Sequence-selective interaction between mercury(II) ions and the DNA dodecamer [d(GCCGATATCGGC)]2 studied by 1H NMR spectroscopy.

The palindromic dodecamer [d(GCCGATATCGGC)]2 has been titrated by Hg(ClO4)2 in order to study sequence dependent HgII ion interactions. The titration pattern as monitored by 1D and 2D 1H NMR is consistent with a transition to a new conformer of the dodecamer induced by HgII ions. At intermediate stages of the titration, the proton signals from the new conformer coexist with those of the original one, indicating slow exchange between the two forms on the NMR timescale. The data clearly show that there is no major alteration in the secondary structure, e.g. B-->Z-form or duplex-->hairpin transition. The intra- and inter-residue sequential walk is completed except for a break between T6 and A7. At a concentration level r = [HgII]/[nucleobase] < 0.20 all four central imino signals are present. This definitely excludes thymine N3 as a possible mercuration site. In the imino region of the spectra HgII ions induce a large upfield shift of the thymine imino resonance T8-N3H, while the other thymine resonance T6-N3H is unperturbed. The guanine imino signal G4-N1H shows a large downfield ring current shift caused by major conformational changes in the duplex. The complete titration experiment indicates that mercury, initially, binds selectively to the A5'-T8 base pair. A tentative model is proposed where mercury is cross-linking the two strands via thymine T8-O4 and the deprotonated amino group of the complementary adenine base A5'.