Fluorescence detection of the endonuclease III reaction using modified oligonucleotides.

We have developed a method for the detection of the endonuclease III reaction by fluorescence. The probes were 13-base-pair hairpin-shaped oligonucleotides containing one of the isomers of thymine glycol or 5,6-dihydrothymine as a damaged base at the center, and had a fluorophore and a quencher at the 5' and 3' ends, respectively. Fluorescence was detected when the probe was cleaved by the enzyme, because the short fragment bearing the fluorophore could not be hybridized to the quencher strand at the incubation temperature. The substrate specificity was shown using Escherichia coli and human enzymes.