title: DNA base flipping by a base pair-mimic nucleoside.
abstract: On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson-Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol(-1) while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol(-1), respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
authors.forename: Shu-ichi
authors.initials: S
authors.lastname: Nakano
authors.forename: Yuuki
authors.initials: Y
authors.lastname: Uotani
authors.forename: Kazuya
authors.initials: K
authors.lastname: Uenishi
authors.forename: Masayuki
authors.initials: M
authors.lastname: Fujii
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D020029:Base Pairing; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D003839:Deoxyadenosines / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
chemical_list: D003839:Deoxyadenosines; C507010:N6-(N'-naphthylcarbamoyl)-2'-deoxyadenosine; C507009:N6-(N'-phenylcarbamoyl)-2'-deoxyadenosine; D004247:DNA