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.
Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan. kseio@bio.titech.ac.jp
Kohji
K
Seio
Ryuya
R
Tawarada
Takeshi
T
Sasami
Masashi
M
Serizawa
Misako
M
Ise
Akihiro
A
Ohkubo
Mitsuo
M
Sekine
D020137:Base Pair Mismatch; D020029:Base Pairing; D002942:Circular Dichroism; D009682:Magnetic Resonance Spectroscopy; D013058:Mass Spectrometry; D008958:Models, Molecular; D008968:Molecular Conformation; D009693:Nucleic Acid Hybridization; D012313:RNA / Q000138:chemical synthesis* / Q000737:chemistry; D014529:Uridine / Q000737:chemistry*
D012313:RNA; D014529:Uridine