Specific binding of Ag+ to central CC mismatched base pair but not terminal CC pair in duplex DNA

Abstract

Metal ion-nucleic acid interactions are important for their contribution in structure formation and their potential applications in nanotechnology. Hg²⁺ and Ag⁺ bind to T–T and CC mismatched base pairs, respectively, at the center of duplex DNA to form T–Hg–T and C–Ag–C. Although primer-extension by DNA polymerases with Hg²⁺ incorporated thymidine 5′-triphosphate to form T–Hg–T, the same reaction with Ag⁺ did not incorporate deoxycytidine 5′-triphosphate to form C–Ag–C. Here, isothermal titration calorimetric analyses to examine the effect of CC position in duplex DNA on Ag⁺ binding demonstrated that Ag⁺ did not bind to the terminal CC base pair in duplex, but it bound to the central CC base pair in duplex at 1:1 molar ratio with 9 × 10⁵ M^–1 binding constant. Ag⁺ did not bind to the terminal and central C–A, C–G, and C–T base pairs in duplex. These findings are useful for developing efficient metal-mediated base pair formation in nanotechnology.