Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.
Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.
Biophys J. 2024 Jan 16;123(2):260-271. doi: 10.1016/j.bpj.2023.12.014. Epub 2023 Dec 18.
XPD helicase is a DNA-unwinding enzyme involved in DNA repair. As part of TFIIH, XPD opens a repair bubble in DNA for access by proteins in the nucleotide excision repair pathway. XPD uses the energy from ATP hydrolysis to translocate in the 5' to 3' direction on one strand of duplex DNA, displacing the opposite strand in the process. We used magnetic tweezers assays to measure the double-stranded DNA unwinding and single-stranded DNA translocation activities of human XPD in isolation. In our experimental setup, hXPD exhibited low unwinding processivity of ∼14 bp and slow unwinding rate of ∼0.3 bp/s. Measurements of the ssDNA translocation activity demonstrated that hXPD translocated on ssDNA at a similar rate as unwinding, revealing that slow rate was an intrinsic property of the hXPD translocation. Individual unwinding and translocation events were composed of pauses and runs with a distribution of lengths and rates. Analysis of these events unveiled similar mean run lengths and rates for unwinding and translocation, indicating that the unwinding behavior was a direct reflection of the translocation activity. The analysis also revealed that hXPD spent similar time stalling and unwinding/translocating. The detailed basal activity of hXPD reported here provides a baseline for future studies on how hXPD activity is regulated by other TFIIH components.
XPD 解旋酶是一种参与 DNA 修复的 DNA 解旋酶。作为 TFIIH 的一部分,XPD 在 DNA 中打开一个修复泡,以便核苷酸切除修复途径中的蛋白质进入。XPD 利用 ATP 水解的能量在双链 DNA 的 5' 到 3' 方向上迁移,在此过程中取代相反的链。我们使用磁镊实验来测量人 XPD 在分离状态下的双链 DNA 解旋和单链 DNA 易位活性。在我们的实验设置中,hXPD 表现出约 14 bp 的低解旋过程性和约 0.3 bp/s 的缓慢解旋速率。ssDNA 易位活性的测量表明,hXPD 在 ssDNA 上的易位速率与解旋相似,表明缓慢的速率是 hXPD 易位的固有特性。单个解旋和易位事件由停顿和运行组成,具有长度和速率的分布。对这些事件的分析揭示了解旋和易位的相似平均运行长度和速率,表明解旋行为是易位活性的直接反映。该分析还表明,hXPD 在停顿和解旋/易位上花费了相似的时间。这里报道的 hXPD 的详细基础活性为研究 hXPD 活性如何被其他 TFIIH 成分调节提供了一个基准。