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Influences of flexible defect on the interplay of supercoiling and knotting of circular dna

Communications in Theoretical Physics 2021年第7期73卷 136-145页

作者： Caiyun Xiong Xiaolin Nie Yixue Peng Xun Zhou Yangtao Fan Hu Chen Yanhui Liu College of Physics Guizhou UniversityGuiyang 550025China School of Physics and Electronic Science Guizhou Normal UniversityGuiyang 550025China Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices PenTung Sah Institute of Micro-Nano Science and TechnologyXiamen UniversityXiamen361005China Research Institute for Biomimetics and Soft Matter Fujian Provincial Key Lab for Soft Functional Materials ResearchDepartment of PhysicsXiamen UniversityXiamen361005China Breeding and Reproduction in The Plateau Mountainous Region Ministry of Education(Guizhou University)Guizhou Guiyang550025China

Knots are discovered in biophysical systems,such as dna and *** portions in knotted dna are significantly bent and their corresponding bending angles are comparable with or larger than the sharp bending angle resulting in flexible *** role of flexible defects in the interplay of supercoiling and knotting of circular dna were predicted by a Monte Carlo *** knotted dna with a particular knot type,a flexible defect noticeably enhances the supercoiling of the knotted dna and the decreasing excitation energy makes the knotted portion more compact.A reduction in twist rigidity and unwinding of flexible defects are incorporated into the numerical simulations,so that interplay of supercoiling and knotting of circular dna is studied under torsional *** unwinding not only results in a wider linking number distribution,but also leads to a drift of the distribution to lower values.A flexible defect has obvious effects on knotting *** summation of equilibrium distribution probability for nontrivial knotted dna with different contour length does not change with excitation energy monotonically and has a maximum at an intermediate value of excitation energy around 5 *** the phase space of knot length and gyration radius of knotted dna,knot length does not anticorrelate with its gyration radius,which is attributed to the flexible defect in the knotted portion,which leads to the release of bending energy and inhibited the competition between entropy and bending energy.

关键词： knot flexible defect dna topology knotted dna Monte-Carlo simulation

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