Hysteresis in Pressure-Driven DNA Denaturation

In the past, a great deal of attention has been drawn to thermal driven denaturation processes. In recent years, however, the discovery of stress-induced denaturation, observed at the one-molecule level, has revealed new insights into the complex phenomena involved in the thermo-mechanics of DNA function. Understanding the effect of local pressure variations in DNA stability is thus an appealing topic. Such processes as cellular stress, dehydration, and changes in the ionic strength of the medium could explain local pressure changes that will affect the molecular mechanics of DNA and hence its stability. In this work, a theory that accounts for hysteresis in pressure-driven DNA denaturation is proposed. We here combine an irreversible thermodynamic approach with an equation of state based on the Poisson-Boltzmann cell model. The latter one provides a good description of the osmotic pressure over a wide range of DNA concentrations. The resulting theoretical framework predicts, in general, the process of denaturation and, in particular, hysteresis curves for a DNA sequence in terms of system parameters such as salt concentration, density of DNA molecules and temperature in addition to structural and configurational states of DNA. Furthermore, this formalism can be naturally extended to more complex situations, for example, in cases where the host medium is made up of asymmetric salts or in the description of the (helical-like) charge distribution along the DNA molecule. Moreover, since this study incorporates the effect of pressure through a thermodynamic analysis, much of what is known from temperature-driven experiments will shed light on the pressure-induced melting issue

Denaturation curves for cylindrical DNA cells.

<p>Typical parameters of linear charge density, , salt concentration, and temperature, °C, are considered.</p

Wigner-Seitz cell model (6 cells shown) for DNA molecules under PB cell model.

<p>Every cylinder has a radius with the radius of a DNA molecule, i.e. , and as stated is the volume fraction.</p

Denaturation curves for spherical DNA cells.

<p>Typical parameters of charge for globular biomolecules, , salt concentration, and temperature, °C, are considered.</p

Reduced osmotic pressure versus energy dissipation for() [No hydrogen bond broken] in cylindrical biomolecules.

<p>Reduced osmotic pressure versus energy dissipation for() [No hydrogen bond broken] in cylindrical biomolecules.</p

Denaturation curves for spherical biomolecules in suspension.

<p>The value of , Temperature is as follows: (a) , (b) , (c) y (d) . All plots correspond to the same sequence.</p

Osmotic pressure versus volume fraction for cylindrical macroions at different salt concentrations.

<p>Osmotic pressure versus volume fraction for cylindrical macroions at different salt concentrations.</p

Normalized isothermal compressibility () for cylindrical macroions at different salt concentrations.

<p>The inset corresponds to the no-salt case.</p

, the fraction of broken hydrogen bonds as a function of the reduced osmotic pressure for cylindrical biomolecules.

<p>This plot corresponds to the low-salt regime . and under charge saturation conditions and at T = . (i.e. the melting temperature for this sequence).</p