DNA Structural Correlation in Short and Long Ranges
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- 作者：Chan Gu ; Jun Zhang ; Y. Isaac Yang ; Xi Chen ; Hao Ge ; Yujie Sun ; Xiaodong Su ; Lijiang Yang ; Sunney Xie ; Yi Qin Gao
- 刊名：Journal of Physical Chemistry B
- 出版年：2015
- 出版时间：November 5, 2015
- 年：2015
- 卷：119
- 期：44
- 页码：13980-13990
- 全文大小：678K
- ISSN：1520-5207
文摘
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.