Simulation Study On The Effect Of Environmental Factors And Geometric Confinement On DNA Condensation

DNA molecules as an important genetic material in the biological world,its properties have been attracted much attention.Current experiments show that temperature and crowding have significant effects on DNA condensation.For example,the increasing temperature can promote DNA condensation,crowding effect can directly lead to DNA condensation.However,the mechanism underlying the temperature and crowding effects that promote DNA condensation by multivalent cations need to be further understood.In view of which,related works carried out by using the Monte Carlo simulation are as the following,(1).Effects of temperature on the DNA condensation process.By incorporating the temperature dependence of DNA persistence length into the strong correlation model of DNA condensation,effects of temperature on the single molecule experiment process of DNA condensation was identified and the results are in agreement with the single molecule experiment.The results indicate that condensed DNA conformations at single molecule level become more compact with increasing temperature.(2).Crowding effects on DNA condensation process was systematically studied in the cross region of de Gennes and Odijk.Based on the DNA strong correlation model,DNA and crowders both confined within the confined space.The results show that,with the addition of crowders,the condensed conformations confined within the spherical space become more compact than those without crowders.The DNA condensed conformations undergo a transition from the initial random coil structure to the toroid structure,followed by the extended rod-like structure,and finally to totally compacted structure,the critical volume fraction is proportional to the diameter of the crowder with the increasing aspect ratio.In capsules confined space,the DNA condensed conformations undergo more complex transition,when the aspect ratio greater than 1.6,with the increasing of volume fraction of crowder,the totally compacted structure was extended to rod-like structure further,mainly due to crowders rearrangement,resulting in the confined space size satisfying the Odijk regimes.For the case with constant radius R,the critical volume fraction inversely proportional to aspect ratio,for the case with constant length L,the critical volume fraction is proportional to the aspect ratio.