ON THE ORIGIN OF THE TEMPERATURE-DEPENDENCE OF THE SUPERCOILING FREE-ENERGY

Monte Carlo simulations using temperature-invariant torsional and bend ing rigidities fail to predict the rather steep decline of the experim ental supercoiling free energy with increasing temperature, and conseq uently fail to predict the correct sign and magnitude of the supercoil ing entropy. To illustrate this problem, values of the twist energy pa rameter (E-tau), which governs the supercoiling free energy, were simu lated using temperature-invariant torsion and bending potentials and c ompared to experimental data on pBR322 over a range of temperatures. T he slope, -dE(T)/dT, of the simulated values is also compared to the s lope derived from previous calorimetric data. The possibility that the discrepancies arise from some hitherto undetected temperature depende nce of the torsional rigidity was investigated, The torsion elastic co nstant of an 1876-bp restriction fragment of pBR322 was measured by ti me-resolved fluorescence polarization anisotropy of intercalated ethid ium over the range 278-323 K, and found to decline substantially over that interval, Simulations of a 4349-bp model DNA were performed using these measured temperature-dependent torsional rigidities, The slope, -dE(T)/dT, of the simulated data agrees satisfactorily with the slope derived from previous calorimetric measurements, but still lies subst antially below that of Duguet's data, Models that involve an equilibri um between different secondary structure states with different intrins ic twists and torsion constants provide the most likely explanation fo r the variation of the torsion constant with T and other pertinent obs ervations.