Synthesis and Properties of Gapmer Oligonucleotides Containing 4′-Carboxy- and 4′-Carbamoyl-Thymidine Analogs

Gapmer oligonucleotides (ONs) contain a gap region consisting of DNA, whose heteroduplex with RNA can be a substrate for RNase H. Herein, the synthesis and properties of gapmer ONs containing 4 '-carboxy- and 4 '-carbamoyl-thymidine analogs at the gap region are reported. Synthesis of the ONs was performed by postsynthetic modification of 4 '-(methoxycarbonyl)thymidine through hydrolysis and nucleophilic substitution. Concerning the synthesis of ONs containing 4 '-(propylcarbamoyl)thymidine, postsynthetic conversion of 4 '-carboxythymidine or 4 '-(phenoxycarbonyl)thymidine on the support is effective. The duplex stabilities of the modified ONs are comparable to those of the unmodified ON. Several types of modified ONs can elicit the RNase H-mediated degradation of target RNA. Furthermore, modified ON containing 4 '-carboxy-thymidine at the gap region shows improved stability in fetal bovine serum solution. The analogs used in this study can be modified nucleosides for the gap region of gapmer ONs.