Conformational determinants of tandem GU mismatches in RNA: Insights from molecular dynamics simulations and quantum mechanical calculations

Molecular dynamics (MD) simulations are performed on a series of 5'-GU-3' and 5'-UG-3' duplexes in different sequence contexts in order to characterize the underlying atomic forces that determine the structural and thermodynamic properties of GU tandem mismatches. The results emphasize the role of GG and GU stacking interactions on the structure and thermodynamics of GU mismatches in RNA.