Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

Area of Science:

• Biophysics
• Computational Biology
• Structural Biology

Background:

• Existing DNA structure data often uses short, linear sequences, limiting understanding of cellular DNA.
• Cells frequently employ bent and supercoiled DNA, necessitating studies on these conformations.

Purpose of the Study:

• To investigate DNA structural distortions in minicircles using atomistic molecular dynamics (MD) simulations.
• To compare simulation results with experimental biochemical data on DNA structural changes.

Main Methods:

• Atomistic molecular dynamics (MD) simulations were performed on DNA minicircles (65-110 base pairs).
• Simulations analyzed structural responses to bending and torsional stress.

Main Results:

• Non-canonical structures, including kinks, denaturation bubbles, and wrinkled conformations, were observed.
• Bending induced kinks in 65 bp minicircles; larger, torsionally relaxed 110 bp circles showed no defects.
• Underwinding in minicircles (65-110 bp) resulted in single-stranded bubbles and wrinkles.

Conclusions:

• Atomistic MD simulations can reveal complex DNA structures under bending and torsional stress.
• Bending and underwinding are critical factors in forming non-canonical DNA structures within minicircles.