Complex phase transition of DNA condensation under crowding confinement conditions
Complex phase transition of DNA condensation under crowding confinement conditions
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拥挤限制条件下DNA凝聚的复杂相变
DOI：
10.1016/j.physa.2018.05.011
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发表时间：
2018-10
期刊：
影响因子：
--
通讯作者：
刘艳辉
中科院分区：
文献类型：
--
作者：
辜凌云;周倩;周海平;高庆庆;彭亦学;刘泳;宋小义;周勋;刘艳辉
多价阳离子在约束下协助缩合过程的拥挤效应的机制尚未报道。在强相关模型的基础上，采用蒙特卡罗模拟方法检测了拥挤效应对胶囊状空间内DNA凝聚的影响，其几何形状由宽高比控制。在球形空间内（宽高比为1）的凝聚构象比没有凝聚构象时更加致密。dna凝聚构象经历了从初始的随机线圈结构到环面结构，再到延伸的棒状结构，最后到完全致密结构的过渡过程。棒状结构向完全压实结构过渡所对应的临界体积分数与颗粒尺寸成正比。此外，相变对应的临界体积分数强烈依赖于约束几何形状，恒定半径情况下的临界体积分数与长径比成反比。相反，当柱长不变时，临界体积分数与长径比成正比。这些现象与在体积分数和纵横比空间中重新表达的相图相一致。阐明了禁闭几何形状和拥挤体大小对DNA凝聚对拥挤响应的影响，并将其推广到纵横比和拥挤体大小空间的空间图中。当纵横比小于1.6且簇尺寸大于2.0 nm或纵横比≥1.6且簇尺寸大于临界dc *时，DNA的构象由初始的随机线圈结构过渡到环状结构，再过渡到完全致密结构；当长径比≥1.6且蜂群尺寸≤d c *时，DNA缩合构象将进一步由完全压缩结构缩合为延伸棒状结构。此外，从完全压实的结构到扩展的棒状结构的过渡完全是由于de Gennes和Odijk政权之间的拥挤尺寸和约束几何。
The mechanism underlying the crowding effects that assist the condensation process by multivalent cations under confinement is not yet reported. Based on the strong correlation model, Monte Carlo simulation was implemented to detect the crowding effects on DNA condensation within a capsule-like space, and its geometry controlled by the aspect ratio. With the addition of crowders, the condensed conformations confined within the spherical space (aspect ratio is 1) become more compact than those without crowders. The DNA-condensed conformations undergo a transition from the initial random coil structure to toroid structure, followed by the extended rod-like structure, and finally to totally compacted structure. The critical volume fraction corresponding to the transition from the rod-like structure to totally compacted structure pertained to the crowder size proportionally. Moreover, the critical volume fraction corresponding to the phase transition strongly depends on the confinement geometry, the critical volume fraction for the case with constant radius is inversely proportional to the aspect ratio. Conversely, the case with constant cylinder length showed that the critical volume fraction is proportional to the aspect ratio. These phenomena are consistent with their corresponding phase diagram re-expressed in the space of volume fraction and aspect ratio. The effects of confinement geometry and crowder size on the response of DNA condensation to crowding are elucidated and generalized into the space diagram in the space of aspect ratio and crowder size. When the aspect ratio less than 1.6 and the crowder size larger than 2.0 nm or when the aspect ratio≥ 1.6 and the crowder size larger than the critical d c∗, the DNA conformation undergo the transition from the initial random coil structure to toroid structure, followed by totally compacted structure; when the aspect ratio≥ 1.6 and the crowder size≤ d c∗, the DNA condensed conformations will be condensed further from the totally compacted structure to the extended rod-like structure. Furthermore, the transition from the totally compacted structure to the extended rod-like structure is entirely due to the crowder size and the confinement geometry between the de Gennes and Odijk regimes.
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DOI：
10.1021/jp2124907
发表时间：
2012-02
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Ce Zhang-;Zongying Gong;Durgarao Guttula;P. Malar;J. A. van Kan;P. Doyle;J. V. D. van der Maarel
通讯作者：
Ce Zhang-;Zongying Gong;Durgarao Guttula;P. Malar;J. A. van Kan;P. Doyle;J. V. D. van der Maarel
影响因子：
5.5
作者：
Muralidhar, Abhiram;Dorfman, Kevin D.
通讯作者：
Dorfman, Kevin D.
影响因子：
8.6
作者：
Dai, Liang;Mu, Yuguang;van der Maarel, Johan R. C.
通讯作者：
van der Maarel, Johan R. C.
DOI：
10.1103/physreve.78.021904
发表时间：
2008-08
期刊：
Physical review. E, Statistical, nonlinear, and soft matter physics
影响因子：
--
作者：
Won Kyu Kim;W. Sung
通讯作者：
Won Kyu Kim;W. Sung
影响因子：
8.6
作者：
Y. Levin;J. J. Arenzon-J.;J. Stilck
通讯作者：
Y. Levin;J. J. Arenzon-J.;J. Stilck