title: Hysteresis in pressure-driven DNA denaturation.
abstract: 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.
authors.affiliation: Computational Genomics Department, National Institute of Genomic Medicine, México, DF, México. ehernandez@inmegen.gob.mx
authors.forename: Enrique
authors.initials: E
authors.lastname: Hernández-Lemus
authors.forename: Luz Adriana
authors.initials: LA
authors.lastname: Nicasio-Collazo
authors.forename: Ramón
authors.initials: R
authors.lastname: Castañeda-Priego
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D008433:Mathematics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009994:Osmolar Concentration; D009997:Osmotic Pressure; D012492:Salts / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
chemical_list: D012492:Salts; D004247:DNA