Discrimination between Different DNA Lesions by Monitoring Single-Molecule Polymerase Stalling Kinetics during Nanopore Sequencing,Nano Letters

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Discrimination between Different DNA Lesions by Monitoring Single-Molecule Polymerase Stalling Kinetics during Nanopore Sequencing
Nano Letters ( IF 9.6 ) Pub Date : 2022-06-17 , DOI: 10.1021/acs.nanolett.2c01833
Jinyue Zhang _{1,

2} , Yu Wang _{1,

2} , Yuqin Wang _{1,

2} , Panke Zhang ₁ , Hong-Yuan Chen ₁ , Shuo Huang _{1,

2}

Affiliation

O⁶-Carboxymethylguanosine (O⁶-CMG), O⁶-methylguanosine (O⁶-MeG), and abasic site (AP site) are DNA lesions induced by alkylating agents. Identification of these lesions in DNA may aid in understanding their relevance to carcinogenesis and may be used for diagnosis. Nanopore sequencing (NPS) may directly report nucleotide modifications solely from the nanopore readout. However, the conventional NPS strategy still suffers from interferences from neighboring sequences. Instead, by observation of the enzymatic stalling kinetics caused by the O⁶-CMG, O⁶-MeG, or AP site, discrimination between different DNA lesions is directly achieved. This strategy is not interfered with by the sequence context around the lesion. The lesion, which retards the movement of the DNA through the pore, efficiently prohibits misreading of the DNA lesion. These results suggest a new strategy in the identification of DNA lesions or DNA modifications. It also provides a high-resolution biophysical tool to investigate enzymatic kinetics caused by DNA lesions and the corresponding enzymes.

中文翻译：

通过监测纳米孔测序过程中的单分子聚合酶停滞动力学来区分不同的 DNA 损伤

O ⁶ -羧甲基鸟苷（O ⁶ -CMG）、O ⁶ -甲基鸟苷（O ⁶ -MeG）和脱碱基位点（AP位点）是由烷化剂诱导的DNA损伤。鉴定 DNA 中的这些病变可能有助于了解它们与致癌作用的相关性，并可用于诊断。纳米孔测序 (NPS) 可以仅从纳米孔读数直接报告核苷酸修饰。然而，传统的 NPS 策略仍然受到相邻序列的干扰。^{相反，通过观察由 O 6} -CMG引起的酶促停滞动力学，O ⁶-MeG，或AP位点，直接实现不同DNA损伤的区分。该策略不受病变周围的序列上下文的干扰。阻碍DNA通过孔的运动的损伤有效地阻止了DNA损伤的误读。这些结果表明了一种识别 DNA 损伤或 DNA 修饰的新策略。它还提供了一种高分辨率的生物物理工具来研究由 DNA 损伤和相应酶引起的酶动力学。

更新日期：2022-06-17

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