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'.

Sequence-selective metal ion binding to DNA oligomers.

Sequence-selective interactions between DNA oligonucleotides and Pt(II) and Pd(II) complexes have been studied by 1D and 2D NMR spectroscopy. Titration of DNA oligomers with diamagnetic metal ion complexes induces chemical shifts of proton resonances close to the site of interaction. Conformational changes in the helical structure were monitored by measuring cross-peak intensities in 2D NOESY maps. Two duplex deoxynucleotides were studied, [d(CGCGCG)]2 and [d(CGCGAATTCGCG)]2, respectively. The hexamer was titrated in the duplex form with cis-[Pt(NH3)2Cl2]2+ (cis-DDP or cisplatin). The dodecamer was titrated with NO(3-)-salts of Pd(aq)2+, [Pd(en)(H2O)2]2+ and [Pd(dien)(H2O)]+, respectively. The reaction between cis-DDP and the hexamer at conditions where the duplex form is retained proceeded exceedingly slowly. In the initial phase of the titration the NOESY map indicates conformational changes induced by noncovalent adduct formation between the intact hexamer and cis-DDP. The more reactive Pd compounds show a tendency towards sequence-selective binding to the duplex dodecamer. The 'naked' Pd ion is very reactive and exhibits selectivity towards the thymine T8 imino proton and N7 on G4. At a Pd(II)/dodecamer ratio of 4:1 the metal ions induce helix-->coil transition. The mono- and bifunctional Pd complexes with 'bulky' ligands attack the dodecamer at the terminal GC base pairs, leaving the central Watson-Crick base pairs intact.

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.