title: Healing length and bubble formation in DNA.
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.
authors.affiliation: Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
authors.forename: Z
authors.initials: Z
authors.lastname: Rapti
authors.forename: A
authors.initials: A
authors.lastname: Smerzi
authors.forename: K O
authors.initials: KO
authors.lastname: Rasmussen
authors.forename: A R
authors.initials: AR
authors.lastname: Bishop
authors.forename: C H
authors.initials: CH
authors.lastname: Choi
authors.forename: A
authors.initials: A
authors.lastname: Usheva
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004260:DNA Repair; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008970:Molecular Weight; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA