Can one predict DNA Transcription Start Sites by studying bubbles?
Biological Physics
2009-11-11 v2 Computational Physics
Abstract
It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we show that the present evidence is unsubstantiated.
Keywords
Cite
@article{arxiv.physics/0508094,
title = {Can one predict DNA Transcription Start Sites by studying bubbles?},
author = {Titus S. van Erp and Santiago Cuesta-Lopez and Johannes-Geert Hagmann and Michel Peyrard},
journal= {arXiv preprint arXiv:physics/0508094},
year = {2009}
}
Comments
4 pages, 3 figures, accepted for publication in physical review letters