Intercalating fluorescence dye YOYO-1 prevents the folding transition in giant duplex DNA

Recently, it has become clear that with the addition of polyamines, giant D NA molecules of size greater than 10 kbp exhibit all-or-none switching betw een elongated coil and folded compact states. Here the effects of the inter calating fluorescent labeling dye, YOYO-1, and the minor-groove binding flu orescent labeling dye, DAPI, on the folding transition of single giant T4 D NA (166 kbp) induced by spermidine(3+) were examined, by use of the experim ental technique of single molecular chain observation with fluorescence mic roscopy. It is found that the intercalating dye, YOYO-1, markedly prevents the folding transition, whereas the minor-groove binding dye, DAPI, exhibit s negligible effect on the folding transition. This action of YOYO-1 is dis cussed in relation to the biological effect of intercalators. (C) 2001 Acad emic Press.