Thermodynamics of the first transition in writhe of a small circular DNA by Monte Carlo simulation.
Monte Carlo simulations are employed to investigate the thermodynamics of the first transition in writhe of a circular model filament corresponding to a 468 base-pair DNA. Parameters employed in these simulations are the torsional rigidity, C = 2.0 x 10(-19) dyne cm2, and persistence length, P = 500 A. Intersubunit interactions are modeled by a screened Coulomb potential. For a straight line of subunits this accurately approximates the nonlinear Poisson-Boltzmann potential of a cylinder with the linear charge density of DNA. Curves of relative free energy vs writhe at fixed linking difference (delta l) exhibit two minima, one corresponding to slightly writhed circles and one to slightly underwrithed figure-8's, whenever delta l lies in the transition region. The free energies of the two minima are equal when delta lc = 1.35, which defines the midpoint of the transition. At this midpoint, the free energy barrier between the two minima is found to be delta Gbar = (0.20) kBT at 298 K. Curves of mean potential energy vs writhe at fixed linking difference similarly exhibit two minima for delta l values in the transition region, and the two minimum mean potential energies are equal when delta l = 1.50. At the midpoint writhe, delta lc = 1.35, the difference in mean potential energy between the minimum free energy figure-8 and circle states is (1.3) kBT, and the difference in their entropies is 1.3 kB. Thus, the entropy of the minimum free energy figure-8 state significantly exceeds that of the circle at the midpoint of the transition. The first transition in writhe is found to occur over a rather broad range of delta l values from 0.85 to 1.85. The twist energy parameter (ET), which governs the overall free energy of supercoiling, undergoes a sigmoidal decrease, while the translational diffusion coefficient undergoes a sigmoidal increase, over this same range. The static structure factor exhibits an increase, which reflects a decrease in radius of gyration associated with the circle to figure-8 transition.
Gebe
J A
JA
Department of Chemistry, University of Washington, Seattle 98195-1700, USA.
Schurr
J M
JM
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004270:DNA, Circular / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry*; D008432:Mathematical Computing; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
D004270:DNA, Circular; D004278:DNA, Superhelical