Thermodynamic investigation of the dinucleotide bulge of domain V of group II intron

Abstract

Group II introns are self‐splicing ribozymes, found in RNA of organelles in fungi, plants, and protists, as well as in bacterial mRNA. Group II introns are composed of six structural domains, which are designated domain I to domain VI. Domain V (DV) is a short stem loop that contains a dinucleotide AC bulge; it is implicated in the catalytic function of the intron, as it is expected to bind the catalytic Mg2+ ion(s). A crystal structure of a group II intron from Oceanobacillus iheyensis shows inner sphere interactions between two Mg2+ ions and the phosphate oxygens of the cytosine of the dinucleotide bulge. In this study, we are examining the role of the dinucleotide sequence on RNA stability along with quantifying the contribution of RNA‐magnesium interactions. Various RNA and DNA constructs of the dinucleotide bulge were designed and thermal denaturation experiments were performed on the wild type and the modified constructs in 1 M KCl and in varying concentrations of Mg2+ ions. Comparative thermodynamic data will be presented on various dinucleotide RNA and DNA constructs and their ion interactions. This work was funded by NSF Grant MCB‐0950582 to NG.