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Nucleic Acids Symposium Series 2005 49(1):221-222; doi:10.1093/nass/49.1.221
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© 2005 Oxford University Press

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

Chunxia Zhao1, Qing Dai1, Takehiro Seino1, Ying-Yu Cui1, Seiichi Nishizawa1,2 and Norio Teramae1,2

1 Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, 2 CREST, Japan Science and Technology Agency (JST)

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 105 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.


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