Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting

Area of Science:

• Biophysics
• Molecular Biology
• Computational Biology

Background:

• Topologically constrained DNA, like circular plasmids, exhibits distinct melting behavior compared to linear DNA.
• The role of topology in DNA denaturation physics remains incompletely understood.
• Experimental data shows DNA melting is less abrupt for constrained molecules.

Purpose of the Study:

• To elucidate the physical mechanisms behind topology's influence on DNA melting.
• To explain the experimentally observed broadened melting transition in circular DNA.
• To investigate the relationship between supercoiling, melting, and denaturation bubble dynamics.

Main Methods:

• Large-scale Brownian dynamics simulations of DNA molecules.
• Development and application of an analytically solvable phenomenological Landau mean field theory.
• Analysis of phase coexistence and denaturation bubble growth in topologically constrained DNA.

Main Results:

• Competition between DNA melting and supercoiling drives phase coexistence of denatured and intact DNA.
• This phase coexistence occurs over a broad temperature range, explaining the broadened melting transition.
• A topology-dependent scaling law for denaturation bubble growth in supercoiled plasmids was identified.

Conclusions:

• DNA topology significantly impacts melting dynamics by inducing phase coexistence.
• The proposed mean field theory successfully explains the observed phenomena, including bubble growth scaling.
• This work provides a deeper understanding of DNA denaturation physics in topologically constrained systems.