Target search on a dynamic DNA molecule

Abstract

We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA contour but close in 3D space. A strongly binding protein that searches by 1D sliding and jumping alone, explores the search space less redundantly when the DNA dynamics is fast on the timescale of protein jumps than in the opposite "frozen DNA" limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in "islands" within random DNA configurations in solution.

manuscript and supplementary material combined into a single document

References in corpus (4)

• Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential
• Spatial effects on the speed and reliability of protein-DNA search
• Effects of intersegmental transfers on target location by proteins
• Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation

Cited by in corpus (4)

• Lévy Noise Induced Switch in the Gene Transcriptional Regulatory System
• Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
• Reverse-time analysis uncovers universality classes in directional biological dynamics
• Linear Response Theory for Nonlinear Stochastic Differential Equations with $\alpha$-stable Lévy Noises