The fundamental role and effects of enzymes in the key processes of DNA replication and transcription have been deeply addressed during the last ten years. In fact, it is well established nowadays that the initiation of DNA transcription is tributary to the synthesis of the polymerase-RNA which is known as the main factor contributing to break the strong hydrogen bonds linking bases in pairs, for the genetic code to be exposed out of the stack. Unlocking the complexity of such a phenomenon has then been shown to mainly depend on the DNA complex structure, as it requires, among the numerous involved degrees of freedom, the unwinding of the double helix. That complexity mainly comes from its structure which is primarily made of random distributions of four types of bases, adenine (A), thymine (T), cytosine (C) and Guanine (G). Besides, the pairing of the bases respects a universal complementarity where A can bind only to T and C to G.
The bases are put together by hydrogen bonds, and the AT pair contains two H-bonds while the GC pair contains three of them. Among the models introduced to describe the dynamics of such a complex molecule, the Peyrard-Bishop (PB) model has been extensively used in the last ten years because of its capability of predicting the occurrence of denaturation bubbles as widely observed in experiments where the so-called first-order phase transition emerges. Furthermore, many studies have been carried out, showing that it support solitonic structures and is rather suitable to observe the localization of the energy which drives the key dynamical processes known as replication and transcription.
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