DNA denaturation bubbles at criticality

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 fewer than ten 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.