Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
권호 표지
DOI QR코드

DOI QR Code

A Linear Beacon System Featuring an Internal Deoxyguanine Quencher Allows Highly Selective Detection of Single Base Mismatches

  • Lee, Young-Ae (Department of Chemistry, Kyungpook National University) ;
  • Hwang, Gil-Tae (Department of Chemistry, Kyungpook National University)
  • Received : 2010.05.12
  • Accepted : 2010.05.27
  • Published : 2010.07.20
Download PDF
⟨ Previous Next ⟩

Abstract

The fluorescence intensity of a single-stranded oligonucleotide containing a fluorene-labeled deoxyuridine $(U^{Fl})$ unit increases by only 1.5-fold upon formation of its perfectly matched duplex. To increase the fluorescence signal during hybridization, we positioned a quencher strand containing a deoxyguanine (dG) nucleobase, functioning as an internal quencher, opposite to the $U^{Fl}$ unit to reduce the intrinsic fluorescence upon hybridization with a probe. From an investigation of the optimal length of the quencher strand and the effect of the neighboring base sequence, we found that a short strand (five-nucleotide) containing all natural nucleotides and dG as an internal quencher was effective at reducing the intrinsic fluorescence of a linear beacon; it also exhibited high total discrimination factors for the formation of perfectly matched and single base-mismatched duplexes. Such assays that function based on clear changes in fluorescence in response to single-base nucleotide mutations would be useful tools for accelerating diagnoses related to various diseases.

Keywords

References

  1. Tyagi, S.; Kramer, F. R. Nat. Biotechnol. 1996, 14, 303. https://doi.org/10.1038/nbt0396-303
  2. Tyagi, S.; Bratu, D.; Kramer, F. R. Nat. Biotechnol. 1998, 16, 49. https://doi.org/10.1038/nbt0198-49
  3. Ho, H. A.; Boissinot, M.; Bergeron, M. G.; Corbeil, G.; Dore, K.; Boudreau, D.; Leclerc, M. Angew. Chem., Int. Ed. 2002, 41, 1548. https://doi.org/10.1002/1521-3773(20020503)41:9<1548::AID-ANIE1548>3.0.CO;2-I
  4. Yamane, A. Nucleic Acids Res. 2002, 30, e97. https://doi.org/10.1093/nar/gnf096
  5. Kumar, T. S.; Wengel, J.; Hrdlicka, P. J. ChemBioChem 2007, 8, 1122. https://doi.org/10.1002/cbic.200700144
  6. Thurley, S.; Roglin, L.; Seitz, O. J. Am. Chem. Soc. 2007, 129, 12693. https://doi.org/10.1021/ja075487r
  7. Lyamichev, V.; Mast, A. L.; Hall, J. G.; Prudent, J. R.; Kaiser, M. W.; Takova, T.; Kwiatkowski, R. W.; Sander, T. J.; de Arruda, M.; Arco, D. A.; Neri, B. P.; Brow, M. A. D. Nat. Biotechnol. 1999, 17, 292. https://doi.org/10.1038/7044
  8. Komiyama, M.; Ye, S.; Liang, X. G.; Yamamoto, Y.; Tomita, T.; Zhou, J. M.; Aburatani, H. J. Am. Chem. Soc. 2003, 125, 3758. https://doi.org/10.1021/ja0295220
  9. Schena, M.; Heller, R. A.; Theriault, T. P.; Konrad, K.; Lachenmeier, E.; Davis, R. W. Trends Biotechnol. 1998, 16, 301. https://doi.org/10.1016/S0167-7799(98)01219-0
  10. Pirrung, M. C. Angew. Chem., Int. Ed. 2002, 41, 1276. https://doi.org/10.1002/1521-3773(20020415)41:8<1276::AID-ANIE1276>3.0.CO;2-2
  11. Taton, T. A.; Mirkin, C. A.; Letsinger, R. L. Science 2000, 289, 1757 https://doi.org/10.1126/science.289.5485.1757
  12. Liu, G.; Lee, T. M. H.; Wang, J. J. Am. Chem. Soc. 2005, 127, 38. https://doi.org/10.1021/ja043780a
  13. Hwang, G. T.; Seo, Y. J.; Kim, B. H. J. Am. Chem. Soc. 2004, 126, 6528. https://doi.org/10.1021/ja049795q
  14. Luo, G.; Zheng, L.; Zhang, X.; Zhang, J.; Nilsson-Ehle, P.; Xu, N. Anal. Biochem. 2009, 386, 161. https://doi.org/10.1016/j.ab.2008.11.032
  15. Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. J. Phys. Chem. 1996, 100, 5541. https://doi.org/10.1021/jp951507c
  16. Cooper, J. P.; Hagerman, P. J. Biochemistry 1990, 29, 9261. https://doi.org/10.1021/bi00491a022
  17. Gait, M. J. Oligonucleotide Synthesis: A Practical Approach; IRL Press: Washington, DC, 1984.
  18. Ryu, J. H.; Seo, Y. J.; Hwang, G. T.; Lee, J. Y.; Kim, B. H. Tetrahedron 2007, 63, 3538. https://doi.org/10.1016/j.tet.2006.10.091
  19. Wagenknecht, H.-A. Angew. Chem., Int. Ed. 2003, 42, 2454. https://doi.org/10.1002/anie.200301629

Cited by

  1. Highly Efficient Quencher-Free Molecular Beacon Systems Containing 2-Ethynyldibenzofuran- and 2-Ethynyldibenzothiophene-Labeled 2′-Deoxyuridine Units vol.14, pp.11, 2013, https://doi.org/10.1002/cbic.201300240
  2. Fluorescent Oligonucleotides Containing a 2-Ethynylfluorene- or 2-Ethynylfluorenone-labeled 2′-Deoxyguanosine Unit: Fluorescence Changes upon Duplex Formation vol.37, pp.8, 2016, https://doi.org/10.1002/bkcs.10856
  3. Photophysical Study of 2-Fluorenyl-1,2,3-Triazole-labeled 2′-Deoxyuridine and Its Oligonucleotide vol.39, pp.1, 2017, https://doi.org/10.1002/bkcs.11349
  4. Single-Labeled Oligonucleotides Showing Fluorescence Changes upon Hybridization with Target Nucleic Acids vol.23, pp.1, 2018, https://doi.org/10.3390/molecules23010124
  5. Quencher-free Linear Beacon Systems with Dual Fluorene-labeled Deoxyuridines vol.32, pp.11, 2010, https://doi.org/10.5012/bkcs.2011.32.11.4129
  6. The linkers in fluorene-labeled 2′-deoxyuridines affect fluorescence discriminating phenomena upon duplex formation vol.10, pp.32, 2010, https://doi.org/10.1039/d0ra01651a
  7. Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing vol.18, pp.30, 2010, https://doi.org/10.1039/d0ob01299h