Healing Length and Bubble Formation in Dna.
From: Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
Physical review. E, Statistical, nonlinear, and soft matter physics
- Publish Date: May 2006
- ISSN: 1539-3755
- Volume: 73
- Issue: 5 Pt 1
- Pages: 051902
- Medium: Print
- Language: English
- Citation (JAMA): Rapti Z, Smerzi A, Rasmussen K O, et al. Healing Length and Bubble Formation in Dna.. May 2006;73:051902
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.
Mesh Headings (Keywords): Base Pairing, Base Sequence, Binding Sites, Computer Simulation, DNA, DNA Repair, Models, Chemical, Models, Molecular, Molecular Sequence Data, Molecular Weight, Nucleic Acid Conformation, Nucleic Acid Denaturation, Sequence Analysis, DNA
Check for Full Text / PubMed Unique Identifier (PMID): 16802962
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