Kinetic signature of cooperativity in the irreversible collapse of a polymer

TL;DR

This study explores the kinetics of polymer collapse caused by irreversible crosslinking, revealing a cooperative pearling transition characterized by a specific length scale, confirmed through simulations and DNA experiments.

Contribution

It introduces a novel kinetic analysis of polymer collapse showing a cooperative pearling instability and links it to experimental DNA data.

Findings

Identification of a sharp conformational transition to pearl-like states.

Dependence of transition time and pearl size on polymer dynamics and crosslinking rate.

Experimental confirmation using DNA conformation capture in yeast.

Abstract

We investigate the kinetics of a polymer collapse due to the formation of irreversible crosslinks between its monomers. Using the contact probability $P(s)$ as a scale-dependent order parameter depending on the chemical distance $s$, our simulations show the emergence of a cooperative pearling instability. Namely, the polymer undergoes a sharp conformational transition to a set of absorbing states characterized by a length scale $\xi$ corresponding to the mean pearl size. This length and the transition time depend on the polymer equilibrium dynamics and the crosslinking rate. We confirm experimentally this transition using a DNA conformation capture experiment in yeast.