Ensemble of DNA Kinks

L V Yakushevich ,L A Krasnobaeva

doi:10.1051/epjconf/201922403005

Abstract

The DNA open states, which are locally unwound regions of the double helix within which hydrogen bonds between complementary nitrous bases are broken, are often modeled as quasiparticles – DNA kinks. Most of the works on the DNA kinks are devoted to the studies of their dynamic properties, as well as their role in the functioning of the molecule. However, if not one but N open states are formed in the DNA molecule it is reasonable to consider the problem of the statistics of the ensemble of N DNA kinks. The statistical properties of such an ensemble are still poorly understood. In the present work, we study these properties applying new data on the dynamic characteristics of DNA kinks.

Highlights

When studying the internal conformational mobility of the DNA molecule by various experimental methods and, in particular, by the method of hydrogen-tritium exchange [1], the researchers found that locally unwound regions called open states or bubbles [2], can be formed in the DNA double helix
It can be seen from formulas (18) - (21) and from the graphs presented in Figures 3, 4 that with increasing temperature, the average energy and the entropy increase, the free the energy decreases, and the heat capacity remains constant for any temperature T
We studied statistical properties of ensemble of the DNA kinks which simulate the open states of the molecule

Summary

Introduction

When studying the internal conformational mobility of the DNA molecule by various experimental methods and, in particular, by the method of hydrogen-tritium exchange [1], the researchers found that locally unwound regions called open states or bubbles [2], can be formed in the DNA double helix. If the DNA molecule is long enough, it can form not one, but several open states, and it is legitimate to raise the question of the statistical properties of such an ensemble. This question was raised in the monograph [3]. A possibility to apply statistical characteristics of kinks in the calculations the dynamic form factor of neutron scattering on DNA was considered in [14]. The question of the statistics of the DNA kinks ensemble is investigated taking into account new data on the DNA dynamic parameters. All calculations are performed for kinks activated in the pBR322 plasmid which is a small circular DNA widely applied in gene research, and its components are used to create new instrumental plasmids [15]

DNA internal dynamics

Dynamic characteristics of DNA kinks

Statistical characteristics of an ensemble of DNA kinks

Velocity distribution function of DNA kinks

Discussion and conclusion