Title: Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity Show Chinese title

Title: 移动DNA上的促进扩散：构型陷阱和序列异质性

Abstract: We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in 3D, and of sequence heterogeneity. We find that in a network of DNA loops, as are thought to be present in bacterial DNA, the search process is very sensitive to the spatial location of the target within such loops. Therefore, specific genes might be repressed or promoted by changing the local topology of the genome. On the other hand, sequence heterogeneity creates traps which normally slow down facilitated diffusion. When suitably positioned, though, these traps can, surprisingly, render the search process much more efficient. Show Chinese abstract

Abstract: 我们展示了对蛋白质在DNA上促进扩散的布朗动力学模拟，其中蛋白质被建模为带有表面结合位点的球体，DNA被建模为半柔性聚合物。我们考虑了DNA在三维中的组织结构以及序列异质性的影响。我们发现，在如细菌DNA中被认为存在的DNA环网络中，搜索过程对目标在这些环内的空间位置非常敏感。因此，特定基因可能通过改变基因组的局部拓扑结构而被抑制或促进。另一方面，序列异质性会产生陷阱，通常会减缓促进扩散。然而，当这些陷阱处于适当的位置时，出人意料地可以使搜索过程更加高效。