Figure 1.
Simplified illustration of the DNA-particle interaction model.
The one-dimensional chain (solid spheres) models the DNA chain considering a single relevant degree of freedom per base pair, and two phenomenological potentials [
and
]. The brownian particle, with coordinate
(dim ellipse), diffuses along the chain interacting with open regions through the potential
.
Figure 2.
First four PCA eigenvectors calculated for three different complete genes.
The promoter region -with the TSS highlighted- and the codifying region are pointed out. Most of the fluctuations appear localized in the promoter region, meaning that bubbles tend to form mostly here. This feature manifests the different mechanical behavior of the promoter and codifying regions, suggesting its key role in the DNA-protein interaction.
Figure 3.
DNA opening versus protein position.
Base pair mean opening (upper panels) and particle histogram (lower panels) calculated for each of the nine studied promoters. The horizontal axis represent the base pair positions counted from the coding starting point ATG (). We use this criterion to label the binding sites of the simulated promoters. The experimentally identified TSSs are shaded and their exact location marked with solid bars. In every case a peak appears close to each TSS, meaning this region is “softer” and thus likely to form bubbles, supporting their key role in regulatory processes. The total A-T content of Anabaena PCC7120 genome is around
[18]. The A-T content of each analyzed sequence is: alr0750 (61%); argC (64%); nifB (68%); conR (57%); furA (66%); furB (65%); petH (62%); petF (63%); ntcA (65%).
Table 1.
Thermo-statistical properties of studied promoters.
Figure 4.
Hierarchical free energy dendrogram for three selected promoters.
Basins of attraction separated by barriers lower than are clustered to define macrostates of the system. Their weight is indicated in the plot together with a representation of the physical state they represent, typically the particle located in a certain site where a bubble opens.