Different chromotropic behaviour of DNA and RNA and of poly(adenylic acid) and poly(uridylic acid) with the dye pinacyanol chloride

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AbstractThe cyanine dye pinacyanol chloride (PCYN) distinguishes various polyanions by exhibiting two distinct types of absorption spectra of the dye‐polyanion system. This dye can also differentiate between the biopolymers DNA and RNA, as well as between poly(adenylic acid) (poly‐A) and poly(uridylic acid) (poly‐U). The dye‐RNA spectra are independent of polymer/dye (P / D) ratio and show a sharp peak at 490 nm and a very broad band around 560 nm indicating not well organized aggregation of dye cations bound to the polymer. The spectra of the dye‐DNA system are similar only at low P / D, but with increase in DNA concentration a sharp band appears at 560 nm with disappearance of the peak at 490 nm. The poly‐U/PCYN system resembles the RNA‐PCYN system and the poly‐A/PCYN system resembles the DNA‐PCYN system. These differences are interpreted to arise from the preferential binding of the dye to purine bases rather than to pyrimidine bases, and from the partial intercalation of the dye within the DNA helix at high P / D. The sharp band at 560 nm of DNA‐PCYN at high P / D is due to dimerization of PCYN — the major, if not the only, state of aggregation of the dye induced by DNA at high P / D.