Competition between supercoils and toroids in single molecule DNA condensation

Area of Science:

• Biophysics
• Molecular Biology
• Polymer Physics

Background:

• DNA condensation into toroidal structures is a known phenomenon facilitated by multivalent ions and polypeptides.
• Recent studies indicate toroid formation persists even under tensile forces applied to DNA molecules.

Purpose of the Study:

• To investigate how combined tension and torsion influence DNA condensation in the presence of condensing agents.
• To identify competing structural states beyond toroids under these conditions.

Main Methods:

• Utilized a fluctuating elastic rod model for DNA.
• Incorporated phenomenological models for DNA interactions with condensing agents.
• Computed minimum energy configurations for DNA under varying tension and end-rotations.

Main Results:

• Introduced supercoiled DNA as a structural state competing with toroids under combined tension and torsion.
• Determined a critical number of end-rotations, above which supercoiled DNA is preferred and below which toroids dominate, for each tension level.
• Observed close agreement between model predictions and experimental data from DNA extension-rotation experiments with spermine.

Conclusions:

• The interplay of tension, torsion, and condensing agents significantly alters DNA's preferred structural states.
• Developed a phase diagram illustrating DNA states (toroids vs. supercoiled structures) as a function of tension and end-rotations.
• Identified a specific region on the phase diagram requiring further experimental or simulation-based investigation to resolve the preferred DNA state.