A Study of Molecular Recognition between DNA and Metal Ions

N. Fukushima (ayui@cray.com)[1]
M. Kanehisa (kanehisa@kuicr.kyoto-u.ac.jp)[2]

[1] Computational Chemistry Group, Cray Research Japan Ltd.
5-5 Shin-Yokohama 2-chome, Kohoku-ku, Yokohama-shi, Kanagawa 222, Japan
[2] Institute for Chemical Research, Kyoto University
Gokasho, Uji, Kyoto 611, Japan

The dissociation energies have been calculated between A, C, G, or T of DNA and divalent metal ions (Mg and Ca) and between a double-stranded DNA dimer d (AT) and a hydration shell including either Mg or Ca 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 O atom of T (T (O)) and the N atom of G (G(N)) played important roles for the recognition of AT and GC base pairs, respectively and that Mg interacted more strongly than Ca to the AT stack-site of the minor groove in B-DNA through the hydration shell.