DNA denaturation bubbles at criticality

TL;DR

This paper investigates the statistical properties of DNA denaturation bubbles near critical temperature using the Peyrard-Bishop-Dauxois model, highlighting the role of nonlinear stacking interactions in bubble formation and shape.

Contribution

It provides a detailed analysis of how nonlinear stacking influences bubble formation and shape, especially near the critical temperature in DNA denaturation models.

Findings

Small bubbles have higher free energy per site than larger ones.

Approaching critical temperature, free energy for bubble growth diminishes.

Nonlinear stacking affects the scaled shape of bubbles.

Abstract

The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of nonlinear base-stacking interactions. Small bubbles extending over less than 10 base pairs are associated with much larger free energies of formation per site than larger bubbles. As the critical temperature is approached, the free energy associated with further bubble growth becomes vanishingly small. An analysis of average displacement profiles of bubbles of varying sizes at different temperatures reveals almost identical scaled shapes in the absence of nonlinear stacking; nonlinear stacking leads to distinct scaled shapes of large and small bubbles.