Defect-facilitated buckling in supercoiled double-helix DNA

Area of Science:

• Statistical mechanics
• Biophysics
• Molecular biology

Background:

• Supercoiled DNA exhibits complex structural transitions under force and ionic conditions.
• Understanding DNA mechanics is crucial for gene regulation and biotechnological applications.

Purpose of the Study:

• To develop a statistical-mechanical model for stretched, twisted double-helix DNA.
• To investigate the influence of thermal fluctuations and DNA defects on plectoneme formation.
• To explain experimental observations of DNA buckling and rebuckling transitions.

Main Methods:

• A Hamiltonian-based statistical-mechanical model was formulated without scaling hypotheses.
• The model explicitly treats thermal fluctuations in DNA elasticity.
• Simulations and comparisons with magnetic tweezer experiments were performed.

Main Results:

• The model predicts the coexistence of multiple plectoneme domains in supercoiled DNA at physiological conditions.
• Ionic strength and stretching force influence the number of plectoneme domains.
• Immobile point defects can spatially pin plectoneme domains by nucleating kinked end loops.
• A kinked end loop reduces bending energy, with a quantified reduction per unpaired base.

Conclusions:

• The model successfully describes DNA structural transitions, including defect-mediated phenomena.
• It explains experimental observations of buckling and rebuckling, providing quantitative insights.
• The model predicts novel three-state coexistence at transitions, suggesting future experimental directions.