Unwrapping of DNA-protein complexes under external stretching

TL;DR

This study investigates how DNA-protein complexes unwrap under external force, revealing different behaviors based on chain stiffness, with implications for interpreting force-extension experiments like those with nucleosomes.

Contribution

It introduces a combined simulation and phenomenological approach to analyze unwrapping dynamics, highlighting the role of chain stiffness in structural transitions.

Findings

Flexible chains show linear extension-force relationship.

Stiff chains exhibit discontinuous unwrapping with force jumps.

Ordered structures resemble nucleosomes with discrete unwinding.

Abstract

A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in space. Without stretching force, the chain is wrapped around the core. By applying an external stretching force, unwrapping of the complex is induced. We study the statics and the dynamics of the unwrapping process by computer simulation and simple phenomenological theory. We find two different scenarios depending on the chain stiffness: For a flexible chain, the extension of the complex scales linearly with the external force applied. The sphere-chain complex is disordered, i.e. there is no clear winding of the chain around the sphere. For a stiff chain, on the other hand, the complex structure is ordered, which is reminiscent to nucleosome. There is a clear winding number and the unwrapping process under external stretching is discontinuous with jumps of the distance-force curve. This is associated to discrete unwinding processes of the complex. Our predictions are of relevance for experiments, which measure force-extension curves of DNA-protein complexes, such as nucleosome, using optical tweezers.