Target search on a dynamic DNA molecule

Details Target search on a dynamic DNA molecule Target search on a dynamic DNA molecule

2011-09-14

arxiv.org/abs/1109.3211v1

Biology

Quantitative Biology

Biomolecules

manuscript and supplementary material combined into a single document

Scientific paper

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.

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