13C relaxation studies of the DNA target sequence for HhaI methyltransferase reveal unique motional properties
13C relaxation studies of the DNA target sequence for HhaI methyltransferase reveal unique motional properties
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DOI：
10.1021/bi7020469
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发表时间：
2008-07-22
期刊：
影响因子：
2.9
通讯作者：
Varani, Gabriele
中科院分区：
文献类型：
--
作者：
Shajani, Zahra;Varani, Gabriele
这项工作的目的是检查DNA中序列依赖的构象灵活性是否在碱基挤压中起作用，碱基挤压是许多DNA修饰酶诱导的常见构象变化。我们通过记录大量的C-13核磁共振弛豫参数，研究了HhaI甲基转移酶双链DNA靶点的动力学。我们观察到胞苷呋喃糖环经历了其他核苷酸中不存在的快速（皮秒到纳秒）运动；甲基化位点具有特别高的流动性。我们还观察到，在HhaI识别序列GCGC中，鸟苷和胞苷残基的碱基运动速度要慢得多（1-100 μ s）。我们将这些观察结果与之前对EcoRI核酸酶靶序列的溶液和固体核磁共振研究以及类似HhaI靶结构的固体核磁共振研究进行了比较。与其他核苷酸相比，胞苷呋喃糖环的迁移率在这两种序列中都有所增加，但仅在HhaI靶DNA中观察到较慢的运动。我们提出，这种固有的灵活性降低了DNA与HhaI甲基转移酶结合时必须发生的能量障碍，以及在甲基化之前挤压胞苷。
The goal of this work was to examine if sequence-dependent conformational flexibility in DNA plays a role in base extrusion, a common conformational change induced by many DNA-modifying enzymes. We studied the dynamics of the double-stranded DNA target of the HhaI methyltransferase by recording an extensive set of C-13 NMR relaxation parameters. We observe that the cytidine furanose rings experience fast (picosecond to nanosecond) motions that are not present in other nucleotides; the methylation site experiences particularly high mobility. We also observe that the bases of guanosine and cytidine residues within the HhaI recognition sequence GCGC experience motions on a much slower (1-100 mu s) time scale. We compare these observations with previous solution and solid-state NMR studies of the EcoRI nuclease target sequence, and solid-state NMR studies of a similar HhaI target construct. While an increased mobility of cytidine furanose rings compared to those of other nucleotides is observed for both sequences, the slower motions are only observed in the HhaI target DNA. We propose that this inherent flexibility lowers the energetic barriers that must occur when the DNA binds to the HhaI methyltransferase and for extrusion of the cytidine prior to its methylation.