Synthesis and properties of 4-(diarylmethylene)imidazolinone-conjugated fluorescent nucleic acids

Abstract A novel fluorescent cytidine derivative ( dC DAIN ) bearing 4-(diarylmethylene)imidazolinones ( DAINs ) at C5-position was successfully synthesized and incorporated into oligonucleotides. The oligonucleotide bearing dC DAIN hybridized with complimentary strand in a sequence specific manner, and the florescence intensity was changed depending on the nucleobases opposite to dC DAIN in the double stranded DNA or RNA. Interestingly, the fluorescence intensity was higher when the dC DAIN -containing oligonucleotide hybridized with a mismatched sequence. Especially, when dC DAIN was located at the opposite position of an abasic site, the fluorescent intensity was four times higher than that observed in a single stranded state.