Synthesis and hybridization of 2′-O-methyl-RNAs incorporating 2′-O-carbamoyluridine and unique participation of the carbamoyl group in U–G base pair Original Research Article

2′-O-Carbamoyluridine (Ucm) was synthesized and incorporated into DNAs and 2′-O-Me-RNAs. The oligonucleotides incorporating Ucm formed less stable duplexes with their complementary and Ucm–U, Ucm–C single-base mismatched DNAs and RNAs in comparison with those without the carbamoyl group. On the contrary, the Tm analyses revealed that the duplexes with a mismatched Ucm–G base pair showed almost the same thermostability as the corresponding unmodified duplexes. Molecular dynamics (MD) simulations of the Ucm-modified 2′-O-Me-RNA/RNA duplexes with Ucm–G mismatched base pair suggested that the carbamoyl group could participate in the Ucm–G base pair by an additional intermolecular hydrogen bond between the carbamoyl oxygen and the H2 of the guanine base.