title: A dimeric form of N-methoxycarbonyl-2-amino-1,8-naphthyridine bound to the A-A mismatch in the CAG/CAG base triad in dsRNA.
abstract: A dimeric form of N-methoxycarbonyl-2-amino-1,8-naphthyridine (MCND) connected at the C2 position with a three-atom linker was examined for the binding to mismatches in double stranded RNA. Despite the fully complementary hydrogen bonding groups to guanine, MCND did not bind to guanine-guanine mismatch but did to adenine-adenine mismatch. The base pairs flanking the mismatch had weak effect on the binding, with showing the strongest binding to the A-A mismatch in the CAG/CAG sequence. The A-A mismatch in the GAC/GAC sequence was a poor substrate for the MCND binding. A monomeric derivative of MCND and another derivative lacking a methylcarbamate group showed negligilble binding to the A-A mismatch and the sequence selectivity. These results are important clues for the better molecular design of RNA binding small molecules.
authors.affiliation: Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan. nakatani@sanken.osaka-u.ac.jp
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Nakatani
authors.forename: Mariko
authors.initials: M
authors.lastname: Toda
authors.forename: Hanping
authors.initials: H
authors.lastname: He
mesh_terms: D000225:Adenine / Q000737:chemistry*; D020137:Base Pair Mismatch; D019281:Dimerization; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009287:Naphthyridines / Q000737:chemistry* / Q000378:metabolism; D009943:Organophosphorus Compounds / Q000737:chemistry / Q000378:metabolism; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000378:metabolism*
chemical_list: C427025:2-amino-1,8-naphthyridine; D009287:Naphthyridines; D009943:Organophosphorus Compounds; D012330:RNA, Double-Stranded; C054324:methoxycarbonyl phosphate; D000225:Adenine