Fluorescence detection of thymidine-related single-nucleotide polymorphisms by 3, 5-diaminopyrazine derivatives.
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.
Zhao
Chunxia
C
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
Dai
Qing
Q
Seino
Takehiro
T
Cui
Ying-Yu
YY
Nishizawa
Seiichi
S
Teramae
Norio
N
D015342:DNA Probes; D005456:Fluorescent Dyes / Q000737:chemistry*; D008024:Ligands; D020641:Polymorphism, Single Nucleotide; D011719:Pyrazines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013936:Thymidine / Q000737:chemistry*
C520213:6-chloro-3,5-diamino-2-pyrazinecarbonitrile; D015342:DNA Probes; D005456:Fluorescent Dyes; D008024:Ligands; D011719:Pyrazines; D013936:Thymidine