Study On The Thermodynamic And Kinetic Properties Of DNA Hairpin Structure Based On Ox-DNA Model

This paper studies the related properties of thermodynamics and kinetics of DNA hairpin structural transformation based on ox-DNA model.By using the method of Langevin dynamics to simulate the two-state transition process of DNA hairpin structure,the following work is carried out mainly from the aspects of temperature and pulling force:(1)DNA hairpin study of the thermodynamic properties of single molecules.the phase transformation behavior of DNA hairpin single molecules of short sequences at different temperatures was studied under ox-DNA model using molecular dynamics simulation.The study found that the DNA hairpin single molecule opening probability of short sequence is related to the temperature of the system.When the temperature is relatively low,DNA hairpin single molecule is almost all in the closed state,the open state will only appear with low probability.as the temperature increases,the frequency of the open state arising from the temperature increases.as the temperature increases to higher,almost all DNA hairpin single molecules are on.DNA hairpin the single molecule opening probability has a quantitative relationship with temperature and can be explained from the perspective of the two-state model.(2)DNA hairpin study of single molecular dynamics.the temperature of the fixed system is constant,its simulation method,model and sequence of DNA hairpin single molecule are unchanged,only a constant pulling force in the opposite direction is applied at both ends of the DNA hairpin single molecule in the system.it is found that at different temperatures,the probability of DNA hairpin single molecule in quantitatively related to the applied constant pulling force size at different temperatures,which can be explained from the angle of the two-state model with pulling force and the Bell model,and the critical force is linearly related to the temperature,and quantitative analysis of the temperature and open a base pair of energy relationship.Also studied the tensile-temperature phase diagram can be obtained by applying linear force at both ends of the DNA hairpin at different temperatures.the phase diagram shows that the fracture force(rupture force)is linearly related to the temperature,and both the tensile force and the temperature are favorable for the opening of the DNA hairpin.this result is consistent with the results of a large number of single molecule experiments.above results can be beneficial to people's understanding of the thermodynamic and kinetic properties of short sequences DNA hairpin single molecules in pulling force action.