Facilitated diffusion on confined DNA

G. Foffano*, D. Marenduzzo, E. Orlandini

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


In living cells, proteins combine three-dimensional bulk diffusion and one-dimensional sliding along the DNA to reach a target faster. This process is known as facilitated diffusion and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: We find that facilitated diffusion is most efficient inside an isotropic volume and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin.

Original languageEnglish
Article number021919
Number of pages8
JournalPhysical Review E - Statistical, Nonlinear and Soft Matter Physics
Issue number2
Publication statusPublished - 22 Feb 2012




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