alexa Force-induced melting of the DNA double helix. 2. Effect of solution conditions.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Computer Science & Systems Biology

Author(s): Rouzina I, Bloomfield VA

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Abstract 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 temperature, the overstretching force, f(ov)(T), is predicted to decrease nearly linearly with temperature. We calculate the slope of this dependence as a function of entropy and heat-capacity changes upon DNA melting. Fitting of the experimental f(ov)(T) dependence allows determination of both of these quantities in very good agreement with their calorimetric values. At temperatures slightly above the regular DNA melting temperature, we predict stabilization of dsDNA by moderate forces, and destabilization by higher forces. Thus the DNA stretching curves, f(b), should exhibit two rather than one 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 calculate the dependence of DNA overstretching force on solution pH, f(ov)(pH), from 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., accepted for publication). Finally, we quantitatively explain the measured dependence of DNA overstretching force on solution ionic strength for crosslinked and noncrosslinked DNA. The much stronger salt dependence of f(ov) in noncrosslinked DNA results from its lower linear charge density in the melted state, compared to crosslinked or double-stranded overstretched S-DNA.
This article was published in Biophys J and referenced in Journal of Computer Science & Systems Biology

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