9KZP

Z-form DNA-RNA hybrid in dynamic simulation

Summary for 9KZP

• Entry DOI: 10.2210/pdb9kzp/pdb
• Descriptor: DNA (5'-D(*(5CM)P*GP*(5CM)P*AP*(5CM)P*GP*(5CM)P*G)-3'), RNA (5'-R(*CP*GP*CP*GP*UP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: z-form dna-rna hybrid, dynamic simulation, okazaki fragment, block dna replication, dna-rna complex, dna/rna
• Biological source: Homo sapiens; More
• Total number of polymer chains: 2
• Total formula weight: 5026.28

Authors

Wang, S.Y.,Xu, Y. (deposition date: 2024-12-11, release date: 2024-12-25, Last modification date: 2025-03-19)

Primary citation

Wang, S.,Xu, Y.
Z-form DNA-RNA hybrid blocks DNA replication.
Nucleic Acids Res., 53:-, 2025

PubMed 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 Å) and a very narrow minor groove (8.3 Å) plays the key role in the repression toward DNA replication.

PubMed: 40037715
DOI: 10.1093/nar/gkaf135

Experimental method

SOLUTION NMR