INTERACTIONS OF METAL CATIONS WITH NUCLEOBASES IN CRYSTALS

Martin Kabelác and Bohdan Schneider

J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic fax number +420 2 858 2307. E-mail address: martin.kabelac@jh-inst.cas.cz,

Possible binding sites of metal cations were localized around adenine, guanine, cytosine, thymine and uracil from structures from the Cambridge Structural Database. The stereochemistry of binding of all transition metals is not significantly influenced by either type of a base, base atom where the metal is bonded, or by types of ligands and the net charge of the metal coordination sphere. The transition metals bind in the plane given by the base atoms and have the highest binding affinity to the N7 atom in purines and the the N3 atom in pyrimidines. The metals from IA and IIA periodic groups prefer interactions with oxygen atoms, O6 of guanine, O2 or O4 atom of thymine, and O2 atom of cytosine. In contrast to the transition metals, geometry of these metals is much more variable and their deviations from the base plane can be quite large.