Effects of pH and 5-Substitution of Templated Thymine on Metal-Mediated Primer Extension Reaction by DNA Polymerases: Insights into Base Selectivity of Metal Ions

We previously reported that Ag^I- and Hg^II-mediated primer extension reactions with a dT template are highly selective for dC and dT triphosphate incorporation, forming T-Ag^I-C and T-Hg^II-T base pairs, respectively. This study investigates the impact of 5-substitution of templated thymine and pH on Klenow fragment (KF) catalyzed metal-mediated primer extension reactions, as well as the thermal stability of DNA duplexes with a 5-substituted uracil derivative. The findings reveal that the selective base recognition of Ag^I and Hg^II ions, leading to T-Ag^I-C and T-Hg^II-T formation in metal-mediated primer extension, is likely governed by the absence of net charge in the resulting base pairs, the abstraction of thymine's N3 imino proton by Ag^I, and the stability of the Hg^II-N3 bond. These findings may be useful for designing novel regulated replicating systems utilizing metal-mediated base pairs.