Nucleic acids, counterion condensation

A number of methodologies have been developed and generalized in recent years to quantitatively describe the ion atmosphere around nucleic acids [11, 12, 17, 28, 29]. These include models based on Poisson-Boltzmann equation [11, 12], counterion condensation [17], and simulation methods, such as Monte Carlo, molecular dynamics, and Brownian dynamics [28, 29]. 

In this chapter, some recent advances in counterion condensation are surveyed. We also discuss how some of these advances have been applied to elucidate the characteristics of nucleic acids. Due to the scope of this chapter, a variety of topics on the ion atmosphere of nucleic acid has been excluded. 

Despite the inherent weaknesses of the Poission-Boltzmann (PB) equation that includes neglect of polyion-polyion interactions and the size of mobile ions, it has nevertheless played an important role in elucidating the characteristics of electrostatic interactions and ion atmopshere in nucleic acids [12]. Two salient results have emerged from such an analysis. First, for cylindrical-shaped molecule of infinite length, there is a critical linear charge density beyond which counterion condensation takes place [33, 34]. Second, the phenomenon of counterion condensation takes place in one and two dimensions only [33, 35], An... 

At higher temperatures, higher concentrations of counterions are needed to induce folding in nucleic acids. This is so because thermal fluctuations resist the propensity of counterions to condense in the vicinity of the polyelectrolyte [108, 109]. This is in agreement with experiments [31, 108-110]. In fact,... 

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