In the base excision repair pathway, the initiating enzymes, DNA glycosylases, remove damaged bases and form long-living complexes with the abasic DNA product, but can be displaced by AP endonucleases. However, many nuclear proteins can move along DNA, either actively (such as DNA or RNA polymerases) or by passive one-dimensional diffusion. In most cases, it is not clear whether this movement is disturbed by other bound proteins or how collisions with moving proteins affect the bound proteins, including DNA glycosylases. We have used a two-substrate system to study the displacement of human OGG1 and NEIL1 DNA glycosylases by DNA polymerases in both elongation and diffusion mode and by D4, a passively diffusing subunit of a viral DNA polymerase. The OGG1–DNA product complex was disrupted by DNA polymerase β (POLβ) in both elongation and diffusion mode, Klenow fragment (KF) in the elongation mode and by D4. NEIL1, which has a shorter half-life on DNA, was displaced more efficiently. Hence, both possibly specific interactions with POLβ and nonspecific collisions (KF, D4) can displace DNA glycosylases from DNA. The protein movement along DNA was blocked by very tightly bound Cas9 RNA-targeted nuclease, providing an upper limit on the efficiency of obstacle clearance.

中文翻译：

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通过 DNA 上的分子交通置换慢转化 DNA 糖基化酶

在碱基切除修复途径中，起始酶 DNA 糖基化酶去除受损碱基并与无碱基 DNA 产物形成长寿命复合物，但可以被 AP 核酸内切酶取代。然而，许多核蛋白可以主动（如 DNA 或 RNA 聚合酶）或被动的一维扩散沿 DNA 移动。在大多数情况下，不清楚这种运动是否受到其他结合蛋白的干扰，或者与运动蛋白的碰撞如何影响结合蛋白，包括 DNA 糖基化酶。我们使用双底物系统研究了 DNA 聚合酶在延伸和扩散模式下以及 D4（病毒 DNA 聚合酶的被动扩散亚基）对人 OGG1 和 NEIL1 DNA 糖基化酶的置换。OGG1-DNA 产物复合物在延伸和扩散模式下被 DNA 聚合酶 β (POLβ) 破坏，在延伸模式下被 Klenow 片段 (KF) 和 D4 破坏。对 DNA 具有较短半衰期的 NEIL1 被更有效地取代。因此，与 POLβ 的可能特异性相互作用和非特异性碰撞（KF、D4）都可以从 DNA 中置换 DNA 糖基化酶。沿着 DNA 的蛋白质运动被非常紧密结合的 Cas9 RNA 靶向核酸酶阻断，为障碍清除效率提供了上限。