2011/09/14 by Thomas Schötz, Richard A. Neher, Ulrich Gerland · 19 citations
Biochemistry, Genetics and Molecular Biology · Engineering · Mathematics · Medicine · Physics and Astronomy · #Artificial intelligence #Biological system #Biology #Biophysics #Computational biology #Computer science #Crossover #DNA #Diffusion and Search Dynamics #Genetics #Limit (mathematics) #Mathematical and Theoretical Epidemiology and Ecology Models #Mathematics #Molecular dynamics #Physics #Plasmonic and Surface Plasmon Research #Quantum mechanics #Statistical physics #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.1103/physreve.84.051911
published in Physical Review E 84(5), 051911 (American Physical Society) · manuscript and supplementary material combined into a single document
arxiv created 2011/09/14 · openalex publication_date 2011/11/17 · arxiv updated 2015/05/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
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 three-dimensional space. A strongly binding protein that searches by one-dimensional sliding and jumping alone explores the search space less redundantly when the DNA dynamics is fast on the time scale 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.