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Updated: Jun 12, 2026
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
Published on: May 2, 2025
Abasic sites preferentially form at regions undergoing DNA replication
Paul D Chastain1, Jun Nakamura, Shangbang Rao
1Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7525, USA. pchastai@med.unc.edu
Summary
Apurinic/apyrimidinic (AP) sites are more frequent in replicating DNA and increase under oxidative stress. DNA fiber analysis reveals higher AP site density in newly replicated DNA, suggesting increased susceptibility to oxidative damage during replication.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Apurinic/apyrimidinic (AP) sites are common DNA lesions.
- Their distribution and frequency during DNA replication and oxidative stress are not fully understood.
Purpose of the Study:
- To investigate the frequency and distribution of AP sites in replicating DNA.
- To determine if oxidative stress impacts AP site frequency in these regions.
Main Methods:
- DNA fiber spreading and fluorescent immunostaining.
- Detection of DNA replication sites and AP lesions on extended DNA fibers.
- Enumeration of AP lesions in bulk DNA and at replication sites.
Main Results:
- Background AP site density was 5.4 AP sites/10(6) nt.
- Newly replicated DNA showed a higher density of 12.9 AP sites/10(6) nt.
- Oxidative stress (20 μM H(2)O(2)) increased AP sites in newly replicated DNA to 20.8/10(6) nt.
- Fiber analysis results agreed with standard slot blot assays.
Conclusions:
- DNA fiber analysis accurately quantifies AP site frequency and distribution.
- Replicating DNA regions exhibit increased susceptibility to oxidative damage.
- This susceptibility may explain the observed clustering of AP sites.
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