Synthesis and hybridization of 2'-O-methyl-RNAs incorporating 2'-O-carbamoyluridine and unique participation of the carbamoyl group in U-G base pair.

2'-O-Carbamoyluridine (U(cm)) was synthesized and incorporated into DNAs and 2'-O-Me-RNAs. The oligonucleotides incorporating U(cm) formed less stable duplexes with their complementary and U(cm)-U, U(cm)-C single-base mismatched DNAs and RNAs in comparison with those without the carbamoyl group. On the contrary, the T(m) analyses revealed that the duplexes with a mismatched U(cm)-G base pair showed almost the same thermostability as the corresponding unmodified duplexes. Molecular dynamics (MD) simulations of the U(cm)-modified 2'-O-Me-RNA/RNA duplexes with U(cm)-G mismatched base pair suggested that the carbamoyl group could participate in the U(cm)-G base pair by an additional intermolecular hydrogen bond between the carbamoyl oxygen and the H2 of the guanine base.