title: Use of abasic site-containing DNA strands for nucleobase recognition in water.
abstract: Nucleobase recognition in water is successfully achieved by the use of an abasic site (AP site) as the molecular recognition field. We intentionally construct the AP site in DNA duplex so as to orient the AP site toward a target nucleobase and examine the complexation of 2-amino-7-methylnaphthyridine (AMND) with nucleobases at the AP site. AMND is found to selectively bind to cytosine (C) base with a 1:1 binding constant of >106 M-1, accompanied by remarkable quenching of its fluorescence. In addition to hydrogen bonding, a stacking interaction with nucleobases flanking the AP site seems responsible for the binding properties of AMND at the AP site. Possible use of AMND is also presented for selective and visible detection of a single-base alternation related to the cytosine base.
authors.affiliation: Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
authors.forename: Keitaro
authors.initials: K
authors.lastname: Yoshimoto
authors.forename: Seiichi
authors.initials: S
authors.lastname: Nishizawa
authors.forename: Masakazu
authors.initials: M
authors.lastname: Minagawa
authors.forename: Norio
authors.initials: N
authors.lastname: Teramae
mesh_terms: D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009287:Naphthyridines / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D009287:Naphthyridines; D014867:Water; D004247:DNA