Theory of Bubble Nucleation and Cooperativity in DNA Melting

TL;DR

This paper investigates DNA melting and bubble formation using a computational model, achieving excellent agreement with experiments and exploring critical factors influencing DNA stability and transition states.

Contribution

It introduces a parameter-free Monte Carlo simulation approach to study DNA denaturation bubbles and compares results with experimental data, providing new insights into DNA melting behavior.

Findings

Excellent agreement between simulations and experiments

Identification of critical DNA segment length for bubble stability

Evidence supporting a two-state transition in DNA melting

Abstract

The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles and the possibility of a two states transition are studied.