Counterions in RNA structure: Structural bioinformatics analysis to identify the role of Mg2+ ions in base pair formation

TL;DR

This study analyzes 1541 RNA crystal structures to understand the role of Mg2+ ions in base pair formation and stability, revealing specific binding patterns and their effects on canonical and non-canonical base pairs.

Contribution

It provides a comprehensive bioinformatics analysis of Mg2+ interactions in RNA structures, highlighting their influence on base pair stability and specific binding sites.

Findings

Mg2+ does not affect G:C W:WC base pairs

Mg2+ often binds to O6 or N7 of guanine in G:G W:HC pairs

Majority of non-canonical G:G pairs involve Mg2+ binding

Abstract

Contribution of metal ions on nucleic acids structures and functions is undeniable. Among the available metal ions like Na+, K+, Ca2+, Mg2+ etc., the role that play the Mg2+ ion is very significant related to the stability of the structures of RNA and this is quite well studied. But it is not possible to grasp the entire functionality of Mg2+ ion in the structure of RNA. So, to have a better understanding of the Mg-RNA complexes, in the present study, we have investigated 1541 non-redundant crystal structures of RNA and generated reports for various statistics related to these Mg-RNA complexes by computing base pairs and Mg2+ binding statistics. In this study, it has also been reported whether the presence of Mg2+ ions can alter the stability of base pairs or not by computing and comparing the base pairs stability. We noted that the Mg2+ ions do not affect the canonical base pair G:C W:WC while majority of the non-canonical base pair G:G W:HC, which is important also in DNA telomere structures, has Magnesium ion binding to O6 or N7 atoms of one of the Guanines.