Thermodynamics of DNA denaturation in a model of bacterial intergenic sequences

We present a detailed investigation of the denaturation process for intergenic sequences of several bacterial species. The reason for analyzing these specific sequences is that these regions are expected to be denaturated to allow for the intrusion of the transcription factors performing the transcription process of genes. Our study relies upon a well known dynamical model of the DNA double-strand proposed by Dauxois-Peyrard-Bishop [44], applied to the collection of intergenic regions from bacterial species. We have performed extended numerical simulations in the presence of a thermostat (canonical setup) and we have found that all of these indicators essentially identify a typical denaturation temperature. This confirms the reliability and robustness of the denaturation thermodynamics described by this model. We want to remark also that the actual value of the denaturation temperature, as expected, varies from species to species, because of the different structural features of the corresponding intergenic sequences. Another important result reported in this manuscript is that the comparison with simulations in the absence of a thermostat (microcanonical setup) yields sensibly higher, irrealistic denaturation temperatures, thus providing evidence that thermal fluctuations play a crucial role in the cooperative effect yielding the denaturation process.