title: Competitive binding of small ligands to nucleobases in AP site-containing DNA duplexes.
abstract: By using lumichrome (Lch) as a masking ligand, we successfully control the binding selectivity of 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) when binding to nucleobases in AP site-containing DNA duplexes (5'-TCT GCG TCC AGX GCA ACG CAC AC-3'/3'-AGA CGC AGG TCN CGT TGC GTG TG-5', X = AP site; Spacer C3, N = C or T). In solutions buffered to pH 7.0 (I = 0.11 M, at 5 degrees C), ATMND binds to cytosine and thymine with a comparable binding affinity (K(d) / nM: C: 7.7, T: 15). By contrast, in the presence of Lch, ATMND shows a clear binding selectivity for cytosine over thymine (K(d)/nM: C: 17, T: 204). Such competitive binding events are discussed with a view towards development of ligand-based fluorescence assay for single-nucleotide polymorphisms (SNPs) typing.
authors.affiliation: Department of Chemistry, Graduate School of Science, Tohoku university, and CREST, Japan Science and Technology Agency (JST), Aoba-ku, Sendai 980-8578, Japan.
authors.forename: Tomoe
authors.initials: T
authors.lastname: Kageyama
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Sato
authors.forename: Seiichi
authors.initials: S
authors.lastname: Nishizawa
authors.forename: Norio
authors.initials: N
authors.lastname: Teramae
mesh_terms: D001667:Binding, Competitive; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D005415:Flavins / Q000737:chemistry*; D008024:Ligands; D009287:Naphthyridines / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D013050:Spectrometry, Fluorescence; D013941:Thymine / Q000737:chemistry*
chemical_list: C528376:2-amino-5,6,7-trimethyl-1,8-naphthyridine; D005415:Flavins; D008024:Ligands; D009287:Naphthyridines; C001559:7,8-dimethylalloxazine; D003596:Cytosine; D004247:DNA; D013941:Thymine