Lengthscales and cooperativity in DNA bubble formationZ. Rapti1, 2, A. Smerzi3, 4, K. Ø. Rasmussen3, A. R. Bishop3, C. H. Choi5 and A. Usheva5
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 in final form 28 February 2006
published online 24 March 2006
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.
87.15.Aa - Theory and modeling; computer simulation.
87.15.Ya - Fluctuations.
87.15.He - Dynamics and conformational changes.
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