Modelling the thermal evolution of enzyme-created bubbles in DNA

Area of Science:

• Biophysics
• Nonlinear Dynamics
• Molecular Biology

Background:

• Nucleic acids (NAs) bubble formation is crucial for DNA replication, repair, and RNA processes.
• Enzymatic complexes typically separate NA regions during these biological functions.

Purpose of the Study:

• To model DNA duplex structure using nonlinear dynamics and coupled oscillators.
• To investigate the origin and characteristics of oscillating localized patterns (breathers) in DNA.
• To analyze the temperature dependence and stability of these breathers.

Main Methods:

• A nonlinear network of coupled oscillators was used to model the DNA duplex.
• The Nosé-Hoover method was employed to simulate the system in contact with a heat bath.
• Analysis focused on radial and torsional breathers associated with H-bond deformations.

Main Results:

• Local structural distortions in DNA can generate radial and torsional breathers, mimicking replication bubbles.
• These oscillating breathers demonstrate stability against thermal perturbations up to room temperature.
• At non-zero temperatures, breathers exhibit coherent movement along the DNA double chain; at T=0, they are standing.

Conclusions:

• Nonlinear dynamics provide a framework for understanding NA bubble formation via breathers.
• Radial and torsional breathers are robust localized structures within the DNA duplex, even under thermal stress.
• The findings offer insights into the physical mechanisms underlying essential NA-related biological processes.