Mechanical response to tension and torque of molecular chains via statistically interacting particles associated with extension, contraction, twist, and supercoiling

TL;DR

This paper extends a statistical mechanical model to analyze how polymeric chains, especially DNA, respond to combined tension and torque, capturing conformational changes and supercoiling phenomena.

Contribution

It introduces a methodology that incorporates torque into the analysis of polymer chains, enabling detailed modeling of twist, supercoiling, and conformational transitions.

Findings

Successfully models B-DNA, S-DNA, and P-DNA conformations.

Describes the conversion between twist and supercoiling during buckling.

Aligns with experimental data on DNA under tension and torque.

Abstract

A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination of tension and torque involves, in the framework of this method of analysis, the (thermal or mechanical) activation of a specific mix of statistically interacting particles carrying quanta of extension or contraction and quanta of twist or supercoiling. The methodology, which is elucidated in applications of increasing complexity, is capable of describing the conversion between twist chirality and plectonemic chirality in quasistatic processes. The control variables are force or extension and torque or linkage (a combination of twist and writhe). The versatility of this approach is demonstrated in two applications relevant and promising for double-stranded DNA under controlled tension and torque. One application describes conformational transformations between (native) B-DNA, (underwound) S-DNA, and (overwound) P-DNA in accord with experimental data. The other application describes how the conversion between a twisted chain and a supercoiled chain accommodates variations of linkage and excess length in a buckling transition.