Abstract
Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation—dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases’ vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.
Highlights
Water is a universal solvent and medium in which most biochemical and biophysical reactions take place in the body
We investigated the mechanical properties of DNA using a mechanical mathematical model
It has been shown that an increase in viscosity leads to the rapid stabilization of angular vibrations, while a decrease in viscosity changes the dynamics of the DNA molecule: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the chains of the DNA molecule increase at each moment of time
Summary
Water is a universal solvent and medium in which most biochemical and biophysical reactions take place in the body. The free energy of the DNA nitrogenous bases pairs interactions [9,10,11,12] as well as the energy localization in it [13] depend on the parameters of the solvent. The dependence of the free energies of the nitrogenous bases stacking on the aqueous environment was noted [14]. It is obvious that it is necessary to consider biopolymers, taking into account the entropy and their interaction with the aqueous environment [16,17,18]. We investigated the mechanical properties of DNA using a mechanical mathematical model. The influence of the viscosity of the external environment on the internal dynamics and stability of the DNA molecule was investigated by the method of mathematical modeling
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
