Zinc ion–DNA polymer interactions
Authors: Jia Xin J. , Marzilli Luigi G. 
Published: December 2004

The adjacent GN7‐M‐GN7 cross‐linking and adjacent G‐M‐G sandwich‐complex models for DNA metal ion binding were evaluated both with native DNAs differing in GC content as well as with the synthetic polymers poly[(dGdC)]2, poly[(dAdT)]2, and poly[(dAdC)(dGdT)]. The effect of Zn2+ was studied in depth, and limited studies were also performed with Co2+ and Mg2+. The results were compared to the extensive information available on Cu2+ binding to native DNAs and poly [(dAdT)]2. At high ratios of metal/base (R), Zn2+ caused all native DNAs to denature with the same melting temperature Tm, ∼ 61°C. A similar pattern was reported previously for Cu2+, but the typical Tm, was ∼ 35°C. The extent of renaturation on cooling DNAs denatured in the presence of Zn2+ increased with GC content, as reported previously for Cu2+. These results, together with previously reported similarities, strongly indicate that the DNA binding characteristics of the two cations are similar. By comparison of the Tm values and hyperchromicity changes monitored at 260 and 282 nm, it is clear that, during thermal denaturation in the presence of Zn2+, both AT and GC regions were denatured, even at high R. The Tm vs R profile for the native DNAs was typical. The rise at low R and subsequent decrease at high R were inversely and directly related, respectively, to GC content. Except for poly[(dAdT)]2, where Tm, increased with R, the other synthetic polymers exhibited the increase/decrease pattern. Poly[(dAdC)(dGdT)] gave a Tm, value a at high R of 54°C. In the absence of Zn2+, this polymer exhibited little hypochromicity on cooling of denatured polymer. However, in the presence of Zn2+, nearly complete hypochromicity was observed, although the midpoint of the cooling curve was lower than the Tm value by ∼ 15°C at R = 10. These characteristics were similar to those with native DNAs, although viscosity and CD studies suggested that the “renatured” polymer was not identical to the unheated polymer. Furthermore, addition of Zn2+ after denaturation nearly completely reversed the absorption increase. This finding contrasts with those for native DNAs, where the Zn2+ must be present during denaturation in order to reverse the absorption increase nearly completely on cooling. With some caveats, poly[(dAdC)(dGdT)] appears to be a good model for native DNAs since its properties, including CD and uv changes on addition of Zn2+ to premelted and melted polymer, parallel those of the native polymers. Based on these findings and the discovery that Zn2+ actually inhibits renaturation of poly[(dGdC)]2, we believe adjacent G‐M‐G complexes are not the primary species responsible for the spectral changes in pre‐ melted DNAs, nor are they the principal species promoting renaturation. Three interrelated hypotheses to explain these phenomena were identified for further study as follows: (a) a kinetic effect–the metal ion promotes renaturation of denatured regions formed during thermal denaturation with metal ion present; (b) an inhibiting effect–the metal ion prevents the initial formation of conformations that otherwise inhibit renaturation; and (c) a CN3 binding effect–the metal ion lowers Tm by stabilizing the denatured state through C binding. We speculate that such CN3 binding may account for the unexpectedly poor ability of Co2+ both to lower Tm and to promote renaturation.