Statistical Mechanics of Multiplectoneme Phases in DNA

TL;DR

This paper develops a simple theoretical model for multiple plectoneme formation in stretched, supercoiled DNA, showing good agreement with simulations and explaining the discrepancy with experimental observations.

Contribution

It extends the two-phase model to include multiple plectonemes by incorporating positional and length entropy, providing a more comprehensive understanding of DNA supercoiling.

Findings

The theory predicts multiple plectonemes in long DNA molecules.

Good agreement with Monte Carlo simulations of the twistable wormlike chain.

Experimental plectoneme counts are lower due to resolution limits.

Abstract

A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled DNA, allowing for the coexistence of multiple plectonemic domains by including positional and length distribution entropies. Such a multiplectoneme phase is favored in long DNA molecules in which the gain of positional entropy compensates for the cost of nucleating a plectoneme along a stretched DNA segment. Despite its simplicity, the developed theory is shown to be in excellent agreement with Monte Carlo simulations of the twistable wormlike chain model. The theory predicts more plectonemes than experimentally observed, which we attribute to the limited resolution of experimental data. Since plectonemes are detected through fluorescence signals, those shorter than the observable threshold are likely missed.