Detection of A/G single nucleotide alteration in RNA using base-discriminating fluorescent oligodeoxynucleotides

We report the fluorescence properties of oligodeoxynucleotides (ODNs) containing a base-discriminating fluorescent nucleoside, benzopyridopyrimidine (BPP), in hybridizing with RNAs possessing different bases opposite BPP. BPP-containing ODN selectively exhibited a strong fluorescence when the RNA base opposite BPP was A, whereas the fluorescence of BPP-containing ODN hybridized with RNA possessing G opposite BPP was very weak. BPP acts as a good base-discriminating fluorescent nucleoside for A/G single base alteration of RNA.