Amine induced Z-DNA in poly(dG-dC)·poly(dG-dC): Circular dichroism and gel electrophoresis study

Abstract

Spermine and [Co(NH3)6]3+ are known to induce the B → Z transition in poly(dG-dC)·poly(dG-dC) DNA. In this paper gel electrophoresis shift assays using the long DNA poly(dG-dC)·poly(dG-dC) are developed to complement circular dichroism (CD) measurements of the conformation of the DNA in the presence of amines including spermine, spermidine, [Co(NH3)6]3+, (+)-[Co(en)3]3+ and (−)-[Co(en)3]3+ (en: ethylenediamine). CD is used to monitor the average conformation of the DNA and the gels show when there is a population of a given type of DNA in the solution. Spermidine is found to induce the transition at very low ionic strength, in contrast to literature wisdom. The cobalt amine-induced Z-DNA melts, with a broad transition, at a lower temperature than B-DNA. The electrophoresis data shows the presence of a DNA more flexible than B-DNA at low amine concentrations. This is ascribed to the existence of B/Z junctions. At higher amine concentrations, a DNA (Z-DNA) that is stiffer than B-DNA is observed. The Z-DNA induced by spermine is stiffer (runs more slowly on the gels) than that induced by the other amines. The spermine–DNA interaction is found to be very cooperative, whereas that of the cobalt amines is uncooperative. The kinetics of the B → Z transition with spermine at room temperature is very slow, whereas the cobalt amines induce it within seconds.