Lengthscales and cooperativity in DNA bubble formation

¹ Center for Nonlinear Studies, Los Alamos National Laboratory Los Alamos, NM 87545, USA
² School of Mathematics, Institute for Advanced Study Einstein Drive 1, Princeton, NJ 08540, USA
³ Theoretical Division and Center for Nonlinear Studies Los Alamos National Laboratory - Los Alamos, NM 87545, USA
⁴ Istituto Nazionale di Fisica per la Materia BEC-CRS, Università di Trento I-38050 Povo, Italy
⁵ Beth Israel Deaconess Medical Center and Harvard Medical School 99 Brookline Avenue, Boston, MA 02215, USA

Received: 11 October 2005
Accepted: 28 February 2006

Abstract

It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of adenine-thymine pairs in specific regions with lengths which at physiological temperatures are of the order of (but not equal to) the size of the bubble. Our analysis is based on the Peyrard-Bishop-Dauxois model, whose equilibrium statistical properties have been accurately calculated here with a transfer integral approach.