Mesoscopic Model Confirms Strong Base Pair Metal Mediated Bonding for T–Hg2+–T and Weaker for C–Ag+–C

Metal mediated DNA are mismatches where a metal ion bridges the base pairs and are of interest for biosensors. Here, we study THg2+ T, which is known to be stabilized by base pair metal mediated bonds, and CAg+ C whose stabilization mechanism is less well understood. We use a mesoscopic model and published melting temperatures of sequences containing CC or TT mismatches in the presence of the metal ions. For THg2+ T we obtain a strong base pair bond potential and moderate one for CAg+ C, only one stacking potential for each configuration is stronger than usual.