Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions.
Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions.
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羟基胞霉素对霍利迪连接结构和稳定性的影响。
DOI：
10.1021/acs.biochem.6b00801
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发表时间：
2016-10-18
期刊：
影响因子：
2.9
通讯作者：
Ho PS
中科院分区：
文献类型：
--
作者：
Vander Zanden CM;Rowe RK;Broad AJ;Robertson AB;Ho PS
5-羟甲基胞嘧啶 (5hmC) 是一种表观遗传标记，最近被证明可以促进同源重组 (HR)。在这项研究中，我们确定了 5hmC 对霍利迪连接体（与 HR 相关的四链 DNA 中间体）天然堆叠 X 形式的结构、热力学和构象动力学的影响。羟甲基和对照甲基取代基置于两性 GxCC 三核苷酸核心序列（其中 xC 是 C、5hmC 或甲基化 5mC）的背景下，该序列也是核酸内切酶 G 识别以促进 HR 的序列的一部分。 5hmC 连接的羟甲基采用两种不同的旋转构象，其中基面内形式比通常在双链体结构中看到的竞争性面外旋转异构体占主导地位。面内旋转异构体被认为通过连接主链的更稳定的分子内氢键而稳定。由 5hmC 中的羟基取代基或 5mC 结构中的桥接水形成的稳定氢键（H 键）为连接点的每次相互作用提供大约 1.5 至 2 kcal/mol 的稳定性，这大部分被熵补偿所抵消，从而使 G5hmCC 结构的整体稳定性与 GCC 核心相似。因此，甲基和羟甲基修饰都可以在不破坏霍利迪连接体的结构或稳定性的情况下进行。 5hmC 和 5mC 都显示打开结构，使连接核心更容易接近。因此，通过直接和间接读出机制，在羟甲基取代基的蛋白质识别特异性的背景下讨论了将 5hmC 掺入 DNA 连接的总体后果。
5-Hydroxymethylcytosine (5hmC) is an epigenetic marker that has recently been shown to promote homologous recombination (HR). In this study, we determine the effects of 5hmC on the structure, thermodynamics, and conformational dynamics of the Holliday junction (the four-stranded DNA intermediate associated with HR) in its native stacked-X form. The hydroxymethyl and the control methyl substituents are placed in the context of an amphimorphic GxCC trinucleotide core sequence (where xC is C, 5hmC, or the methylated 5mC), which is part of a sequence also recognized by endonuclease G to promote HR. The hydroxymethyl group of the 5hmC junction adopts two distinct rotational conformations, with an in-base-plane form being dominant over the competing out-of-plane rotamer that has typically been seen in duplex structures. The in-plane rotamer is seen to be stabilized by a more stable intramolecular hydrogen bond to the junction backbone. Stabilizing hydrogen bonds (H-bonds) formed by the hydroxyl-substituent in the 5hmC or from a bridging water in the 5mC structure provide approximately 1.5 to 2 kcal/mol per interaction of stability to the junction, which is mostly offset by entropy compensation, thereby leaving the overall stability of the G5hmCC constructs similar to the GCC core. Thus, both methyl and hydroxymethyl modifications are accommodated without disrupting the structure or stability of the Holliday junction. Both 5hmC and 5mC are shown to open up the structure to make the junction core more accessible. The overall consequences of incorporating 5hmC into a DNA junction are thus discussed in the context of the specificity in protein recognition of the hydroxymethyl substituent through direct and indirect readout mechanisms.