Work

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

Year: 2025

Type: article

Abstract: We previously reported that AgI- and HgII-mediated primer extension reactions with a dT template are highly selective for dC and dT triphosphate incorporation, forming T-AgI-C and T-HgII-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 AgI and HgII ions, leading to T-AgI-C and T-HgII-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 AgI, and the stability of the HgII-N3 bond. These findings may be useful for designing novel regulated replicating systems utilizing metal-mediated base pairs.

Source: Chemical and Pharmaceutical Bulletin

DOI: 10.1248/cpb.c25-00390

Authors: Hidehito Urata, Tatsuya Funai, Sanako Yoshimura, Shun-ichi Wada

Institution: Osaka Medical and Pharmaceutical University

Language: English

Topic: DNA and Nucleic Acid Chemistry

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: diamond

Funder: Japan Society for the Promotion of Science

Awards: Regulation of DNA polymerase-catalyzed primer extension reaction based on formation of metal-mediated base pairs, Recognition of metal-mediated base pairs by DNA polymerases