Analysis of dimeric cyanine-nucleic acid dyes by capillary zone electrophoresis in N,N-dimethylacetamide as non-aqueous organic solvent.

A method based on capillary zone electrophoresis is presented for the determination of the purity of commercial dimeric cyanine dyes (TOTO, YOYO, BOBO, all -1 and -3 species, LOLO-1, POPO-1) that are common as fluorescent probes for nucleic acid staining. These dyes are tetracharged cations, and have a strong tendency to interact with negatively charged centres, where they are rapidly adsorbed, especially from aqueous solutions. Thus anionic sites at the capillary wall must be avoided, and aqueous buffers are not suitable. The method introduced here avoids both complications, using non-aqueous N,N-dimethylacetamide as solvent, and suppressing the dissociation of silanol groups at the capillary surface due to selection of acidic separation conditions (20 mmol/l perchloric acid as background electrolyte). The present method enables the determination of the purity of all 10 dyes in less than 15 min. The selectivity of the method allows separation of at least five main and differentiating a number of unresolved minor contaminants as demonstrated in detail for TOTO-3 as an example. Quantitation (with 100% normalisation of the peak areas) of nine lots of this dye results in a purity between 33 and 87%.