DNA Polymerase Catalyzes Successive Formation of Cytosine-AgI-Thymine Base Pairs
Abstract
To explore the constraints of forming consecutive C-AgI-T base pairs during DNA polymerase-catalyzed primer extension reactions, we examined the incorporation of deoxythymidine triphosphate (dTTP) into consecutive C sites in the presence of AgI ions. The results demonstrated that AgI-promoted primer extension enables the formation of up to three consecutive C-AgI-T base pairs. Importantly, suppression of C-AgI-C base pair formation resulting from dCTP incorporation was demonstrated to be essential for achieving this outcome. Furthermore, by using MnII ions, the formation of up to five consecutive C-AgI-T base pairs was achieved. The formation of consecutive T-AgI-C base pairs, which involves the incorporation of dCTP into templating T sites, is more difficult than the formation of consecutive C-AgI-T base pairs, because much higher concentrations of dTTP compete with the template thymine for the AgI ion that abstracts the N3 imino proton. Thermal denaturation studies demonstrated that Ag+ ions effectively stabilized duplexes containing consecutive C–T mismatches, whereas stabilization by consecutive C-Ag+-C base pairs was limited because of electrostatic repulsion between neighboring positively charged base pairs. These results suggest that charge-neutral and thermally stable metal-mediated base pairs are critical for efficient polymerase-catalyzed synthesis of metal-containing DNA. These insights could be beneficial for the enzymatic synthesis of DNA-based AgI nanowires.
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BibTeX
@article{funai2026polymerase,
title = {{DNA Polymerase Catalyzes Successive Formation of Cytosine-AgI-Thymine Base Pairs}},
author = {Tatsuya Funai and Keiko Morita and Ayaka Tani and Shun-ichi Wada and Hidehito Urata},
journal = {Chemical and Pharmaceutical Bulletin},
year = {2026},
month = oct,
doi = {10.1248/cpb.c26-00271},
url = {https://www.jstage.jst.go.jp/article/cpb/74/10/74_c26-00271/_article},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - DNA Polymerase Catalyzes Successive Formation of Cytosine-AgI-Thymine Base Pairs
AU - Tatsuya Funai
AU - Keiko Morita
AU - Ayaka Tani
AU - Shun-ichi Wada
AU - Hidehito Urata
PY - 2026
DA - 2026/10/24
JO - Chemical and Pharmaceutical Bulletin
DO - 10.1248/cpb.c26-00271
UR - https://www.jstage.jst.go.jp/article/cpb/74/10/74_c26-00271/_article
AB - To explore the constraints of forming consecutive C-AgI-T base pairs during DNA polymerase-catalyzed primer extension reactions, we examined the incorporation of deoxythymidine triphosphate (dTTP) into consecutive C sites in the presence of AgI ions. The results demonstrated that AgI-promoted primer extension enables the formation of up to three consecutive C-AgI-T base pairs. Importantly, suppression of C-AgI-C base pair formation resulting from dCTP incorporation was demonstrated to be essential for achieving this outcome. Furthermore, by using MnII ions, the formation of up to five consecutive C-AgI-T base pairs was achieved. The formation of consecutive T-AgI-C base pairs, which involves the incorporation of dCTP into templating T sites, is more difficult than the formation of consecutive C-AgI-T base pairs, because much higher concentrations of dTTP compete with the template thymine for the AgI ion that abstracts the N3 imino proton. Thermal denaturation studies demonstrated that Ag+ ions effectively stabilized duplexes containing consecutive C–T mismatches, whereas stabilization by consecutive C-Ag+-C base pairs was limited because of electrostatic repulsion between neighboring positively charged base pairs. These results suggest that charge-neutral and thermally stable metal-mediated base pairs are critical for efficient polymerase-catalyzed synthesis of metal-containing DNA. These insights could be beneficial for the enzymatic synthesis of DNA-based AgI nanowires.
SN - 1347-5223
SN - 0009-2363
ER -