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.

Keywords:

• Ag⁺ ion
• C:C mismatched base pair
• thermodynamics
• isothermal titration calorimetry
• circular dichroism

Acknowledgments

This work was partly supported by the Casio Science Promotion Foundation; Iketani Science and Technology Foundation; Nakatani Foundation of Electronic Measuring Technology Advancement; and Tateishi Science and Technology Foundation. This work was also supported in part by Grant-in-Aid for JSPS Fellows (08J07706 to T.K.) from the Ministry of Education, Science, Sports, and Culture of Japan.

Notes

^a Not applicable as the titration plots were fitted to a model of one binding site.