Hybridization ability and base pair geometry of modified deoxycytidine derivatives having a 4-N-carbamoyl group

Modified oligodeoxyribonucleotides incorporating 4-N-carbamoyldeoxycytidine derivatives were synthesized. The 1H-NMR of 4-N-carbamoyldeoxycytidine suggests that the carbamoyl group forms an intramolecular hydrogen bond with the cytosine ring nitrogen atom and this geometry would inhibit formation of the Watson-Crick base pair with a guanine base. However, the Tm analysis of the modified oligodeoxynucleotides revealed that, in the process of their hybridization with the complementary oligodeoxynucleotides, the orientation of the carbamoyl group changed in a manner where the stable Watson-Crick base pair can be formed with the guanine base.