Competitive binding of small ligands to nucleobases in AP site-containing DNA duplexes.

Tomoe Kageyama, Yusuke Sato, Seiichi Nishizawa, Norio Teramae

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)119-120
Number of pages2
JournalNucleic acids symposium series (2004)
Issue number52
Publication statusPublished - 2008 Dec 1
Externally publishedYes

ASJC Scopus subject areas

  • Medicine(all)

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