biostudies-literatureWang SJapan Society for the Promotion of Sciencegkaf135https://www.ebi.ac.uk/biostudies/studies/S-EPMC11879439biostudies-literatureUnknown53(5)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 Å) and a very narrow minor groove (8.3 Å) plays the key role in the repression toward DNA replication.Nucleic acids researchZ-form DNA-RNA hybrid blocks DNA replication.PMC1187943924K0164821H02081Wang SXu YfalseZ-form DNA-RNA hybrid blocks DNA replication.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 Å) and a very narrow minor groove (8.3 Å) plays the key role in the repression toward DNA replication.2025-01-01T00:00:00Z2025 Feb2026-06-01T11:16:45.37Z2025-04-07T11:26:53.212ZS-EPMC118794394003771510.1093/nar/gkaf135