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. 2013 Oct 8;42(2):727–738. doi: 10.1093/nar/gkt907

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© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Influence of macromolecular crowding on gene regulation kinetics. (A) NAPs cause shrinking of available searching volume by linking and bending of DNA chains. NAPs when bound to DNA disturb non-specific association of TFs and 1D diffusion along DNA (12). Macromolecular crowding increases viscosity of the cytoplasm and diminishes TF 1D and 3D-mobility constants [Equations (1–2)]. The viscosity experienced by a translocating macromolecule is a stretched exponential function of size of the macromolecule (13,14). (B) TF searches for specific site on DNA through numerous DNA–non-specific associations. Three-dimensional diffusion brings TF close to DNA. Next, TF binds to DNA with microscopic association rate constant k_i (8). Non-specifically bound TF slides performing curvilinear motion (16,19) along DNA and dissociates with rate constant λ.