Ratio of AT and GC Pairs in the Zones of Open States Genesis in DNA Molecules.

Abstract

Background: There is an assumption about the presence of a specific nucleotides sequence in DNA molecule, which contributes to the genesis of open states (OS). In addition, it would be logical to assume that OS zones should form in DNA regions with a large proportion of Adenine-Thymine (AT) pairs, since they contain fewer hydrogen bonds than Guanine- Cytosine (GC) base pairs. However, studies have shown that in areas rich in AT pairs, the probability of open states will not always be higher.

Methods: In this work, for two genes containing different numbers of regions with a large AT pairs proportion, we calculated the ratio of AT and GC pairs in the OS zones. For calculations, we used a coarse-grained angular mechanical DNA model.

Results: It has been established that small OS zones can appear on any part of the DNA molecule. They mainly consist of AT pairs, but as the size of OS zones increases, the content of AT pairs in them decreases.

Conclusions: The occurrence of long-length OS zones is "tied" to regions of the DNA molecule with a large proportion of AT pairs; if there are several such areas, then, depending on the magnitude of the torque, OS zones can arise in different areas of the gene. Thus, the genesis probability of large OS zones in a DNA segment depends not only on the "strength" of the nucleotide sequence of this area, but also on the factors determining the dynamics of DNA.