Supercoiling DNA with a free end

Area of Science:

• Biophysics
• Polymer Physics
• Computational Biology

Background:

• DNA supercoiling is crucial for genomic functions.
• Understanding DNA mechanics under torque is essential.
• Open DNA end dynamics present unique challenges.

Purpose of the Study:

• Investigate supercoiling dynamics in open DNA under constant torque.
• Analyze steady-state twist and writhe profiles.
• Explore the transition between DNA phases.

Main Methods:

• Coarse-grained Brownian dynamics simulations.
• Mean-field theory analysis.
• Modeling of DNA polymer under applied torque.

Main Results:

• Observed a critical torque threshold for phase transition (swollen to plectonemic).
• Identified non-linear, inhomogeneous twist profiles in the plectonemic phase.
• Demonstrated diffusive twist accumulation and negligible writhe diffusion.

Conclusions:

• DNA supercoiling is torque-dependent, even with a free end.
• Plectoneme formation is localized near the torque application point.
• Results provide a framework for single-molecule experiment comparisons.