Sequence-selective metal ion binding to DNA hexamers.

Base-selective interaction between divalent metal ions and DNA oligomers has been studied by 1D and 2D NMR spectroscopy. Titration with paramagnetic metal ions induces selective line broadening of resonances from protons close to the binding site. Also the intensities of 2D NOESY cross-peaks involving paramagnetic affected protons will be quenched. Two hexamers, 5'-d(CGTACG)2 (I) and 5' (GCATGC)2 (II) have been titrated with Mn(II) ions. Manganese binds selectively to the terminal guanine, G1, in sequence II as manifested through pronounced paramagnetic line broadening and loss of intensities of NOESY cross-peaks involving G-H8 protons. The second guanine, G5, and the non-guanine residues are appreciably less affected. In sequence I both guanines, G2 and G6, are the targets for selective metal binding as judged from G-H8 line broadening. The extent of interaction is almost identical for the two G-residues and comparable to that observed for G1 in sequence II. The metal binding site in the duplexes is most likely nitrogen G-N7. Selective metal binding to oligonucleotides may be related to sequence-dependent variation in molecular electrostatic potentials (MEP) along the chain.