Deoxyinosine mismatch parameters calculated with a mesoscopic model result in uniform hydrogen bonding and strongly variable stacking interactions

Abstract

Here we apply a technique which uses mesoscopic models to calculate hydrogen bond strengths and stacking interactions from experimental deoxyinosine melting temperatures. Our results confirm an uniform hydrogen bond strength for all deoxyinosine mismatches of the same order of AT base pairs, with the only exception of II mismatches which show a reduced hydrogen bonding. The resulting stacking interactions however are far from uniform, with IG showing the largest variations. The highly asymmetric stacking directly influences the duplex stability and calculated opening profiles show that for some mismatches there can be a localised breakdown of the melting cooperativity.