Lengthscales and cooperativity in DNA bubble formation

Year: 2006

Authors: Rapti Z., Smerzi A., Rasmussen K.O., Bishop A.R., Choi CH., Usheva A.

Autors Affiliation: Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA; Inst Adv Study, Sch Math, Princeton, NJ 08540 USA; Los Alamos Natl Lab, Theoret Div, Los Alamos, NM 87545 USA; Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA; Univ Trent, Ist Nazl Fis Mat, BEC, CRS, I-38050 Trento, Italy; Beth Israel Deaconess Med Ctr, Boston, MA 02215 USA; Harvard Univ, Sch Med, Boston, MA 02215 USA.

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.

Journal/Review: EUROPHYSICS LETTERS

Volume: 74 (3)      Pages from: 540  to: 546

KeyWords: Peyrard-bishop Model; Statistical-mechanics; Transcription; Denaturation; Transition; Initiation
DOI: 10.1209/epl/i2005-10543-x

ImpactFactor: 2.229
Citations: 28
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