Elastic stability of DNA configurations. II. Supercoiled plasmids with self-contact

Area of Science:

• Biophysics
• Polymer Physics
• Computational Biology

Background:

• Understanding the three-dimensional configurations of DNA is crucial for its biological functions.
• Protein-free DNA miniplasmids offer a simplified model to study DNA mechanics.
• Previous work established stability criteria for DNA configurations.

Purpose of the Study:

• To calculate and analyze the stable configurations of protein-free DNA miniplasmids.
• To investigate the role of impenetrability and self-contact forces in DNA structure.
• To identify regions of stability on bifurcation diagrams using established criteria.

Main Methods:

• Exact solutions of Kirchhoff's equations for elastic rods of circular cross-section were employed.
• Bifurcation diagrams plotting excess link (DeltaL) versus writhe (W) were generated.
• Stability criteria from prior research were applied to locate stable configurations.

Main Results:

• Primary bifurcation branches exhibit D(m) symmetry, with secondary and tertiary branches showing lower symmetries.
• A specific configuration in the primary branch (m=2, branch alpha) is stable if dDeltaL/dW > 0.
• Nonplanar, contact-free configurations outside branch alpha are generally unstable.

Conclusions:

• The study identifies specific stable configurations for protein-free DNA miniplasmids based on elastic properties.
• The findings highlight the importance of symmetry and the DeltaL-W relationship for DNA stability.
• A previously observed rule regarding self-contact and DeltaL magnitude holds for these miniplasmid configurations.