A molecule that detects the length of DNA by using chain fluctuations

TL;DR

This paper proposes a physical mechanism based on DNA chain fluctuations that explains how nucleosome remodeling motors detect and compare DNA lengths, facilitating nucleosome repositioning.

Contribution

It introduces a novel physical model linking DNA fluctuation frequency to length detection by remodeling motors, explaining their translocation behavior.

Findings

Shorter DNA chains have higher fluctuation frequencies.

Binding rates of the motor are higher for shorter chains.

Dimerization enables length comparison and nucleosome translocation.

Abstract

A class of nucleosome remodeling motors translocate nucleosomes, to which they are attached, toward the middle of DNA chain in the presence of ATP during in vitro experiments. Such a biological activity is likely based on a physical mechanism for detecting and comparing the lengths of the flanking polymer chains. Here we propose that a pivoting mode of DNA fluctuation near the surface of the nucleosome coupled with binding reaction with a DNA binding site of the motor provides a physical basis for length detection. Since the mean frequency of fluctuation is higher for a shorter chain than a longer one due to its lower drag coefficient, a shorter chain has a higher rate of receptor binding, which triggers the ATP-dependent activity of the remodeling motor. Dimerization of such units allows the motor to compare the length of the flanking DNA chains, enabling the translocation of the nucleosome toward the center of the DNA.