Design and synthesis of a novel fluorescent benzo[g]imidazo[4,5-c]quinoline nucleoside for monitoring base-pair-induced protonation with cytosine: distinguishing cytosine via changes in the intensity and wavelength of fluorescence†
A novel fluorescent benzo[g]imidazo[4,5-c]quinoline nucleoside BIQA (1) comprising a 3-deaza-2′-deoxyadenosine skeleton was developed and used to monitor BIQA–C base-pair formation in oligodeoxynucleotide (ODN) duplexes. The newly synthesized BIQA exhibited distinct photophysical properties associated with its protonated/deprotonated forms (monomer: pKa 6.2) via dramatic changes in its absorption and fluorescence spectra. In ODN duplexes, the induced protonation of BIQA occurred, even under alkalescent conditions when cytosine was the opposite base on the complementary strand; the resulting BIQA–C base pairs were stable. By monitoring the protonation of BIQA under neutral and alkalescent conditions, we could clearly discriminate cytosine through spectral changes in absorption and fluorescence. Similarly, we found that the demonstrated 3-deaza-2′-deoxyadenosine 3zA forms a stable base pair with cytosine via N1 protonation in ODN duplexes under neutral and acidic conditions (pH < 7.0). At lower pH values, 3zA-containing ODNs could clearly discriminate cytosine through melting temperature (Tm) measurements. Therefore, ODN probes containing indicator nucleosides, such as BIQA and 3zA, exhibit great potential as bioprobes for genetic analysis and structural studies of nucleic acids.