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Induced Coalescence of Cations through Low-Temperature Poisson-Boltzmann Calculations

Department of Chemistry, University of Louisville, Louisville, Kentucky 40292

Correspondence: Address reprint requests to George R. Pack, Professor and Chair, Dept. of Chemistry, University of Louisville, 2320 South Brook St., Louisville, KY 40292. Tel.: 502-852-6798; E-mail: george.pack{at}louisville.edu.

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.

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