Dramatic selectivity differences in the association of DNA and RNA models with new ethylene- and propylene diamine...

The affinities of polyamines consisting of ethylenediamine units equipped with either one or two terminal naphthyl-, anthryl-, or acridyl units towards PolyA.PolyU as an RNA model, and Poly(dA).Poly(dT) as a DNA model are screened by measuring the melting point changes (DeltaT(m)) of the double strands, and also partially by a fluorimetric binding assay using ethidium bromide. The larger aromatic moieties with long spacers between them allow bisintercalation; this leads to an increased preference for DNA in comparison to RNA, where ion pairing of the ammonium centers with the major RNA groove phosphates dominates. Allosteric affinity control by metalation is achieved e.g. with Cu(2+) ions, which induce conformational distortions within the chains. With anthryl- in contrast to naphthyl derivatives intercalation can be so strong that distortion of the ethylenediamine chain by metalation is not powerful enough. A particularly high concentration of positive charges is accessible with tripodal derivatives built up from ethylenediamine and propylenediamine units; in the absence of aryl parts, which interfere with the RNA groove preference, one observes the highest affinity difference known until today, reflected in a melting point ratio of DeltaT(m(RNA))/DeltaT(m(DNA)) = 40, whereas other synthetic ligands reach only a DeltaT(m(RNA))/DeltaT(m(DNA)) ratio of about 3.