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 Mg2+ 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.