Drug binding by branched DNA: selective interaction of the dye stains-all with an immobile junction.

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.