Force-induced melting of the DNA double helix. 2. Effect of solution conditions

In this paper, we consider the implications of the general theory developed in the accompanying paper, to interpret experiments on DNA overstretching that involve variables such as solution temperature, pH, and ionic strength . We find the DNA helix-coil phase boundary in the force-temperature space. At temperatures significantly below the regular (zero force) DNA melting t emperature, the overstretching force, f(ov)(T), is predicted to decrease ne arly linearly with temperature. We calculate the slope of this dependence a s a function of entropy and heat-capacity changes upon DNA melting. Fitting of the experimental f(ov)(T) dependence allows determination of both of th ese quantities in very good agreement with their calorimetric values. At te mperatures slightly above the regular DNA melting temperature, we predict s tabilization of dsDNA by moderate forces, and destabilization by higher for ces. Thus the DNA stretching curves, f(b), should exhibit two rather than o ne overstretching transitions: from single stranded (ss) to double stranded (ds) and then back at the higher force. We also predict that any change in DNA solution conditions that affects its melting temperature should have a similar effect on DNA overstretching force. This result is used to calcula te the dependence of DNA overstretching force on solution pH, f(ov)(pH), fr om the known dependence of DNA melting temperature on pH. The calculated f( ov)(pH) is in excellent agreement with its experimental determination (M. C . Williams, J. R. Wenner, I. Rouzina, and V. A. Bloomfield, Biophys. J., ac cepted for publication). Finally, we quantitatively explain the measured de pendence of DNA overstretching force on solution ionic strength for crossli nked and noncrosslinked DNA. The much stronger salt dependence of f(ov) in noncrosslinked DNA results from its lower linear charge density in the melt ed state, compared to crosslinked or double-stranded overstretched S-DNA.