Binding of molecules to DNA and other semiflexible polymers

TL;DR

This paper develops a theory for how small molecules bind to semiflexible polymers like DNA, highlighting the role of chain fluctuations in mediating interactions and how tension influences binding.

Contribution

It introduces a model for binding on semiflexible polymers, bridging the gap between flexible and stiff polymers, and explores the effects of chain stiffness and tension on binding behavior.

Findings

Fluctuations induce long-range attractive interactions between bound molecules.

Binding can become highly cooperative when it affects local chain stiffness.

External tension suppresses fluctuation-induced interactions, altering binding dynamics.

Abstract

A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers (e.g. DNA) represent an intermediate case between flexible polymers and stiff, rod-like ones, whose association with small molecules was previously studied. The chains are not flexible enough to actively participate in the self-assembly, yet their fluctuations induce long-range attractive interactions between bound molecules. In cases where the binding significantly affects the local chain stiffness, those interactions lead to a very sharp, cooperative association. This scenario is of relevance to the association of DNA with surfactants and compact proteins such as RecA. External tension exerted on the chain is found to significantly modify the binding by suppressing the fluctuation-induced interaction.