A Study of Molecular Recognition between DNA and Metal Ions

Abstract

The dissociation energies have been calculated between A, C, G, or T of DNA and divalent metal ions (Mg²⁺ and Ca²⁺) and between a double-stranded DNA dimer d (AT) and a hydration shell including either Mg²⁺ or Ca²⁺ in order to investigate the ability of the sequence recognition of the ions. All calculations were carried out using the Hartree-Fock and the density functional methods on CRAY supercomputers. From the results of calculations it was shown that the O₂ atom of T (T (O₂)) and the N₇ atom of G (G (N₇)) played important roles for the recognition of AT and GC base pairs, respectively and that Mg²⁺ interacted more strongly than Ca²⁺ to the AT stack-site of the minor groove in B-DNA through the hydration shell.