DNA Structural Correlation in Short and Long Ranges
DNA Structural Correlation in Short and Long Ranges
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短距离和长距离的 DNA 结构相关性
DOI：
10.1021/acs.jpcb.5b06217
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发表时间：
2015-11-05
影响因子：
3.3
通讯作者：
Gao, Yi Qin
中科院分区：
文献类型：
--
作者：
Gu, Chan;Zhang, Jun;Gao, Yi Qin
最近的单分子测量揭示了蛋白质/DNA结合中的DNA变构。分子动力学模拟表明，这种变构效应与DNA的形变性质有关。在这项研究中，我们使用MD模拟来进一步研究DNA结构相关性的机制、它对DNA序列的依赖以及碱基的化学修饰。除了随机序列外，聚d(AT)和聚d(GC)也被用作更简单的模型系统，它们表现出不同的弯曲和扭转灵活性。碱基-堆积作用和胸腺嘧啶5-碳位上的甲基导致两个模型体系的局部结构和柔性有很大的不同，进而导致构象变形的明显不同趋势，包括远程变构效应。
Recent single-molecule measurements have revealed the DNA allostery in protein/DNA binding. MD simulations showed that this allosteric effect is associated with the deformation properties of DNA. In this study, we used MD simulations to further investigate the mechanism of DNA structural correlation, its dependence on DNA sequence, and the chemical modification of the bases. Besides a random sequence, poly d(AT) and poly d(GC) are also used as simpler model systems, which show the different bending and twisting flexibilities. The base-stacking interactions and the methyl group on the 5-carbon site of thymine causes local structures and flexibility to be very different for the two model systems, which further lead to obviously different tendencies of the conformational deformations, including the long-range allosteric effects.