Equilibrium fluctuations of DNA plectonemes

Area of Science:

• Biophysics
• Molecular Biology
• Polymer Physics

Background:

• Plectonemes, or intertwined helical loops, form in supercoiled DNA and are crucial in cellular contexts.
• Understanding the physical properties of supercoiled DNA, including its fluctuations, is vital for molecular biology and biophysics.
• Previous research has explored both experimental and modeling approaches to study DNA's physical behavior.

Purpose of the Study:

• To investigate the fluctuations in end-point distance (z) of supercoiled linear DNA molecules subjected to external stretching forces.
• To identify the dominant mechanisms contributing to extension fluctuations (variance 〈Δz^{2}〉) in supercoiled DNA.
• To validate a two-phase model for supercoiled DNA behavior under force.

Main Methods:

• Development and application of a two-phase model describing supercoiled DNA as a combination of stretched and plectonemic phases.
• Analysis of extension fluctuations using Monte Carlo simulations of the twistable wormlike chain model.
• Investigation of various fluctuating quantities to compare simulation results with theoretical predictions.

Main Results:

• Phase-exchange fluctuations, involving the transient shrinking and expansion of plectonemes and length exchange between phases, are identified as the dominant contributor to extension variance 〈Δz^{2}〉.
• Monte Carlo simulations of the twistable wormlike chain show results consistent with the predictions of the two-phase model.
• The two-phase model accurately captures DNA extension and its variance at high forces, particularly when exceeding quadratic approximations.

Conclusions:

• Phase-exchange dynamics are the primary driver of extension fluctuations in supercoiled DNA under stretching forces.
• The developed two-phase model provides a robust framework for understanding the physical behavior of supercoiled DNA, especially at high forces.
• Further refinement of the two-phase model beyond quadratic approximations is essential for precise prediction of DNA extension and variance.