Analytical Approaches to Investigating the Dynamics of Genes with a Single Coding Region

Abstract

The question of how the heterogeneity of DNA, such as the presence of functionally important sites (promoters, terminators, and coding regions) in its sequence, affects the dynamic properties of the molecule, is one of the core concerns in the biophysics of DNA. Research in this field is expected to provide a deeper understanding of the role of dynamic mechanisms in the functioning of the molecule. In this paper, the dynamics of the interferon alpha 17 gene were studied. In particular, the McLaughlin–Scott analytical method was applied to solve the problem concerning the motion of transcription bubbles, which are commonly termed DNA kinks. The energy profile of the gene was constructed. The time dependencies of the kink velocity, coordinate, and total energy are found. The mechanism by which the coding region influences the kink dynamics was investigated.