Two-phase dynamics of DNA supercoiling based on DNA polymer physics.

Area of Science:

• Biophysics
• Molecular Biology
• Genomics

Background:

• DNA supercoiling is crucial for genome regulation processes like transcription and replication.
• Under tension, DNA supercoils exhibit coexistence of plectonemic and stretched phases with dynamic behaviors.

Purpose of the Study:

• To develop a dynamic model for DNA supercoiling that captures essential behaviors across multiple timescales.
• To represent the conformational changes and dynamics of DNA supercoils, including plectoneme behavior.

Main Methods:

• Developed a two-phase dynamic model based on timescale separation of DNA supercoil dynamics.
• Identified two-phase boundaries as collective slow variables to describe essential dynamics.
• Compared numerical results with the DNA polymer physics-based worm-like chain model.

Main Results:

• The two-phase model accurately represents DNA supercoiling dynamics, including plectoneme nucleation, diffusion, and hopping.
• The model captures physiologically relevant events across vastly different timescales.
• Achieved accurate reproduction of supercoiling dynamics at significantly reduced computational cost.

Conclusions:

• The developed two-phase dynamic model provides an efficient and accurate method for studying DNA supercoiling.
• This model can be applied to explore multiscale physical mechanisms underlying DNA supercoiling-dependent physiological processes.