Healing length and bubble formation in DNA

Z. Rapti, A. Smerzi, K. Rasmussen, A. R. Bishop, C. H. Choi, A. Usheva

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article number051902
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Issue number5
StatePublished - 2006

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics


Dive into the research topics of 'Healing length and bubble formation in DNA'. Together they form a unique fingerprint.

Cite this