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DNA 的关联运动:超越 DNA 柔韧性的碱基对步模型。

Correlated motions in DNA: beyond base-pair step models of DNA flexibility.

机构信息

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri i Reixac 10-12, 08028 Barcelona, Spain.

Department of Biochemistry and Biomedicine, University of Barcelona, 08028 Barcelona, Spain.

出版信息

Nucleic Acids Res. 2023 Apr 11;51(6):2633-2640. doi: 10.1093/nar/gkad136.

Abstract

Traditional mesoscopic models of DNA flexibility use a reductionist-local approach, which assumes that the flexibility of DNA can be expressed as local harmonic movements (at the base-pair step level) in the helical space, ignoring multimodality and correlations in DNA movements, which have in reality a large impact in modulating DNA movements. We present a new multimodal-harmonic correlated model, which takes both contributions into account, providing, with a small computational cost, results of an unprecedented local and global quality. The accuracy of this method and its computational efficiency make it an alternative to explore the dynamics of long segments of DNA, approaching the chromatin range.

摘要

传统的 DNA 柔性介观模型采用简化局部方法,该方法假设 DNA 的柔性可以表达为螺旋空间中的局部调和运动(在碱基对步级),而忽略了 DNA 运动中的多模态和相关性,而实际上这些相关性对调节 DNA 运动有很大影响。我们提出了一种新的多模态调和相关模型,同时考虑了这两个因素,以较小的计算成本提供了前所未有的局部和全局质量的结果。该方法的准确性和计算效率使其成为探索长段 DNA 动力学的替代方法,可用于接近染色质范围。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e3f0/10085700/20a1497ff060/gkad136fig1.jpg

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