A Pyrazine-based Fluorescence-enhancing Ligand with a High Selectivity for Thymine in AP Site-containing DNA Duplexes

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  • ZHAO Chunxia
    Department of Chemistry, Graduate School of Science, Tohoku University, and CREST, Japan Science and Technology Agency (JST)
  • RAJENDRAN Arivazhagan
    Department of Chemistry, Graduate School of Science, Tohoku University, and CREST, Japan Science and Technology Agency (JST)
  • DAI Qing
    Department of Chemistry, Graduate School of Science, Tohoku University, and CREST, Japan Science and Technology Agency (JST)
  • NISHIZAWA Seiichi
    Department of Chemistry, Graduate School of Science, Tohoku University, and CREST, Japan Science and Technology Agency (JST)
  • TERAMAE Norio
    Department of Chemistry, Graduate School of Science, Tohoku University, and CREST, Japan Science and Technology Agency (JST)

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Abstract

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°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 µM. The binding of DCPC is accompanied by a significant enhancement of its fluorescence (λmax, 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.

Journal

  • Analytical Sciences

    Analytical Sciences 24 (6), 693-695, 2008

    The Japan Society for Analytical Chemistry

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