A pyrazine-based fluorescence-enhancing ligand with a high selectivity for thymine in AP site-containing DNA duplexes.
A fluorescent pyrazine derivative, 3,5-diamino-6-chloro-2-pyrazine carbonitrile (DCPC), is presented as a promising light-up ligand for single-nucleotide polymorphisms (SNPs) typing. In solutions buffered to pH 7.0 (I = 0.11 M, at 5 degrees C), DCPC can bind to thymine selectively over other nucleobases opposite an abasic site in DNA duplexes (5'-GTGTG CGTTG ANA TGGAC GCAGA-3'/3'-CACAC GCAAC TXT ACCTG CGTCT-5', X = abasic site, N = target nucleotide) with a dissociation constant of 2.6 microM. The binding of DCPC is accompanied by a significant enhancement of its fluorescence (lambda(max), 412 nm), and the response is highly selective to thymine base. These binding and sensing properties allow a clear detection of thymine-related mutations present in polymerase chain reaction (PCR) amplification products.
Zhao
Chunxia
C
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba, Sendai, Japan.
Rajendran
Arivazhagan
A
Dai
Qing
Q
Nishizawa
Seiichi
S
Teramae
Norio
N
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D005453:Fluorescence; D008024:Ligands; D011119:Polynucleotides; D011719:Pyrazines / Q000737:chemistry*; D013379:Substrate Specificity; D013941:Thymine / Q000737:chemistry*
C520213:6-chloro-3,5-diamino-2-pyrazinecarbonitrile; D008024:Ligands; D011119:Polynucleotides; D011719:Pyrazines; C001790:apyrimidinic acid; D004247:DNA; D013941:Thymine