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Updated: Jul 1, 2026

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
Published on: January 7, 2017
Competitive binding of small ligands to nucleobases in AP site-containing DNA duplexes
Tomoe Kageyama1, Yusuke Sato, Seiichi Nishizawa
1Department of Chemistry, Graduate School of Science, Tohoku university, and CREST, Japan Science and Technology Agency (JST), Aoba-ku, Sendai 980-8578, Japan.
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.
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