Contribution of 3′T and 3′TT overhangs to the thermodynamic stability of model siRNA duplexes

Abstract Herein, we report comprehensive thermodynamic studies on 36 RNA/DNA duplexes designed as siRNA mimics to determine the energetic contribution of 3′T and 3′TT dangling ends. The thermodynamic effect induced by the presence of 3′T overhangs on the stability of RNA duplexes ranges from −0.28 to −0.92 kcal/mol and strongly depends on the type and orientation of the adjacent base pair. Further extension of the 3′-dangling end length, by a second T residue, results in additional stabilization of 0.14 to 0.21 kcal/mol. The results revealed that the thermodynamic contribution of 3′-dangling T and TT on RNA duplexes differs from the influence of 3′-dangling U and UU on RNA duplexes and 3′-dangling T and TT on DNA duplexes. This data suggests that using the contribution of 3′-dangling T values for RNA duplexes, instead of 3′-dangling T values for DNA duplexes or 3′-dangling U values for RNA duplexes, would improve the prediction of the stability of siRNA duplexes.