DNA strand breaks with chemically modified termini are a critical form of damage caused by ionizing radiation, environmental genotoxins, and therapeutic agents. Among them, 3'-phosphoglycolate (3'-PG) termini are particularly problematic, as they obstruct DNA repair and contribute to genome instability. Several indirect detection strategies have provided valuable insights into 3'-PG lesions; however, the lack of a method for direct and specific labeling of 3'-PG termini continues to limit detailed analyses of their distribution and repair in biological systems. We report a novel chemical labeling method that enables the selective conjugation of biotin to the 3'-PG terminus of synthetic oligonucleotides. The method involves carbodiimide-mediated activation of the 3'-PG carboxyl group using EDC·HCl (1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride) and NHS (N-hydroxysuccinimide), followed by coupling with Biotin-PEG11-Amine to form a stable amide bond. This reaction proceeds specifically at the 3'-PG terminus without modifying 3'-phosphate ends. Under the conditions used, the labeling efficiency was approximately 50%. Our results demonstrate the feasibility of chemically tagging 3'-PG ends with high specificity in vitro, providing a foundation for future studies aimed at visualizing and quantifying 3'-PG lesions in more complex biological systems.
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Ryosuke Morozumi
Naoto Shimizu
Tomoko Amimoto
Nucleosides Nucleotides & Nucleic Acids
The University of Osaka
National Human Genome Research Institute
Hiroshima University
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Morozumi et al. (Fri,) studied this question.
www.synapsesocial.com/papers/69bf86ecf665edcd009e9074 — DOI: https://doi.org/10.1080/15257770.2026.2645371
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