Is the kinetoplast DNA a percolating network of linked rings at its critical point?
Is the kinetoplast DNA a percolating network of linked rings at its critical point?
复制标题
动质体 DNA 在其临界点上是一个由环相连的渗透网络吗？
作者：
D. Michieletto;D. Marenduzzo;E. Orlandini
在这项工作中，我们提出了一个计算研究的动基体基因组，建模为大量的半柔性unknotted环，这是允许相互连接。随着DNA密度的增加，系统显示出一个非连接环的气体和连接环的网络之间的渗透过渡，跨越整个系统。接近渗透转变，我们发现网络的平均价，即连接到任何一个环的环的平均数，大约是3，实验发现的动基体DNA（kDNA）。更重要的是，通过模拟限制性内切酶消化的网络，我们表明，寡聚体的分布，即由几个环，消化后保持连接形成的结构，定量匹配从凝胶电泳获得的实验数据，只要密度是，再一次，接近渗滤过渡。相对于以前的工作，我们的分析建立在减少假设的基础上，但仍然可以充分解释实验数据。我们的研究结果表明，kDNA可以被看作是一个网络的链接环定位非常接近的渗滤过渡，我们讨论了可能的生物学意义，这一显着的事实。
In this work we present a computational study of the kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation transition between a gas of unlinked rings and a network of linked loops which spans the whole system. Close to the percolation transition, we find that the mean valency of the network, i.e. the average number of loops which are linked to any one loop, is around three, as found experimentally for the kinetoplast DNA (kDNA). Even more importantly, by simulating the digestion of the network by a restriction enzyme, we show that the distribution of oligomers, i.e. structures formed by a few loops which remain linked after digestion, quantitatively matches experimental data obtained from gel electrophoresis, provided that the density is, once again, close to the percolation transition. With respect to previous work, our analysis builds on a reduced number of assumptions, yet can still fully explain the experimental data. Our findings suggest that the kDNA can be viewed as a network of linked loops positioned very close to the percolation transition, and we discuss the possible biological implications of this remarkable fact.
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影响因子：
7.015
作者：
Michieletto, Davide;Marenduzzo, Davide;Turner, Matthew S.
通讯作者：
Turner, Matthew S.
影响因子：
11.4
作者：
Chen, JH;Englund, PT;Cozzarelli, NR
通讯作者：
Cozzarelli, NR
影响因子：
1.5
作者：
Hines, JC;Ray, DS
通讯作者：
Ray, DS
体内与动质体 DNA 网络相关的蛋白质的分离。
DOI：
10.1073/pnas.90.5.1786
发表时间：
1993
影响因子：
11.1
作者：
Xu,C;Ray,DS
通讯作者：
Ray,DS