The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA

Abstract

We have used gel electrophoresis to measure the progress of local denaturation in closed circular pBR322 DNA as a function of temperature and linking deficiency, delta Lk. Local denaturation is closely coupled to supercoiling in closed DNA, requiring statistical mechanical methods for analysis. We have applied these methods to the experimental data to evaluate the free energies for three associated molecular processes. These processes are changes in the residual linking deficiency, delta Lkr, initiation of local denaturation, and twisting of denatured strands about one another. Our results confirm the quadratic dependence of the supercoiling free energy upon delta Lk, with a free energy coefficient of 740/N kcal/mol at 37 degrees C, where N is the number of base-pairs. The free energy of initiation of denaturation is 10.2(+/- 0.7) kcal/mol. The free energy of interstrand twisting of denatured regions varies with the square of the twist density, with proportionality coefficient C tau = 1.62 (+/- 0.11) kcal/rad2 at 37 degrees C. We have also calculated the entropy and enthalpy of these three processes, using the temperature dependence of the respective free energies. We find that both the entropy and the enthalpy of supercoiling are positive and vary quadratically with delta Lk. The free energy of initiation of denaturation is independent of temperature, hence arises primarily from a change in enthalpy. The entropy and enthalpy of interstrand twisting of denatured regions are both positive, and the twisting force constant decreases with temperature. These results differ considerably from expectations based solely upon considerations of chain configuration in vacuo, indicating the importance of solvent-dependent factors in determining the structure of closed circular DNA.