Facilitated diffusion on confined DNA

Abstract

In living cells, proteins combine 3D bulk diffusion and 1D 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.

References in corpus (4)

• First-passage times in complex scale-invariant media
• Effects of intersegmental transfers on target location by proteins
• Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model
• Facilitated diffusion of DNA-binding proteins: Simulation of large systems

Cited by in corpus (6)

• Distance matters: the impact of gene proximity in bacterial gene regulation
• In vivo facilitated diffusion model
• Intracellular facilitated diffusion: searchers, crowders and blockers
• Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
• The effects of transcription factor competition on gene regulation
• Physical constraints determine the logic of bacterial promoter architectures