Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, United States.
Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, United States.
Biophys Chem. 2023 May;296:106992. doi: 10.1016/j.bpc.2023.106992. Epub 2023 Mar 3.
In bacterial endospores, a cross-linked thymine dimer, 5-thyminyl-5,6-dihydrothymine, commonly referred to as the spore photoproduct (SP), is found as the dominant DNA photo lesion under UV radiation. During spore germination, SP is faithfully repaired by the spore photoproduct lyase (SPL) for normal DNA replication to resume. Despite this general mechanism, the exact way in which SP modifies the duplex DNA structure so that the damaged site can be recognized by SPL to initiate the repair process is still unclear. A previous X-ray crystallographic study, which used a reverse transcriptase as a DNA host template, captured a protein-bound duplex oligonucleotide containing two SP lesions; the study showed shortened hydrogen bonds between the AT base pairs involved in the lesions and widened minor grooves near the damaged sites. However, it remains to be determined whether the results accurately reflect the conformation of SP-containing DNA (SP-DNA) in its fully hydrated pre-repair form. To uncover the intrinsic changes in DNA conformation caused by SP lesions, we performed molecular dynamics (MD) simulations of SP-DNA duplexes in aqueous solution, using the nucleic acid portion of the previously determined crystal structure as a template. After MD relaxation, our simulated SP-DNAs showed weakened hydrogen bonds at the damaged sites compared to those in the undamaged DNA. Our analyses of the MD trajectories revealed a range of local and global structural distortions of DNA induced by SP. Specifically, the SP region displays a greater tendency to adopt an A-like-DNA conformation, and curvature analysis revealed an increase in the global bending compared to the canonical B-DNA. Although these SP-induced DNA conformational changes are relatively minor, they may provide a sufficient structural basis for SP to be recognized by SPL during the lesion repair process.
在细菌芽孢中，一种交联的胸腺嘧啶二聚体，5-胸腺嘧啶-5,6-二氢胸腺嘧啶，通常被称为芽孢光产物（SP），是在紫外线辐射下发现的占主导地位的 DNA 光损伤。在芽孢萌发过程中，SP 通过芽孢光产物裂合酶（SPL）被忠实修复，以便正常的 DNA 复制恢复。尽管存在这种普遍机制，但 SP 修饰双链 DNA 结构的具体方式，使得受损部位可以被 SPL 识别以启动修复过程，目前仍不清楚。先前的一项 X 射线晶体学研究使用逆转录酶作为 DNA 宿主模板，捕获了一种含有两个 SP 损伤的结合蛋白的双链寡核苷酸；该研究表明，损伤涉及的 AT 碱基对之间的氢键缩短，并且在受损部位附近的小沟变宽。然而，仍有待确定这些结果是否准确反映了修复前完全水合的 SP 含 DNA（SP-DNA）的构象。为了揭示 SP 损伤引起的 DNA 构象的内在变化，我们在水溶液中对 SP-DNA 双链进行了分子动力学（MD）模拟，使用先前确定的晶体结构的核酸部分作为模板。在 MD 弛豫后，与未受损 DNA 相比，我们模拟的 SP-DNAs 在受损部位的氢键较弱。我们对 MD 轨迹的分析揭示了 SP 引起的 DNA 局部和全局结构扭曲的范围。具体而言，SP 区域显示出更大的倾向采用 A 型-DNA 构象，曲率分析显示与典型的 B-DNA 相比，整体弯曲增加。尽管这些 SP 诱导的 DNA 构象变化相对较小，但它们可能为 SPL 在损伤修复过程中识别 SP 提供了足够的结构基础。
