Interaction of manganese(II), cobalt(II) and nickel(II) with DNA oligomers studied by 1H NMR spectroscopy

Abstract

The metal binding properties of three different oligodeoxyribonucleotides, one decamer and two dodecamers, have been studied by 1D and 2D 1H NMR spectroscopy. The sequential composition of the oligomers was chosen so as to provide a multitude of different binding site contexts: 5′-GACGGCCGTC ( I), 5′-CGCGAATTCGCG ( II), and 5′-ATGGGTACCCAT ( III). Salts of three different metal ions: Mn(II), Co(II) and Ni(II), were used in titration experiments. The binding studies were carried out under duplex conditions. The influence of paramagnetic metal ions on protons adjacent to the binding site were followed by measuring line broadening and T 1 relaxation times. We have previously proposed a rule for sequence-selective metal binding to G-N7 in oligodeoxyribonucleotides where the metal prefer the 5′-guanine residue in the order: 5′-GG ≥ GA > GT ≫ GC. This binding pattern is also observed in the present study for Mn( II) and Co(II). However, in sequence I Ni(II) does not follow the established selectivity rule showing greater affinity for 5′-G in the context 5′-GC than in the context 5′-GA. For II and III Ni(II) ions are seen to follow the selectivity rule. Fluctuation in the nucleophilicity of G-N7 along the duplex is probably a consequence of sequence-dependent variation in π-stacking interaction between base residues.