title: A new modified cytosine base capable of base pairing with guanine using four hydrogen bonds.
abstract: Oligonucleotides, containing 4-N-(1H-pyrrol-2-ylcarbonyl)deoxycytidine (dC(Pyc)) and related derivatives, were synthesized via deprotection using 1.5 M NaOMe/MeOH. Among them, oligodeoxynucleotides containing dC(Pyc) exhibited a higher hybridization affinity for DNA and RNA than the unmodified oligodeoxynucleotides. Comparative analysis between dC(Pyc) and its derivatives by molecular dynamic simulation indicated that the C(Pyc) residue could form four hydrogen bonds with the opposite G nucleobase keeping a more planar structure than the C(Inc) residue where the Pyc group was replaced with a 1H-indol-2-ylcarbonyl group.
authors.affiliation: Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501 Japan. msekine@bio.titech.ac.jp.
authors.forename: Ken
authors.initials: K
authors.lastname: Yamada
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Masaki
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: D020029:Base Pairing; D003596:Cytosine / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D006147:Guanine; D003596:Cytosine