Application of the Poisson Boltzmann polyelectrolyte model for analysis of thermal denaturation of DNA in the presence of Na+ and polyamine cations Original Research Article

The Poisson Boltzmann (PB) cell model of polyelectrolyte solution has been used for calculation of the electrostatic free energy difference, ΔGel, between double- and single-stranded DNA. The calculations have been performed for conditions relevant to describe the DNA helix-coil transition in NaCl solution in the presence of the natural polyamines putrescine2+, spermidine3+, spermine4+ and their synthetic homologs with different spacing between the charged amino groups, for which experimental values of the DNA ‘melting’ transition temperature (Tm) are available. Using the PB theory and the polyamine ion radius as an adjusting parameter provides quantitative agreement between experimental and theoretical Tm—salt concentration dependencies only by using physically unreasonable radii for the polyamine. Thus, modeling the linear and flexible polyamines as charged spheres within the PB cell model is an implausible oversimplification. We propose another explanation for the experimental observations, still within the frame of the ‘primitive’ PB polyelectrolyte theory. This explanation is based on an analysis of the ΔGel dependence on the stoichiometry of polyamine-polyanion binding to double- and single-stranded DNA.