Quantitative approach to facilitated diffusion with intersegmental jumping

TL;DR

This paper presents a quantitative model showing how DNA coiling and intersegmental jumps enhance protein search efficiency along DNA, supported by experimental data on restriction enzymes.

Contribution

It introduces a new quantitative approach to understanding facilitated diffusion that incorporates DNA coiling and intersegmental jumping effects.

Findings

Intersegmental jumps increase search rate for DNA sites.

DNA coiling facilitates more efficient protein diffusion.

Model aligns with experimental observations of EcoRV enzymes.

Abstract

We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be captured by foreign DNA segments that have looped back close to the original segment. These intersegmental jumps are shown to enhance the search rate for a specific site on the DNA by lowering the tendency to resample previously visited sites on the DNA. The model developed here offers a quantitative description of recent single molecule experiments on facilitated diffusion of restriction enzymes EcoRV.