Easy method for the synthesis of labeled oligonucleotides

Abstract We developed a new strategy for labeling oligonucleotides. Labels bearing an acceptor substituted azide moiety, e.g. a sulfonyl azide substituent are used during oligonucleotide synthesis instead of conventional dye phosphoramidites. Azides are well known to react with trivalent phosphor compounds to phosphor amidates and therefore they could be used instead of an oxidizer during oligonucleotide synthesis. Because N-Alkyl or N-Aryl phosphor amidates are hydrolyzed especially under acidic conditions, we used acceptor substituted azides as reactants, which results in remarkable stabilization of the corresponding amidates. This method is suitable to introduce labels at any internucleosidic linkage of an oligonucleotide and could be used for synthesis of any kind of labeled or polylabeled detection probes. Probes synthesized with these new labeling reagents are evaluated in Real Time PCR. They show the same performance like probes synthesized by conventional means. Since the labeling reagents could be easily synthesized and since excess reagent could be recycled and used for further labeling reactions, this method represents a very cost effective way for the synthesis of labeled oligonucleotides.