Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA

Area of Science:

• Structural biology
• Biophysics
• Computational biology

Background:

• DNA can adopt complex structures like plectonemes under supercoiling.
• Transitions between different DNA structural phases are not fully understood.

Purpose of the Study:

• To predict and characterize a novel DNA conformational regime involving denaturation bubbles at plectoneme tips.
• To investigate the properties and implications of this regime using computational simulations.

Main Methods:

• Coarse-grained simulations were employed to model DNA behavior.
• The study focused on DNA under negative supercoiling conditions.

Main Results:

• A novel conformational regime was predicted where denaturation bubbles form at plectoneme tips.
• This regime explains the broad transition between bubble-dominated and plectoneme-dominated DNA phases observed experimentally.
• Tip bubbles localize plectonemes in AT-rich sequences and can pin them, suppressing diffusion.
• These phenomena occur under biologically relevant supercoiling densities and forces.

Conclusions:

• The predicted DNA conformational regime with tip bubbles offers a new perspective on DNA structure and dynamics.
• This finding has potential implications for biological control of genomic processes in vivo.