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.
Lamm
Gene
G
Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
Pack
George R
GR
D000465:Algorithms; D001665:Binding Sites; D002412:Cations / Q000737:chemistry; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D046911:Macromolecular Substances / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D013696:Temperature
D002412:Cations; D046911:Macromolecular Substances; D004247:DNA; D008274:Magnesium