Statistical Mechanics of Multiplectoneme Phases in DNA

new preprint: https://arxiv.org/pdf/2410.23145

Collaboration with Midas Segers(1), Enrico Skoruppa(2) and Helmut Schiessel(2) ((1):Physics of Life KU Leuven and (2):Physics of Life TU Dresden)

Summary: DNA plectonemes are intertwined loops which form when a single DNA molecule is stretched and twisted. Plectonemes are found in bacterial and eukaryotic cells and play important role in several biochemical processes as gene expression etc... By combining modeling and simulations we investigate the properties of a multiplectonemic phase, in which more than one plectoneme nucleate in a DNA molecule.

Entropy favors the proliferation of multiple plectonemes, but each new plectoneme has a nucleation free energy cost.

The theory is in excellent agreement with simulations reproducing the average number of plectonemes at various applied forces and supercoil densities (solid lines: theory, symbols: Monte Carlo simulations)...

.. the plectoneme lengths distributions (solid lines: theory, bars: MC simulations) and other quantities.

The theory predicts more plectonemes than experimentally observed, indicating a limited resolution of fluorescence experiments, likely missing plectonemes shorter than 1kb