The Base-Pairing Properties of 7-Deaza-2′-deoxyisoguanosine and 2′-Deoxyisoguanosine in Oligonucleotide Duplexes with Parallel and Antiparallel Chain Orientation

Oligonucleotides with parallel (ps) or antiparallel (aps) chain orientation containing 7-deaza-2′-deoxyisoguanosine (1) or 2′-deoxyisoguanosine (2) were prepared. The phosphoramidite and phosphonate building blocks 3 – 6 were synthesized and used in solid-phase synthesis. The diphenylcarbamoyl (dpc) residue was used for the 2-oxo group protection and the isobutyryl (iBu=ib) residue for the amino function. Hybridization experiments were performed with oligonucleotides containing 7-deazaisoguanine or isoguanine. Regarding 7-deazapurine-containing oligonucleotides, the 7-deazaisoguanine⋅cytosine base pair was the strongest in ps-duplexes, while that of 7-deazaisoguanine⋅5-methylisocytosine was the most stable one in aps-DNA. Ambiguous base pairing of 7-deazaisoguanine with cytosine, 5-methylisocytosine, thymine, and guanine was observed in the case of aps-duplexes, whereas in ps-duplexes, the ambiguity was extended to adenine. The 7-deazaisoguanine-containing duplexes showed almost identical base-pair stabilities as those containing isoguanine. According to this, various base-pair motifs are proposed. The 7-deaza-2′-deoxyisoguanosine was found to be an effective substitute of 2′-deoxyisoguanosine.