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

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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 (7 = 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-373’-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.

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References

  1. J. M. Gottesfeld, L. Neely, J. W. Trauger, E. E. Baird, and P. B. Dervan, Nature, 1997, 387, 202.

    Article  CAS  Google Scholar 

  2. P. B. Dervan, Bioorg. Med. Chem., 2001, 9, 2215.

    Article  CAS  Google Scholar 

  3. T. G. Uil, H. J. Haisma, and M. G. Rots, Nucleic Acids Res., 2003, 31, 6064.

    Article  CAS  Google Scholar 

  4. D. R. Spring, Chem. Soc. Rev., 2005, 34, 472.

    Article  CAS  Google Scholar 

  5. M. Chicurel, Nature, 2001, 412, 580.

    Article  CAS  Google Scholar 

  6. K. Yoshimoto, S. Nishizawa, M. Minagawa, and N. Teramae, J. Am. Chem. Soc, 2003, 125, 8982.

    Article  CAS  Google Scholar 

  7. K. Yoshimoto, C.-Y. Xu, S. Nishizawa, T. Haga, H. Satake, and N. Teramae, Chem. Commun., 2003, 2960.

    Google Scholar 

  8. S. Nishizawa, K. Yoshimoto, T. Seino, C.-Y. Xu, M. Minagawa, H. Satake, A. Tong, and N. Teramae, Talanta, 2004, 63, 175.

    Article  CAS  Google Scholar 

  9. Q. Dai, C.-Y. Xu, Y. Sato, K. Yoshimoto, S. Nishizawa, and N. Teramae, Anal. Sci., 2006, 22, 201.

    Article  CAS  Google Scholar 

  10. C. Zhao, Q. Dai, T. Seino, Y.-Y. Cui, S. Nishizawa, and N. Teramae, Chem. Commun., 2006, 1185.

    Google Scholar 

  11. N. B. Sankaran, S. Nishizawa, T. Seino, K. Yoshimoto, and N. Teramae, Angew. Chem., Int. Ed, 2006, 45, 1563.

    Article  CAS  Google Scholar 

  12. S. Nishizawa, N. B. Sankaran, T. Seino, Y.-Y. Cui, Q. Dai, C.-Y. Xu, K. Yoshimoto, and N. Teramae, Anal. Chim. Acta, 2006, 556, 133.

    Article  CAS  Google Scholar 

  13. H. Satake, S. Nishizawa, and N. Teramae, Anal. Sci., 2006, 22, 195.

    Article  CAS  Google Scholar 

  14. B. Rajendar, Y. Sato, S. Nishizawa, and N. Teramae, Bioorg. Med. Chem. Lett, 2007, 17, 3682.

    Article  CAS  Google Scholar 

  15. K. Morita, Y. Sato, T. Seino, S. Nishizawa, and N. Teramae, Org. Biomol. Chem., 2008, 6, 266.

    Article  CAS  Google Scholar 

  16. B. Rajendar, S. Nishizawa, and N. Teramae, Org. Biomol. Chem., 2008, 6, 670.

    Article  CAS  Google Scholar 

  17. S. Takenaka, K. Yamashita, M. Takagi, Y. Uto, and H. Kondo, Anal. Chem., 2000, 72, 1334.

    Article  CAS  Google Scholar 

  18. I. Haq, J. E. Ladbury, B. Z. Chowdhry, T. C. Jenkins, and J. B. Chaires, J. Mol. Biol, 1997, 271, 244.

    Article  CAS  Google Scholar 

  19. J. M. Jean and K. B. Hall, Proc. Natl. Acad. Sci. U. S. A., 2001, 98, 37.

    Article  CAS  Google Scholar 

  20. S. E. Kern, K. W. Kinzler, A. Bruskin, D. Jarosz, P. Friedman, C. Prives, and B. Vogelstein, Science, 1991, 252, 1708.

    Article  CAS  Google Scholar 

  21. M. A. Innis, K. B. Myambo, D. H. Gelfand, and M. A. D. Brow, Proc. Natl. Acad. Sci. U. S. A., 1988, 85, 9436.

    Article  CAS  Google Scholar 

  22. Asymmetric PCR21 amplification of 141-mer sense strands of p53 gene20 was done with a 24-mer forward primer (5’-GTAGTGGTAATCTACTGGGACGGA-3’) and a 23-mer reverse primer (5’-CTCGCTTAGTGCTCCCTGGGGGC-3’). The reaction solution (100 μl) contained dNTPs (2.5 mM each, 8 μl), 10 x PCR buffer (10 μl; TaKaRa), forward primer (300 pmol), reverse primer (20 pmol), template (0.2 pmol), and Ex-Taq (2.5 U; TaKaRa). PCR conditions: 94°C for 5 min, followed by 50 cycles of 96°C for 30 s, 57°C for 30 s, and 72°C for 30 s, and then 72°C for 5 min and kept at 4°C. 141-mer PCR product: 5’-GT AGT GGT AAT CTA CTG GGA CGG AAC AGC TTT GAG GTG CGT GTT TGT GCC TGT CCT GGG AYA GAC CGG CGC ACA GAG GAA GAG AAT CTC CGC AAG AAA GGG GAG CCT CAC CAC GAG CTG CCC CCA GGG AGC ACT AAG CGA G-3’ (wild type, Y = G; mutant type, Y = T); 21-mer probe DNA: 5’-GCG CCG GTC TXT CCC AGG ACA-3’ (X = AP site; Spacer-C3).

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Author notes

  1. Chunxia Zhao

    Present address: Chinese Academy of Science, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, 457 Zhongshan Road, Dalian, 116023, China

Authors and Affiliations

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

    Chunxia Zhao, Arivazhagan Rajendran, Qing Dai, Seiichi Nishizawa & Norio Teramae

  2. Chinese Academy of Science, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, 457 Zhongshan Road, Dalian, 116023, China

    Arivazhagan Rajendran, Qing Dai, Seiichi Nishizawa & Norio Teramae

Authors
  1. Chunxia Zhao
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  2. Arivazhagan Rajendran
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  3. Qing Dai
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  4. Seiichi Nishizawa
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  5. Norio Teramae
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Corresponding author

Correspondence to Norio Teramae.

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Zhao, C., Rajendran, A., Dai, Q. et al. A Pyrazine-based Fluorescence-enhancing Ligand with a High Selectivity for Thymine in AP Site-containing DNA Duplexes. ANAL. SCI. 24, 693–695 (2008). https://doi.org/10.2116/analsci.24.693

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  • DOI: https://doi.org/10.2116/analsci.24.693

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