DNA melting in the presence of fluorescent intercalating oxazole yellow dyes measured with a gel-based assay

We measured the effect of the intercalating oxazole yellow DNA dye quinolinium,4-(3-methyl-2(3H)-benzoxazolylidene)methyl]-1-3-(trimethylammonio)propyl]-,diiodide (YO-PRO) and its homodimer (YOYO) on the melting of self-complementary DNA duplexes using a gel-based assay. The assay, which requires a self-complementary DNA sequence, is independent of the optical properties of the molecules in solution. The melting temperature of the DNA is observed to increase in direct proportion to the number of occupied intercalation sites on the DNA, irrespective of whether the dye molecules are in monomer or dimer form. The increase is approximately 2.5 degrees C for each intercalation site occupied in the presence of 38 mM Na(+)], for dye/duplex ratios in which less than 1/5 of the available intercalation sites are occupied.