Emission of characteristic fluorescence from the ligand-cytosine complex in U_A/ACU bulged RNA duplex.

Here we show that N,N-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine (DANP) binds to the single cytosine bulge in RNA duplexes. When the base pairs flanking the C-bulge were A-U base pairs, a characteristic fluorescence was emitted from the DANP-C-bulge complex. The fluorescence would be useful for detecting the C-bulge in RNA secondary structures.