Detection and Discrimination of DNA Adducts Differing in Size, Regiochemistry, and Functional Group by Nanopore Sequencing.

Intawat Nookaew, Piroon Jenjaroenpun, Hua Du, Pengcheng Wang, Jun Wu, Thidathip Wongsurawat, Sun Hee Moon, En Huang, Yinsheng Wang, Gunnar Boysen

Chemical research in toxicology 2020 Dec 21

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Chemically induced DNA adducts can lead to mutations and cancer. Unfortunately, because common analytical methods (e.g., liquid chromatography-mass spectrometry) require adducts to be digested or liberated from DNA before quantification, information about their positions within the DNA sequence is lost. Advances in nanopore sequencing technologies allow individual DNA molecules to be analyzed at single-nucleobase resolution, enabling us to study the dynamic of epigenetic modifications and exposure-induced DNA adducts in their native forms on the DNA strand. We applied and evaluated the commercially available Oxford Nanopore Technology (ONT) sequencing platform for site-specific detection of DNA adducts and for distinguishing individual alkylated DNA adducts. Using ONT and the publicly available ELIGOS software, we analyzed a library of 15 plasmids containing site-specifically inserted O6- or N2-alkyl-2'-deoxyguanosine lesions differing in sizes and regiochemistries. Positions of DNA adducts were correctly located, and individual DNA adducts were clearly distinguished from each other.

Citation

Intawat Nookaew, Piroon Jenjaroenpun, Hua Du, Pengcheng Wang, Jun Wu, Thidathip Wongsurawat, Sun Hee Moon, En Huang, Yinsheng Wang, Gunnar Boysen. Detection and Discrimination of DNA Adducts Differing in Size, Regiochemistry, and Functional Group by Nanopore Sequencing. Chemical research in toxicology. 2020 Dec 21;33(12):2944-2952