding via hydrogen bonding interaction with the first shell water molecules. In the crystal structures, the latter two modes are associated with a buckled and propeller twisted geometry of the base pair. Interestingly, respective optimized geometries of these different Mg²⁺ binding modes (optimized at B3LYP) are consistent with their corresponding experimental geometries. Subsequent interaction energy calculations at MP2 level, and decomposition of its components, suggest that for G:C W:W Trans, Mg²⁺ binding can fine tune the base pair geometries without compromising with their stability. Our results, therefore, underline the importance of the mode of binding of Mg²⁺ ions in shaping RNA structure, folding and function.