Fluorescence detection of thymidine-related single-nucleotide polymorphisms by 3, 5-diaminopyrazine derivatives.

Chunxia Zhao, Qing Dai, Takehiro Seino, Ying Yu Cui, Seiichi Nishizawa, Norio Teramae

Research output: Contribution to journalArticlepeer-review

Abstract

We report on a highly selective fluorescence ligand for thymine (T) base opposite an abasic site (AP site) in DNA duplexes. From the examination of the binding behaviors in solutions buffered to pH 7.0, we find that 6-chloro-3,5-diamino-2-pyrazinecarbonitrile (CDPC) can selectively recognize T with high affinity (Ka = 2.9 x 10(5) M(-1)), and the fluorescence intensity at 424 nm is significantly quenched only when binding to T. It is highly likely that the selective interaction of CDPC with T is explained by a pseudo-base pairing, for which three point hydrogen bonds are formed along the Watson-Crick edge of the target T. These binding functions of CDPC at the AP site are presented to develop ligand-based fluorescence assay for SNPs (single-nucleotide polymorphisms) typing.

Original languageEnglish
Pages (from-to)221-222
Number of pages2
JournalNucleic acids symposium series (2004)
Issue number49
DOIs
Publication statusPublished - 2005

ASJC Scopus subject areas

  • Medicine(all)

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