Skip to main content
SpringerLink
Log in

A highly efficient fluorescence-based switch-on detection method of 5-formyluracil in DNA

  • Research Article
  • Published:
Nano Research Aims and scope Submit manuscript

Abstract

The identification of hydroxylmethyl- and formylpyrimidines in genomic DNA was a landmark event in epigenetics. Numerous laboratories in related fields are investigating the biology of these and other nucleic acid modifications. However, limitations in the ability to detect and synthesize appropriate modifications are an impediment. Herein, we explored a remarkable development in the selective detection of 5-formyluracil in both single-stranded and double-stranded DNA under mild conditions. The “switch-on” specificity towards 5-formyluracil enabled a high signal-to-noise ratio in qualitatively and quantitatively detecting materials containing 5-formyluracil, which is not affected by the presence of abasic sites and 5-formylcytosine, the modified cytosine counterpart of 5-formyluracil. In summary, the innoxiousness, convenience, and cost-efficiency of the 5-formyluracil phosphoramidite synthetic routine would promote the understanding of the epigenetic role of this natural thymidine modification.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Gommers-Ampt, J. H.; Borst, P. Hypermodified bases in DNA. FASEB J. 1995, 9, 1034–1042.

    Google Scholar 

  2. Frankham, R. Genetics and extinction. Biol. Conserv. 2005, 126, 131–140.

    Article  Google Scholar 

  3. Wu, H.; Wu, X. J.; Shen, L.; Zhang, Y. Single-base resolution analysis of active DNA demethylation using methylaseassisted bisulfite sequencing. Nat. Biotechnol. 2014, 32, 1231–1240.

    Article  Google Scholar 

  4. Suzuki, M. M.; Bird, A. DNA methylation landscapes: Provocative insights from epigenomics. Nat. Rev. Genet. 2008, 9, 465–476.

    Article  Google Scholar 

  5. Williams, K.; Christensen, J.; Pedersen, M. T.; Johansen, J. V.; Cloos, P. A. C.; Rappsilber, J.; Helin, K. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011, 473, 343–348.

    Article  Google Scholar 

  6. Schübeler, D. Function and information content of DNA methylation. Nature 2015, 517, 321–326.

    Article  Google Scholar 

  7. Pfaffeneder, T.; Hackner, B.; Truß, M.; Münzel, M.; Müller, M.; Deiml, C. A.; Hagemeier, C.; Carell, T. The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew. Chem., Int. Ed. 2011, 50, 7008–7012.

    Article  Google Scholar 

  8. Pfaffeneder, T.; Spada, F.; Wagner, M.; Brandmayr, C.; Laube, S. K.; Eisen, D.; Truss, M.; Steinbacher, J.; Hackner, B.; Kotljarova, O. et al. Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat. Chem. Biol. 2014, 10, 574–581.

    Article  Google Scholar 

  9. Kasai, H.; Iida, A.; Yamaizumi, Z.; Nishimura, S.; Tanooka, H. 5-Formyldeoxyuridine: A new type of DNA damage induced by ionizing radiation and its mutagenicity to Salmonella strain TA102. Mutat. Res. Lett. 1990, 243, 249–253.

    Article  Google Scholar 

  10. Privat, E. J.; Sowers, L. C. A proposed mechanism for the mutagenicity of 5-formyluracil. Mutat. Res. 1996, 354, 151–156.

    Article  Google Scholar 

  11. Hong, H. Z.; Cao, H. C.; Wang, Y. S.; Wang, Y. S. Identification and quantification of a guanine-thymine intrastrand cross-link lesion induced by Cu(II)/H2O2/ascorbate. Chem. Res. Toxicol. 2006, 19, 614–621.

    Article  Google Scholar 

  12. Hong, H. Z.; Wang, Y. S. Derivatization with girard reagent T combined with LC-MS/MS for the sensitive detection of 5-formyl-2′-deoxyuridine in cellular DNA. Anal. Chem. 2007, 79, 322–326.

    Article  Google Scholar 

  13. Liu, C. K.; Hsu, C. A.; Abbott, M. T. Catalysis of three sequential dioxygenase reactions by thymine 7-hydroxylase. Arch. Biochem. Biophys. 1973, 159, 180–187.

    Article  Google Scholar 

  14. Yoshida, M.; Makino, K.; Morita, H.; Terato, H.; Ohyama, Y.; Ide, H. Substrate and mispairing properties of 5-formyl-2′-deoxyuridine 5′-triphosphate assessed by in vitro DNA polymerase reactions. Nucleic Acids Res. 1997, 25, 1570–1577.

    Article  Google Scholar 

  15. Rogstad, D. K.; Heo, J.; Vaidehi, N.; Goddard, W. A., III; Burdzy, A.; Sowers, L. C. 5-Formyluracil-induced perturbations of DNA function. Biochemistry 2004, 43, 5688–5697.

  16. Smiley, J. A.; Kundracik, M.; Landfried, D. A.; Barnes, V. R., Sr.; Axhemi, A. A. Genes of the thymidine salvage pathway: Thymine-7-hydroxylase from a Rhodotorula glutinis cDNA library and iso-orotate decarboxylase from Neurospora crassa. Biochim. Biophys. Acta 2005, 172, 256–264.

    Article  Google Scholar 

  17. Guo, J. U.; Su, Y. J.; Zhong, C.; Ming, G. L.; Song, H. J. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011, 145, 423–434.

    Article  Google Scholar 

  18. Cortellino, S.; Xu, J. F.; Sannai, M.; Moore, R.; Caretti, E.; Cigliano, A.; Le Coz, M.; Devarajan, K.; Wessels, A.; Soprano, D. et al. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 2011, 146, 67–79.

    Article  Google Scholar 

  19. Yu, M.; Song, C. X.; He, C. Detection of mismatched 5-hydroxymethyluracil in DNA by selective chemical labeling. Methods 2015, 72, 16–20.

    Article  Google Scholar 

  20. Song, C. X.; Szulwach, K. E.; Dai, Q.; Fu, Y.; Mao, S. Q.; Lin, L.; Street, C.; Li, Y. J.; Poidevin, M.; Wu, H. et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 2013, 153, 678–691.

    Article  Google Scholar 

  21. Pastor, W. A.; Pape, U. J.; Huang, Y.; Henderson, H. R.; Lister, R.; Ko, M.; McLoughlin, E. M.; Brudno, Y.; Mahapatra, S.; Kapranov, P. et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011, 473, 394–397.

    Article  Google Scholar 

  22. Song, C. X.; Szulwach, K. E.; Fu, Y.; Dai, Q.; Yi, C. Q.; Li, X. K.; Li, Y. J.; Chen, C. H.; Zhang, W.; Jian, X. et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 2011, 29, 68–72.

    Article  Google Scholar 

  23. Samanta, B.; Seikowski, J.; Hö bartner, C. Fluorogenic labeling of 5-formylpyrimidine nucleotides in DNA and RNA. Angew. Chem., Int. Ed. 2016, 55, 1912–1916.

    Article  Google Scholar 

  24. Hardisty, R. E.; Kawasaki, F.; Sahakyan, A. B.; Balasubramanian, S. Selective chemical labeling of natural T modifications in DNA. J. Am. Chem. Soc. 2015, 137, 9270–9272.

    Article  Google Scholar 

  25. Hirose, W.; Sato, K.; Matsuda, A. Selective detection of 5-formyl-2′-deoxyuridine, an oxidative lesion of thymidine in DNA by a fluorogenic reagent. Angew. Chem., Int. Ed. 2010, 49, 8392–8394.

    Article  Google Scholar 

  26. Guo, P.; Xu, X. W.; Qiu, X. Y.; Zhou, Y. M.; Yan, S. Y.; Wang, C. C.; Lu, C. J.; Ma, W.; Weng, X. C.; Zhang, X. Z. et al. Synthesis and spectroscopic properties of fluorescent 5-benzimidazolyl-2′-deoxyuridines 5-fdU probes obtained from o-phenylenediamine derivatives. Org. Biomol. Chem. 2013, 11, 1610–1613.

    Article  Google Scholar 

  27. Xia, B.; Han, D. L.; Lu, X. Y.; Sun, Z. Z.; Zhou, A. K.; Yin, Q. Z.; Zeng, H.; Liu, M. H.; Jiang, X.; Xie, W. et al. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat. Methods 2015, 12, 1047–1050.

    Article  Google Scholar 

  28. Key, J. A.; Li, C. S.; Cairo, C. W. Detection of cellular sialic acid content using nitrobenzoxadiazole carbonyl-reactive chromophores. Bioconjugate Chem. 2012, 23, 363–371.

    Article  Google Scholar 

  29. Sugiyama, H.; Matsuda, S.; Kino, K.; Zhang, Q.-M.; Yonei, S.; Saito, I. New synthetic method of 5-formyluracil-containing oligonucleotides and their melting behavior. Tetrahedron Lett. 1996, 37, 9067–9070.

    Article  Google Scholar 

  30. Sato, K.; Hirose, W.; Matsuda, A. Synthesis of 5-formyl-2′-deoxyuridine and its incorporation into oligodeoxynucleotides. In Current Protocols in Nucleic Acid Chemistry. John Wiley & Sons, Inc.: New York, 2008.

    Google Scholar 

  31. Schröder, A. S.; Steinbacher, J.; Steigenberger, B.; Gnerlich, F. A.; Schiesser, S.; Pfaffeneder, T.; Carell, T. Synthesis of a DNA promoter segment containing all four epigenetic nucleosides: 5-methyl-, 5-hydroxymethyl-, 5-formyl-, and 5-carboxy-2′-deoxycytidine. Angew. Chem., Int. Ed. 2014, 53, 315–318.

    Article  Google Scholar 

  32. Frelon, S.; Douki, T.; Ravanat, J.-L.; Pouget, J.-P.; Tornabenen, C.; Cadet, J. High-performance liquid chromatographytandem mass spectrometry measurement of radiation-induced base damage to isolated and cellular DNA. Chem. Res. Toxicol. 2000, 13, 1002–1010.

    Article  Google Scholar 

Download references

Acknowledgements

We thank the National Basic Research Program of China (Nos. 2012CB720600 and 2012CB720603), the National Natural Science Foundation of China (Nos. 21432008, 91413109, and 81373256).

Author information

Author notes

  1. These authors contributed equally to this work.

Authors and Affiliations

  1. College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, 430072, China

    Chaoxing Liu, Yuqi Chen, Yafen Wang, Fan Wu, Xiong Zhang, Wei Yang, Jiaqi Wang, Yi Chen, Zhiyong He, Guangrong Zou, Shaoru Wang & Xiang Zhou

Authors
  1. Chaoxing Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuqi Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yafen Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fan Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jiaqi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yi Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Zhiyong He
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Guangrong Zou
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Shaoru Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Xiang Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiang Zhou.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, C., Chen, Y., Wang, Y. et al. A highly efficient fluorescence-based switch-on detection method of 5-formyluracil in DNA. Nano Res. 10, 2449–2458 (2017). https://doi.org/10.1007/s12274-017-1445-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12274-017-1445-2

Keywords

Search

Navigation