Structural Changes during the Photorepair and Binding Processes of Xenopus (6-4) Photolyase with (6-4) Photoproducts in Single- and Double-Stranded DNA
Structural Changes during the Photorepair and Binding Processes of Xenopus (6-4) Photolyase with (6-4) Photoproducts in Single- and Double-Stranded DNA
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DOI：
10.1021/acs.biochem.1c00413
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发表时间：
2021-10-18
期刊：
影响因子：
2.9
通讯作者：
Kandori, Hideki
中科院分区：
文献类型：
--
作者：
Yamada, Daichi;Yamamoto, Junpei;Kandori, Hideki
光分解酶（PHRs）将紫外线（UV）诱导的DNA光产物修复为正常碱基。在这项研究中，我们通过光诱导差分傅里叶变换红外光谱（FT-IR）测量了PHR及其特定底物（6-4）PHR和嘧啶（64）嘧啶光产物（(6-4)PP）在光激活和光修复过程中的构象变化。将（6-4）PP单链DNA （ss(6-4)PP）作为底物，与（6-4）PP双链DNA （ds(6-4)PP）的FT-IR光谱进行比较。在酶的过量底物中，以光照时间依赖的方式获得不同的ss(6-4)PP光修复FT-IR信号。据报道，ds(6-4)PP光反应的早期阶段仅涉及ss(6-4)PP的变化，而反应的后期阶段涉及ss(6-4)PP修复相关的变化和（6-4）PHR的解离。从这些光谱中提取出来自结合/解离光谱的差异光谱。初步确定了单链和双链DNA中（6-4）PP和修复胸腺嘧啶C = O片段的信号。（6-4）PP的C = O延伸以反映水溶液中单链和双链DNA环境的频率进行观察，反映了不同的氢键环境。PHR与ss(6-4)PP和ds(6-4)PP结合后的构象变化相似，表明构象变化仅限于（6-4）PP结合袋区。我们解释说，ds(6-4)PP可能结合在一起，没有任何特殊的机制翻转。
Photolyases (PHRs) repair ultraviolet (UV)-induced DNA photoproducts into normal bases. In this study, we measured the conformational changes upon photoactivation and photorepair processes of a PHR and its specific substrates, (6-4)PHR and a pyrimidine(64)pyrimidone photoproduct ((6-4)PP), by light-induced difference Fourier transform infrared (FT-IR) spectroscopy. The single-stranded DNA with (6-4)PP (ss(6-4)PP) was used as a substrate and the resultant FT-IR spectra were compared with the previous results on double-stranded DNA with (6-4)PP (ds(6-4)PP). In the excess amount of substrate to the enzyme, different ss(6-4)PP photorepair FT-IR signals were obtained in an illumination time-dependent manner. As reported for ds(6-4)PP, the early stages of the photoreaction involve the changes in the ss(6-4)PP only, while the late stages of the reaction involve the ss(6-4)PP repair-associated changes and dissociation from (6-4)PHR. From these spectra, difference spectra originating from the binding/dissociation spectrum were extracted. The signals of the C = O stretches of (6-4)PP and repaired thymines in the single- and double-stranded DNA were tentatively assigned. The C = O stretches of (6-4)PP were observed at frequencies that reflect single- and double-stranded DNA environments in aqueous solution, reflecting the different hydrogen-bonding environments. The conformational changes of PHR upon binding of ss(6-4)PP and ds(6-4)PP were similar, suggesting that the conformational change is limited to the (6-4)PP binding pocket region. We interpreted that ds(6-4)PP may be bound together without any special mechanism for flipping out.