Haesong Lee 1, Ji Eon Kim 1,2, Eun-Ae Shin 1, Yangie Pinanga 1, Kyung-hee Pyo 1, Eun Hae Lee 1, Wonsik Kim 1, Soyeon Kim 1, Chang Sup Lim 3, Kyung Chul Yoon 3, Jung Weon Lee 1,2,
Posted: March 4, 2025
Abstract
We discovered that the Z-form DNA-RNA hybrid stabilized by methylated CpG repeats impacts on the initiation and elongation of Okazaki fragments, contributing to blocking DNA replication at first time. We further present the first Z-form DNA-RNA hybrid structure by using NMR spectroscopy and dynamic computation, revealing the molecular mechanism of inhibition, indicating that a distinctive zig-zag strand pattern of the Z-form hybrid with a smaller helical diameter (15 Ã…) and a very narrow minor groove (8.3 Ã…) plays the key role in the repression toward DNA replication.
NeoBiotechnologies’ products were used in this study:
E. coli DNA polymerase I (pol I) and 3′-5′ exonuclease were commercially obtained from TaKaRa Bio. They were used according to the manufacturer’s instructions without any additional treatment. Human polymerase δ catalytic subunit p125 (pol δ) was ordered from Funakoshi and prepared as 1 μM in stock solution after dilution at -20 °C before use. The full-length ZBP1 was purchased from ORIGENE Technologies, Inc. (US). It’s use follows manufacturing suggestion without further treatment. It’s conservation by using Milli-Q with 10 mM EDTA under -70 °C until next use. Full-length human PCNA protein was ordered from NeoBiotechnologies and used following manufacturing suggestion.
Publication History:
Nucleic Acids Res. 2025 Mar 4;53(5):gkaf135. doi: 10.1093/nar/gkaf135
