Synthesis of 8-aza-3,7-dideaza-2′-deoxyadenosines possessing a new adenosine skeleton as an environmentally sensitive fluorescent nucleoside for monitoring the DNA minor grooveElectronic supplementary information (ESI) available: 1H- and 13C-NMR spectra of newly synthesized compounds, optimized structure of N9-methylated 3n7zA, absorption and excitation spectra of 3n7zA in various solvents, and HPLC profiles, MALDI-TOF-mass, CD, absorption and excitation spectra of 3n7zA-containing ODNs. See DOI

• Main Authors: Suzuki, Azusa, Saito, Mio, Katoh, Ryuzi, Saito, Yoshio
• Format: Journal Article
• Language: English
• Published: 02.07.2015
• ISSN: 1477-0520; 1477-0539
• DOI: 10.1039/c5ob00862j

8-Aza-3,7-dideaza-2′-deoxyadenosine 1 and its C3-naphthylethynylated derivative 3n7z A ( 2 ) comprising a 8-aza-3,7-dideazapurine (pyrazolo[4,3- c ]pyridine) skeleton were synthesized for the first time. In particular, nucleoside 3n7z A ( 2 ) exhibited environmentally sensitive intramolecular charge transfer (ICT) emission because of electron transition in the coplanar conformer formed by nucleobase and naphthalene moieties. Its incorporation into oligodeoxynucleotide (ODN) probes enable a clear identification of a perfectly matched thymine (T) in the complementary strand by a distinct change in the emission wavelength. In addition, the fluorescence emission of the duplexes containing a cytosine/guanine (C/G) base pair flanking 3n7z A ( 2 ) was strongly quenched by guanine only when the opposite base of the modified nucleoside was mismatched, enhancing its base identification ability. Thus, ODN probes containing 3n7z A ( 2 ) acted as effective reporter probes for homogeneous single nucleotide polymorphism (SNP) typing. Fluorescent ODN probes containing 3n7z A ( 2 ) acted as effective reporter probes for homogeneous single nucleotide polymorphism (SNP) typing.