The structure and energy of the guanine (G)-adenine (A) base pairs in the G(anti)-A(anti) and G(anti)A(syn) conformations as well as their complexes with hydrated zinc(II) ions have been investigated by the self-consistent field for molecular interaction (SCF-MI) ab initio method. The formation of covalent bonds between the Zn(II) ions and the N7 sites of the guanine bases results in an increase of the binding energy of the G-A pairs. In addition, the SCF-MI calculations have also been performed for the guanine (G)-guanine (G)-cytosine (C) (G-GC) base triplet and for its complex with a hydrated Zn(II) ion bound to the N7 site of the third-strand guanine. The Zn(II) binding causes a significant stabilization of the G-GC triplet. Possible implications for the conformational changes in alternating d(GA)(n) sequences are discussed.