Can one predict DNA Transcription Start Sites by studying bubbles?

Details Can one predict DNA Transcription Start Sites by studying bubbles? Can one predict DNA Transcription Start Sites by studying bubbles?

2005-08-15

arxiv.org/abs/physics/0508094v2

Physics

Biological Physics

4 pages, 3 figures, accepted for publication in physical review letters

Scientific paper

10.1103/PhysRevLett.95.218104

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.

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