Drug Binding by Branched DNA: Selective Interaction of the Dye Stains-All with an Immobile Junction

Min Lu, Qiu Guo, Nadrian C. Seeman, Neville R. Kallenbach

Research output: Contribution to journalArticle


The thiacarbocyanine dye Stains-All (4,5:4′,5′-dibenzo-3,3′-diethyl-9-methylthiacarbocyanine bromide) is one of a large number of cyanine dyes introduced as photosensitizers in the photographic industry. Stains-All is used in histology as a stain for nucleic acids, proteins, polysaccharides, and lipids. We report here that the dye colors branched DNA molecules differently from linear duplexes and use footprinting experiments with methidiumpropyl-EDTA•Fe(II) [MPE•Fe(II)] and bis(o-phenanthroline)copper(I) [(O-P)2Cu(I)] to show that Stains-All interacts preferentially at the branch point of a four-arm DNA structure. A titration experiment allows us to estimate that the interaction of the dye with the branch has a dissociation constant below 45 nM, tighter than that of ethidium or methidium by over 2 orders of magnitude. Probing the interaction with the purine-specific reagent diethyl pyrocarbonate (DEPC) implies that the dye induces an asymmetric distortion near the branch in the major grooves of double helix in the junction.

Original languageEnglish (US)
Pages (from-to)3407-3412
Number of pages6
Issue number13
StatePublished - Apr 1 1990


ASJC Scopus subject areas

  • Biochemistry

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