Abstract
We measured the fluorescence intensity of DNAβbound fluorescent dyes YOβPROβ1 (oxazole yellow) and YOYOβ1 (dimer of oxazole yellow) at various spermidine concentrations to determine how counterions on DNA are exchanged in the process of DNA condensation. A decrease of fluorescence intensity was observed with an increase of spermidine. Considering the chemical equilibrium under the competition between the dye and spermidine for counterion condensation on DNA, the theoretical curve well describes the decrease of the fluorescence intensity. These results indicate that dyes are exchanged for spermidine at the binding site on DNA; that is, the exchange of counterions occurs. The parameters associated with the decrease of the fluorescence intensity show that the relative affinity of the dye and spermidine for DNA depends on the state of DNA. Moreover, YOYOβ1 prevents the DNA condensation, but the effect of YOβPROβ1 on the condensation is very slight, though both dyes intercalate for DNA; the high affinity of YOYOβ1 compared to YOβPROβ1 enables prevention of the condensation. Β© 2005 Wiley Periodicals, Inc. Biopolymers 77: 354β360, 2005