Conformation and reactivity of DNA. IV. Base binding ability of transition metal ions to native DNA and effect on helix conformation with special references to DNA–Zn(II) complex

Abstract The effects of metal ions of the first‐row transition and of alkaline earth metals on the DNA helix conformation have been studied by uv difference spectra, circular dichroism, and sedimentation measurements. At low ionic strength (10 −3 M NaClO 4 ) DNA shows a maximum in the difference absorption spectra in the presence of Zn 2+ , Mn 2+ , Co 2+ , Cd 2+ , and Ni 2+ but not with Mg 2+ or Ca 2+ . The amplitude of this maximum is dependent on GC content as revealed by detailed studies of the DNA‐Zn 2+ complex of eight different DNA's. Pronounced changes also occur in the CD spectra of DNA transition metal complexes. A transition appears up to a total ratio of approximately 1 Zn 2+ per DNA phosphate at 10 −3 M NaClO 4 ; then no further change was observed up to high concentrations. The characteristic CD changes are strongly dependent on the double‐helical structure of DNA and on the GC content of DNA. Differences were also observed in hydrodynamic properties of DNA metal complexes as revealed by the greater increase of the sedimentation coefficient of native DNA in the presence of transition metal ions. Spectrophotometric acid titration experiments and CD measurements at acidic pH clearly indicate the suppression of protonation of GC base‐pair regions on the addition of transition metal ions to DNA. Similar effects were not observed with DNA complexes with alkaline earth metal ions such as Mg 2+ or Ca 2+ . The data are interpreted in terms of a preferential interaction of Zn 2+ and of other transition metal ions with GC sites by chelation to the N ‐7 of guanine and to the phosphate residue. The binding of Zn 2+ to DNA disappears between 0.5 M and 1 M NaClO 4 , but complex formation with DNA is observable again in the presence of highly concentrated solutions of NaClO 4 (3−7.2 M NaClO 4 ) or at 0.5 to 2 M Mn 2+ . At relatively high cation concentration Mg 2+ is also effective in changing the DNA comformation. These structural alterations probably result from both the shielding of negatively charged phosphate groups and the breakdown of the water structure along the DNA helix. Differential effects in CD are also observed between Mn 2+ , Zn 2+ on one hand and Mg 2+ on the other hand under these conditions. The greater sensitivity of the double‐helical conformation of DNA to the action of transition metal ions is due to the affinity of the latter to electron donating sites of the bases resulting from the d electronic configuration of the metal ions. An order of the relative phosphate binding ability to base‐site binding ability in native DNA is obtained as follows: Mg 2+ , Ba 2+ , < Ca 2+ < Fe 2+ , Ni 2+ , Co 2+ < Mn 2+ , Zn 2+ < Cd 2+ < Cu 2+ . The metal‐ion induced conformational changes of the DNA are explained by alternation of the winding angle between base pairs as occurs in the transition from B to C conformation. These findings are used for a tentative molecular interpretation of some effects of Zn 2+ and Mn 2+ in DNA synthesis reported in the literature.