Hybridization-dependent fluorescence of oligodeoxynucleotides incorporating new pyrene-modified adenosine residues

. We report the synthesis and properties of oligonucleotides incorporating N 6-[ N-(pyren-1-ylmethyl)carbamoyl]-deoxyadenosine (dA pymcm). We designed the ODN which incorporated two consecutive dA pymcm residues. It was revealed that on hybridization with the target DNA and RNA oligomers, the fluorescence spectra of ODNs having two consecutive dA pymcm molecules near the 5′-terminal position can change from the pyrene monomer emission to the excimer, depending on the chain length of the target DNA and RNA. These results indicated that dA pymcm-modified ODNs can be used as interesting hybridization sensors that are sensitive to the size of the target strand.