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.

RNA; RNase H; gapmer oligonucleotides; modified nucleosides; postsynthetic modifications.