title: Properties of 5- and/or 2-modified 2'-O-cyanoethyl uridine residue: 2'-O-cyanoethyl-5-propynyl-2-thiouridine as an efficient duplex stabilizing component.
abstract: We systematically synthesized eight types of 5- and/or 2-modified uridine derivatives and evaluated their effect on duplex stability. The incorporation of 2'-O-cyanoethyl-2-thio-5-propynyluridine (p(5)s(2)UOCE) into RNA was significantly effective for stabilization of RNA/RNA (+8.5 °C) and DNA/RNA (+10.4 °C) duplexes. These striking effects were maintained in oligonucleotides with different sequences or multiple incorporations. In addition, p(5)s(2)UOCE increased selectivity toward the correct AU Watson-Crick base pair over the most stable mismatched base pair in both RNA/RNA and DNA/RNA duplexes. Hence, p(5)s(2)UOCE could be useful for various applications of modified oligonucleotides that need high duplex stability and base pairing selectivity.
authors.affiliation: Department of Life Science, Tokyo Institute of Technology, 4259 J2-12 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, Japan. msekine@bio.titech.ac.jp.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Masaki
authors.forename: Ryuta
authors.initials: R
authors.lastname: Miyasaka
authors.forename: Kunihiro
authors.initials: K
authors.lastname: Hirai
authors.forename: Takashi
authors.initials: T
authors.lastname: Kanamori
authors.forename: Hirosuke
authors.initials: H
authors.lastname: Tsunoda
authors.forename: Akihiro
authors.initials: A
authors.lastname: Ohkubo
authors.forename: Kohji
authors.initials: K
authors.lastname: Seio
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
mesh_terms: D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013891:Thiouridine / Q000031:analogs & derivatives* / Q000737:chemistry; D014529:Uridine / Q000031:analogs & derivatives / Q000138:chemical synthesis* / Q000737:chemistry
chemical_list: D013891:Thiouridine; D012313:RNA; D004247:DNA; D014529:Uridine