Induced coalescence of cations through low-temperature Poisson-Boltzmann calculations.

The computational determination of preferred binding regions of divalent counterions to nucleic acids is either inaccurate (standard Poisson-Boltzmann approaches) or extremely time-consuming (Monte Carlo or molecular dynamics simulations). A novel "selective low-temperature" Poisson-Boltzmann method is introduced that, although approximate in nature, qualitatively accounts for ion correlation and charge-transfer effects and allows for the rapid determination of such regions through an "induced coalescence" of divalent ions. The method is illustrated here for the binding of Mg(2+) to a double-helical sequence of B-form DNA (CGCGAATTCGCG) but the technique is readily applicable to locating divalent cations in other systems such as DNA-endonuclease complexes and ribozymes.