Fluorescent oligonucleotide incorporating 5-(1-ethynylpyrenyl)-2′-deoxyuridine: sequence-specific fluorescence changes upon duplex formation

We describe the design and properties of a pyrene-labeled deoxyuridine that can be inserted efficiently into oligodeoxynucleotides using phosphoramidite chemistry. An oligonucleotide incorporating the pyrene-labeled deoxyuridine is a sensitive fluorescence probe that can discriminate between perfect and single-base-mismatched pairing by changes in its fluorescence intensity.