Metal complex induced changes in DNA conformation and template activity

Abstract

It is now well-known that the interaction of metal ions with DNA leads to dramatic changes in nucleic acid structure [1] and recently it has become apparent that even the handedness of the double helix [2] and its compaction into aggregates [3, 4] is affected by such interaction. As recently demonstrated, DNA can exist in left-handed (Z) as well as the familiar right-handed conformations. The Z-structure is produced by DNA molecules containing alternating guanine (G) and cytosine (C) bases [poly(dGdC)· poly(dGdC) [5]. Compacted states have been known for some time to exist in vivo, and it is believed that these as well as left-handed conformations may be involved in the control of genetic information transfer. It is therefore important to understand how transitions between the DNA conformers take place, and whether such transitions affect the biological activities of DNA. We have addressed both of these problems. We have found that [Co(NH 3) 6]Cl 3 brings about reversible transitions in the structure of poly(dGdC)· poly(dGdC) so that the right-handed B-form is first converted to Z-DNA and then to another structure that resembles A-DNA and finally to the highly compacted ψ-DNA [6]. The metal complex is thus able to induce three transitions among four conformers of DNA. By manipulating the concetrations of [Co(NH 3) 6]Cl 3 and poly(dGdC)·poly(dGdC), as well as other factors such as reaction time and temperature, each of these conformations can be stabilized, and identified by its circular dichroism spectrum; or labilized and converted into another structure. We believed that the mechanism for these interconversions depends on the fact that increasing concentrations of the Co(III) complex stabilize conformations in which the phosphate groups of DNA are closer together. Conformational change in DNA, as demonstrated for the B → Z conversion leads to the biologically important consequence that the ability of the DNA to act as a template for RNA synthesis is affected. Figure 1 illustrates the correlation of the B → Z ▪ transition of poly(dGdC)·poly(dGdC) which occurs at ∼60 μM Co(NH 3) 6 3+, with a decrease in RNA synthesis to ∼ 1 2 the original rate, in the presence of E. coli RNA polymerase. A decrease in RNA synthesis also accompanies the conversion of a similar double helix in which the guanines are methylated, poly(dGdm 5C)·poly(dGdm 5C), from the B to the Z form, even though this transition occurs at a much lower (∼3 μ M) Co(III) concentration. Clearly the metal complex has profound effects on the DNA conformation, and the DNA conformation affects the ability of the DNA to act as a template for RNA synthesis.