We present Brownian dynamics simulations of the facilitated diffusion of a protein, modeled as a sphere with a binding site on its surface, along DNA, modeled as a semiflexible polymer. We consider both the effect of DNA organization in three dimensions and of sequence heterogeneity. We find that in a network of DNA loops, which 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.

• Received 16 July 2012

DOI:https://doi.org/10.1103/PhysRevLett.109.168103