Nucleation at the DNA supercoiling transition

Area of Science:

• Biophysics
• Molecular Biology
• Computational Biology

Background:

• DNA can transition into a supercoiled plectoneme structure when subjected to torsional stress.
• Understanding the kinetics of this transition is crucial for various biological processes.

Purpose of the Study:

• To theoretically predict the rate of plectoneme nucleation in DNA.
• To reconcile theoretical predictions with experimental observations.
• To investigate the role of intrinsic DNA bending in the plectoneme transition.

Main Methods:

• Application of transition-state theory to model plectoneme nucleation.
• Analytic and numerical calculations using an elastic rod model.
• Simulation of the elastic rod model with and without sequence disorder.

Main Results:

• Predicted plectoneme nucleation rate of approximately 10^4 Hz.
• Identified viscous drag on experimental manipulation beads as a factor limiting measured rates.
• Demonstrated the significance of intrinsic base-pair sequence bending for the free-energy barrier.

Conclusions:

• The intrinsic properties of DNA, including sequence-dependent bending, play a critical role in plectoneme formation.
• Theoretical models can explain discrepancies between predicted and experimentally observed transition rates.
• Advanced computational methods are valuable for simulating complex biophysical phenomena.