Healing length and bubble formation in DNA
Year: 2006
Authors: Rapti Z., Smerzi A., Rasmussen K.O., Bishop A.R., Choi C.H., Usheva A.
Autors Affiliation: Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA; Univ Illinois, Dept Math, Urbana, IL 61801 USA; Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA; Univ Trent, INFM, CNR, BEC, I-38050 Trento, Italy; Beth Israel Deaconess Med Ctr, Dept Med, Boston, MA 02215 USA; Harvard Univ, Sch Med, Boston, MA 02115 USA.
Abstract: It has been suggested that thermally induced separations (bubbles) of the DNA double-strand may play a role in the initiation of gene transcription, and an accurate understanding of the sequence dependence of thermal strand separation is therefore desirable. Based on the Peyrard-Bishop-Dauxois model, we show here that the bubble forming ability of DNA can be quantified in terms of a healing length L(n), defined as the length (number of base-pairs) over which a base-pair defect affects bubbles involving n consecutive base-pairs. The probability for a bubble of size n is demonstrated to be proportional to the number of adenine-thymine base-pairs found within this length. The method for calculating bubble probabilities in a given sequence derived from this notion requires several order of magnitude less numerical effort than direct evaluation.
Journal/Review: PHYSICAL REVIEW E
Volume: 73 (5) Pages from: 51902-1 to: 51902-5
KeyWords: ModelDOI: 10.1103/PhysRevE.73.051902ImpactFactor: 2.438Citations: 32data from “WEB OF SCIENCE” (of Thomson Reuters) are update at: 2024-11-10References taken from IsiWeb of Knowledge: (subscribers only)
