Silver(I)-Ion-Mediated Cytosine-Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases.

Spectroscopic characterization of AgI -ion-mediated C-AgI -A and C-AgI -T base pairs found in primer extension reactions catalyzed by DNA polymerases was conducted. UV melting experiments revealed that C-A and C-T mismatched base pairs in oligodeoxynucleotide duplexes are specifically stabilized by AgI ions in 1:1 stoichiometry in the same manner as a C-C mismatched base pair. Although the stability of the mismatched base pairs in the absence of AgI ions is in the order C-A≈C-T>C-C, the stabilizing effect of AgI ions follows the order C-C>C-A≈C-T. However, the comparative susceptibility of dNTPs to AgI -mediated enzymatic incorporation into the site opposite templating C is dATP>dTTP≫dCTP, as reported. The net charge, as well as the size and/or shape complementarity of the metal-mediated base pairs, or the stabilities of mismatched base pairs in the absence of metal ions, would be more important than the stability of the metallo-base pairs in the replicating reaction catalyzed by DNA polymerases.

Regulated incorporation of two different metal ions into programmed sites in a duplex by DNA polymerase catalyzed primer extension.

Metal-mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag(I) ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C-Ag(I)-T base pair, as well as the previously reported C-Ag(I)-A base pair. The comparative susceptibility of dNTPs to Ag(I)-mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP>dTTP≫dCTP. Furthermore, two kinds of metal ions, Ag(I) and Hg(II), selectively mediate the incorporation of thymidine 5'-triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved.