Molecular dynamics study on clustered DNA damage: AP sites on the same strand

IF 3.3 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biophysical chemistry Pub Date : 2025-01-25 DOI:10.1016/j.bpc.2025.107394

Kazushi Terakawa , Susumu Fujiwara , Tomoko Mizuguchi , Hiroaki Nakamura , Ken Akamatsu , Naoya Shikazono , Yoshiteru Yonetani

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Abstract

Although radiation-induced clustered DNA damage can have critical biological consequences, the underlying molecular mechanisms remain unclear. To explore the effect of clustered DNA damage on DNA structure and dynamics, we performed molecular dynamics simulations on damaged DNA with two AP sites on the same strand, that is, a tandem AP cluster. The results showed that the cluster insertion of the two AP sites had a significant impact on the DNA's local and global structures. Local structural deformations as well as the extrahelical form, AP-base pairs, and irregular base pairs were frequently observed. Unlike a single AP site, the tandem AP cluster revealed that these local structural features occurred simultaneously within a small separation. Moreover, we found that the presence of tandem AP sites induced global bending of DNA. This suggests that the present case with tandem AP sites may have a non-negligible impact on the biological function of damage repair.

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来源期刊

Biophysical chemistry 生物-生化与分子生物学

CiteScore

6.10

自引率

10.50%

发文量

121

审稿时长

20 days

期刊介绍： Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal.