Nicolae Radu Zabet, Boris Adryan
(Submitted on 27 Mar 2013)
We performed stochastic simulations of transcription factor (TF) molecules translocating by facilitated diffusion (a combination of 3D diffusion in the cytoplasm and 1D random walk on the DNA), and consider various abundances of cognate and non-cognate TFs to assess the influence of competitor molecules that also move along the DNA. We show that molecular crowding on the DNA always leads to longer times required by TF molecules to locate their target sites as well as to lower occupancy, which may confer a general mechanism to control gene activity levels globally. Finally, we show that crowding on the DNA may increase transcriptional noise through increased variability of the occupancy time of the target sites.