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.
Seio
Kohji
K
Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan. kseio@bio.titech.ac.jp
Tawarada
Ryuya
R
Sasami
Takeshi
T
Serizawa
Masashi
M
Ise
Misako
M
Ohkubo
Akihiro
A
Sekine
Mitsuo
M
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