Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study
Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study
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DOI：
10.1063/1.1799613
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发表时间：
2004-10-22
影响因子：
4.4
通讯作者：
Benham, CJ
中科院分区：
文献类型：
--
作者：
Mielke, SP;Fink, WH;Benham, CJ
RNA聚合酶沿着双链DNA产生的扭矩可以潜在地诱导远程结构变形，这在原核生物和真核生物中都具有生物学意义。在本文中，我们引入了一个动态计算机模型来研究这一现象。双链DNA被表示为一条流体动力学珠链，通过线性弹性拉伸、弯曲和扭曲以及排除体积的电位相互作用。该链在松弛时呈线性，然后形成两个开放但拓扑约束的子域。这允许通过中心施加的扭矩动态引入扭转应力。我们用布朗动力学模拟了一个477碱基对的B-DNA模板对原核转录集合产生的局域扭矩的100 μ s响应。在早期急剧上升之后，分布扭转在两个子域中呈现出几乎恒定的值，并且随着超螺旋应力越来越多地被划分为扭曲而发生一连串的超螺旋变形。当结构在扭转载荷作用下达到力学平衡时，扭扭的大小超过扭转的大小，然后趋于平稳。正如“转录诱导的双超螺旋结构域”模型所预测的那样，超螺旋在一个子结构域同时是右旋的，在另一个子结构域同时是左旋的。刘福峰，王建昌，中华人民共和国。学会科学。[美国法典84,7024(1987)]。链在扭动开始时的性质与理论预测一致，产生的压力足以驱动生理DNA的二级结构转变。(C) 2004年美国物理研究所。
The torque generated by RNA polymerase as it tracks along double-stranded DNA can potentially induce long-range structural deformations integral to mechanisms of biological significance in both prokaryotes and eukaryotes. In this paper, we introduce a dynamic computer model for investigating this phenomenon. Duplex DNA is represented as a chain of hydrodynamic beads interacting through potentials of linearly elastic stretching, bending, and twisting, as well as excluded volume. The chain, linear when relaxed, is looped to form two open but topologically constrained subdomains. This permits the dynamic introduction of torsional stress via a centrally applied torque. We simulate by Brownian dynamics the 100 mus response of a 477-base pair B-DNA template to the localized torque generated by the prokaryotic transcription ensemble. Following a sharp rise at early times, the distributed twist assumes a nearly constant value in both subdomains, and a succession of supercoiling deformations occurs as superhelical stress is increasingly partitioned to writhe. The magnitude of writhe surpasses that of twist before also leveling off when the structure reaches mechanical equilibrium with the torsional load. Superhelicity is simultaneously right handed in one subdomain and left handed in the other, as predicted by the "transcription-induced twin-supercoiled-domain" model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, 7024 (1987)]. The properties of the chain at the onset of writhing agree well with predictions from theory, and the generated stress is ample for driving secondary structural transitions in physiological DNA. (C) 2004 American Institute of Physics.