Study On The Influencing Factors Of Confined DNA Condensation Phase Transition

Whether in viruses or cells,DNA molecules exist in a compact state.Experiments show that under confined conditions,the macromolecular crowding effect can further promotes DNA condensation,and the DNA condensation process is related to the diameter of the crowder.At the same time,temperature also has a prominent effect on DNA condensation,and the increasing of temperature will promote DNA condensation,DNA condensation becomes more compact.However,the promotion mechanism of temperature on DNA condensation under confined conditions and the effect of macromolecular crowding on the DNA condensation process need to be further study.In view of this,this paper uses Monte Carlo simulation method to carry out the following work:(1)The persistence length of DNA molecules is related to temperature.Therefore,we will determine the effect of temperature on DNA condensation under confined spherical conditions.The results show that,in a spherical confined space,with increasing temperature,DNA condensation undergoes a first-order phase change,and the temperature corresponding to the phase change point is approximately linearly related to the size of the confined spherical radius.By comparing the auto-correlation function of the DNA condensation conformation before and after phase transition,the DNA molecule conformation became more compact.(2)In the confined spherical space,we compare the temperature effects and macromolecular crowding effect on the promotion of DNA molecule condensation.The results show that in the confined spherical conditions,as the volume fraction of crowders increases in the confined space,DNA molecules condensation suddenly transform from the initial linear structure into a more compact structure.Moreover,the critical volume fraction of the crowding particles has a linear relationship with itsdiameter of crowding particle;As compared with the crowding effect,the temperature effect has no prominent effect on the DNA condensed phase transition.It can be seen that under the spherical confined space condition,the effect of crowding on the phase transition of DNA condensation is stronger than that of temperature.(3)In the confined cylindrical space,the influence of aspect ratio,temperature effect and macromolecular crowding effect on DNA condensation have been determined.The results show that under the condition of cylinder confinement(the diameter of the added crowders is not changed),the temperature has an effect on DNA condensation with and without crowding effect.With the increase of temperature,the radius of DNA gyration without crowding effect decreases gradually,while the radius of DNA gyration decreases sharply with crowding effect,while the temperature has no obvious effect on DNA condensation.For the determined temperature and aspect ratio(the same kind of crowding particles),with the increase of the volume fraction of crowding particles,the dimensionless DNA radius of gyration first decreases sharply,then fluctuates within a certain volume fraction range,and finally increases sharply,corresponding to the transformation of DNA conformation from the coiled structure to the condensed state,and finally to the rod structure.When the aspect ratio is fixed,the radius R or length L of the column is constant.With the increase of the temperature,the effect of the temperature on the phase transition of DNA molecular condensation is not prominent.The phase diagram is constructed in the phase space composed of the volume fraction of crowding particles,the aspect ratio and the dimensionless radius of gyration.The results show that the critical volume fraction is inversely proportional to the aspect ratio when R is constant.When L is constant,the critical volume fraction is proportional to the aspect ratio.