title: Site-selective RNA cleavage by DNA bearing a base pair-mimic nucleoside.
abstract: We have synthesized the deoxyadenosine derivative tethering a phenyl group (X), which mimics the Watson-Crick A/T base pair. The RNA/DNA hybrid duplexes containing X in the middle of the DNA sequence showed a similar thermal stability regardless of the ribonucleotide species (A, G, C, or U) opposite to X, probably because of the phenyl group stacking inside of the duplex accompanied by the opposite ribonucleotide base flipped in an extrahelical position. The RNA strand hybridized with the DNA strand bearing X was cleaved on the 3'-side of the ribonucleotide opposite to X in the presence of MgCl2, and the RNA sequence to be cleaved was not restricted. The site-specific RNA hydrolysis suggests that the DNA strand bearing X has the advantage of the site-selective base flipping in the target sequence and the development of a "universal deoxyribozyme" to exclusively cleave a target RNA sequence.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research and Department of Chemistry, Faculty of Science and Engineering, 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: D000241:Adenosine / Q000031:analogs & derivatives* / Q000737:chemistry; D020029:Base Pairing; D001483:Base Sequence; D040761:Biomimetic Materials / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D003839:Deoxyadenosines / Q000737:chemistry* / Q000378:metabolism; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000378:metabolism; D010671:Phenylurea Compounds / Q000138:chemical synthesis / Q000737:chemistry*; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D003839:Deoxyadenosines; D009692:Nucleic Acid Heteroduplexes; D010671:Phenylurea Compounds; D012313:RNA; D004247:DNA; D000241:Adenosine