Two-phase stretching of molecular chains

TL;DR

This paper introduces a unified theory explaining the two-phase stretching behavior of polymer chains, such as DNA, linking force-extension features to the energy convexity of monomer units, supported by models and experiments.

Contribution

The paper presents a novel, general theory connecting polymer stretching behavior with monomer energy profiles, validated through models and experiments on DNA and alpha-helix structures.

Findings

Polymer chains with non-convex monomer energy profiles exhibit two-phase stretching.

The force-extension plateau arises from phase separation in monomers due to energy convexity.

DNA and alpha-helix structures demonstrate the two-phase stretching mechanism.

Abstract

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a non-convex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that when the secondary structure of a polymer is mostly due to weak non-covalent interactions, the stretching is two-phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We demostrate in detail how the two-phase scenario is realized in the \alpha-helix, and in DNA double helix. The predicted plateau parameters are consistent with single molecules experiments. Detailed analysis of DNA stretching demonstrates that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double-helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.