Thermodynamic Properties of the Specific Binding Between Ag+ Ions and C:C Mismatched Base Pairs in Duplex DNA

Abstract

Metal-mediated base pairs formed by the interaction between metal ions and artificial bases in oligonucleotides have been developed for potential applications in nanotechnology. We recently found that a natural C:C mismatched base pair bound to an Ag+ ion to generate a novel metal-mediated base pair in duplex DNA. Preparation of the novel C-Ag-C base pair involving natural bases is more convenient than that of metal-mediated base pairs involving artificial bases because time-consuming base synthesis is not required. Here, we examined the thermodynamic properties of the binding between the Ag+ ion and each of single and double C:C mismatched base pair in duplex DNA by isothermal titration calorimetry. The Ag+ ion specifically bound to the C:C mismatched base pair at a 1:1 molar ratio with 106 M−1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. The specific binding between the Ag+ ion and the single C:C mismatched base pair was mainly driven by the positive dehydration entropy change and the negative binding enthalpy change. In the interaction between the Ag+ ion and each of the consecutive and interrupted double C:C mismatched base pairs, stoichiometric binding at a 1:1 molar ratio was achieved in each step of the first and second Ag+ binding. The binding affinity for the second Ag+ binding was similar to that for the first Ag+ binding. Stoichiometric binding without interference and negative cooperativity may be favorable for aligning multiple Ag+ ions in duplex DNA for applications of the metal-mediated base pairs in nanotechnology.