Can one predict DNA transcription start sites by studying bubbles?
It has been speculated that bubble formation of several base pairs due to thermal fluctuations is indicatory for biologically active sites. Recent evidence, based on experiments and molecular dynamics 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 molecular dynamics. Using this method, we show that the present evidence is unsubstantiated.
van Erp
Titus S
TS
Centre Européen de Calcul Atomique et Moléculaire (CECAM), 46 allée d'Italie, 69364 Lyon Cedex 07, France.
Cuesta-Lopez
Santiago
S
Hagmann
Johannes-Geert
JG
Peyrard
Michel
M
D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D000229:Dependovirus / Q000235:genetics; D008956:Models, Chemical; D011401:Promoter Regions, Genetic; D024363:Transcription Initiation Site
D004247:DNA