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Copper tetrapyridino 'phthalocyanin' (Cuprolinic blue) differs in shape from the palladium and platinum analogues, and this affects staining of polynucleotides.

Palladium and platinum homologues of the copper-containing tetrapyridinotetraazaporphin cationic dye Cuprolinic blue were prepared. The affinities of all three dyes for a series of polyanions, with and without nucleotide bases, were assessed using the CEC (critical electrolyte concentration) approach, and expressed as molarities of MgCl2. Whereas Cuprolinic blue bound to RNA with much greater avidity than to DNA, the Pt and Pd analogues showed very high affinity for both. Patterns of affinities for non-nucleotide polyanions showed no differences. 1H and 13C NMR spectra showed that, although the Cu compound was planar, the Pt and Pd homologues must be non-planar. Taken together with previous findings, on e.g. methyl green and pyronin, these results suggest that DNA finds it easier to accommodate pairs of out-of-plane aromatic rings than RNA in stable complexes. CEC analyses can, as demonstrated here, uncover quite subtle differences between molecular recognition patterns of very closely related reagents.