Synthesis and properties of oligonucleotides containing fluorescent ethenodeoxyadenosine and ethenodeoxycytidine

Fluorescent ethenodeoxyadenosine (dA′) or/and ethenodeoxycytidine (dC′) were site-specifically inserted into four oligonucleotides through phosphoramidite chemistry on an automated DNA synthesizer, their nucleoside compositions were confirmed by enzymatic digestion analysis. The UV melting behaviors indicate that the conformation of modified duplex is not affected when incorporated into modified nucleosides. The introduction of dA′ to the oligonucleotide slightly increases the duplex stability relative to the corresponding unmodified oligonucleotide while the introduction of dC′ slightly decreases the duplex stability. Fluorescence is greatly quenched when dA′ or dC′ is inserted into an oligonucleotide and quenched further when the dA′ or dC′-modified oligonucleotide binds with its complementary DNA. The fluorescence intensity of an oligonucleotide can be increased by inserted two or more molecules of dA′.