拓扑异构酶II存在下环形纳米通道中dsDNA多连环体与网络形成的粗粒度模拟
Coarse-grained simulations of dsDNA polycatenanes and network formation in annular nanochannels with topoisomerase II
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中文总结 AI 辅助
本研究通过粗粒度模拟，探究TopoII存在下环形纳米通道内缺刻dsDNA环的行为，分析通道限制对连环化、结形成的影响，为TopoII模型选择及dsDNA互锁材料制备提供方法。
中文摘要 AI 辅助
我们数值研究了在拓扑异构酶II（TopoII）存在下，被限制在环形方形纳米通道内的初始未连接的缺刻双链DNA（dsDNA）环系统的行为。通道限制可通过使不同环的高度弯曲区域靠近来提高连环化概率，同时减少结的出现。环形通道拓扑结构通过消除周期性边界条件简化了系统表征，并可能导致形成环形网络。为表征稳态系统的平衡和动力学性质，包括连环化数量及系统探索的拓扑结构，我们在模型的不同参数和不同限制水平下进行了研究。我们认为，类似的设置可在特征明确且可控的条件下实现实验与模拟的直接对比，从而为选择和调整TopoII的计算模型提供途径，也为以可控方式获取dsDNA互锁材料提供方法。
英文摘要
We numerically investigate the behavior of a system of initially unlinked nicked dsDNA rings confined into an annular square nanochannel in the presence of TopoII. Channel confinement can enhance the catenation likelihood by bringing highly bent regions from different rings in close proximity, while at the same time reducing the emergence of knots. The annular channel topology simplifies the characterization of the system by removing periodic boundary conditions and can lead to the formation of circular catenanes.We characterize the equilibrium and dynamical properties of the steady-state system, including the amount of catenation and the topologies explored by the system, under different parameters of the model and for different levels of confinement. We argue that a similar setup could allow for a direct comparison between experiments and simulations under well characterized and controlled conditions, thus providing a way to select and tune computational models of TopoII, as well as provide a way to obtain dsDNA interlocked materials in a controlled fashion.
发表机构
- Università di Trento（特伦托大学）
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications（意大利国家核物理研究所-特伦托基础物理与应用研究所）
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