"Post-assay" covalent labeling of phosphorothioate-containing nucleic acids with multiple fluorescent markers

A simple protocol has been developed which allows the covalent introduction of multiple fluorescent markers into DNA fragments after gel electrophoresis techniques, that is, while the nucleic acid is imbedded in the polyacrylamide gel matrix. "Post-assay" fluorescent labeling in this manner employs DNA fragments containing phosphorothioate diesters, which can be easily incorporated during chemical and enzymatic synthesis procedures, and can be alkylated with the fluorescent marker monobromobimane. Labeling the internucleotidic phosphorus residue in this manner allows the introduction of a fluorescent marker for each nucleotide residue present. Roughly a linear increase in emitted fluorescence, thus detection sensitivity, is observed with an increasing number of bimane markers. With this technique, oligodeoxynucleotides and DNA fragments can be observed in the gel matrix, without sophisticated electronic detection devices in the low femtomolar (10(-15) mol) range.