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.

Figure 1

The probability of bubble opening as a function of bubble size and position for the AAVP5 promoter and the mutant sequence at 300 K. Probabilities in each row are normalized by a different factor $\varphi (m)=\mathrm{MAX}[⟨{\theta }_i^{[m]}{⟩}_{\mu }]$ for $i\in [1:N]$ given in the lower panel. The 69 bp sequences start at index $-46$ and end at $+23$. The TSS is at $+1$, the mutation is at $(+1,+2)$ where $(\mathrm{A},\mathrm{T})$ bases are replaced by $(\mathrm{G},\mathrm{C})$. Contrary to Ref. 3, the mutation effect is very local.

Figure 2

The probabilities for bubbles larger than 10 bp for the AAVP5 promoter and the mutant at 300 K. Both semi-PBC (threefold replicated system) and loose ends (single chain) are compared and two values for the opening threshold $y_0=1.0$ and $y_0=1.5$. MD results (black) for $y_0=1.5$ with PBC are also given with corresponding error bars. A change of scale in the $y$ axis is applied to include the higher openings at the free boundaries. All results agree but are different from the less accurate results of Ref. 3. The mutation and the free boundaries have only a local impact on the bubble statistics.

Figure 3

Same as Fig. 2 for the 86 bp AdMLP and the 63 bp nonpromoter control sequences. The biologically nonactive control sequence shows considerable opening probability, even more than the biologically active AdMLP promoter.