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| Modeling Mechanical Properties of DNA: Allosteric Protein Binding, Loop Formation, and Longitudinal Fluctuations |
| 2014-11-14
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| Institute of Theoretical Physics | | Chinese Academy of Sciences | | State Key Laboratory of Theoretical Physics | | Seminar | | | | Title 题目 | Modeling Mechanical Properties of DNA: Allosteric Protein Binding, Loop Formation, and Longitudinal Fluctuations | | Speaker 报告人 | Prof. Xin-Liang Xu (徐辛亮） | | Affiliation 所在单位 | 北京计算科学研究中心 | | Date 日期 | 11月14日，11:00-12:00 | | Venue 地点 | ITP New Building 6420 | | Abstract 摘要 | The deformability of DNA has great impacts on its overall shape as well as on many biological functions, such as protein-DNA binding, chromosomal DNA packaging, DNA damage repair, and regulation of gene expression. Here we present our recently developed coarse grained mechanical model of DNA that studies the local deformations of DNA from its canonical structure. In collaboration with recent experimental studies, the correlation between local deformations is unveiled and identified as the underlying mechanism for the observed allosteric protein binding. This newly discovered correlation improves our understanding of the flexibility of DNA and suggests modification of the traditional description of DNA as an elastic rod, which is valid only for long DNA chains and has been challenged by recent experimental studies at shorter length scales. With explicit consideration of the length scale over which local deformations are correlated, our improved model predicts a length dependent flexibility. While our model reduces to the traditional worm-like chain model in the long chain limit, it predicts that DNA becomes much more flexible at shorter sizes that are of biological importance, in good agreement with recent loop formation measurements of short DNA fragments around 100 base pairs. | | Contact Person 所内合作者 | 周海军 |
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