Skip to main content
SpringerLink
Log in

A simple and novel method for the quantitative detection of 5-hydroxymethylcytosine using carbon nanotube field-effect transistors

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

Abstract

5-hydroxymethylcytosine (5-hmC) is an important epigenetic derivative of cytosine and quantitative detection of 5-hmC could be used as a reliable biomarker for a variety of human diseases. Current technologies used in 5-hmC detection are complicated and time/cost inefficient. In this work, we report the first application of antibody-functionalized carbon nanotube field-effect transistors (CNT-FETs) in quantitative detection of 5-hmC from mouse tissues. This method achieves facile and ultra-sensitive 5-hmC detection based on electrical performance device and avoids complicated processing for DNA samples. The 5-hmC content percentages of normal mouse cerebrum, cerebellum, spleen, lung, liver, and heart samples presented in the genomic DNA were measured as 0.653, 0.573, 0.002, 0.020, 0.076, and 0.009, respectively, which is consistent with previous reports. This technology could be developed into facile routine 5-hmC monitoring devices for clinic human disease diagnoses.

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. Wyatt, G. R.; Cohen, S. S. A new pyrimidine base from bacteriophage nucleic acids. Nature 1952, 170, 072–1073.

    Article  Google Scholar 

  2. Penn, N. W.; Suwalski, R.; O’Riley, C.; Bojanowski, K.; Yura, R. The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem. J. 1972, 126, 81–790.

    Article  Google Scholar 

  3. Kriaucionis, S.; Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324, 29–930.

    Article  Google Scholar 

  4. Tahiliani, M.; Koh, K. P.; Shen, Y. H.; Pastor, W. A.; Bandukwala, H.; Brudno, Y.; Agarwal, S.; Iyer, L. M.; Liu, D. R.; Aravind, L. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324, 30–935.

    Article  Google Scholar 

  5. Li, W. W.; Liu, M. Distribution of 5-hydroxymethylcytosine in different human tissues. J. Nucleic Acids. 2011, 2011, 870726.

    Article  Google Scholar 

  6. Feinberg, A. P.; Ohlsson, R; Henikoff, S. The epigenetic progenitor origin of human cancer. Nat. Rev. Genet. 2006, 7, 1–33.

    Article  Google Scholar 

  7. Suzuki, M. M.; Bird, A. DNA methylation landscapes: Provocative insights from epigenomics. Nat. Rev. Genet. 2008, 9, 65–476.

  8. Kroeze, L. I.; van der Reijden, B. A.; Jansen, J. H. 5-Hydroxymethylcytosine: An epigenetic mark frequently deregulated in cancer. Biochim. Biophys. Acta 2015, 1855, 44–154.

    Google Scholar 

  9. Szulwach, K. E.; Li, X. K.; Li, Y. J.; Song, C. X.; Wu, H.; Dai, Q.; Irier, H.; Upadhyay, A. K.; Gearing, M.; Levey, A. I. et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat. Neurosci. 2011, 14, 607–1616.

    Article  Google Scholar 

  10. Sherwani, S. I.; Khan, H. A. Role of 5-hydroxymethylcytosine in neurodegeneration. Gene 2015, 570, 7–24.

    Article  Google Scholar 

  11. Al-Mahdawi, S.; Virmouni, S. A.; Pook, M. A. The emerging role of 5-hydroxymethylcytosine in neurodegenerative diseases. Front. Neurosci. 2014, 8, 397.

    Article  Google Scholar 

  12. Clark, S. J.; Harrison, J.; Paul, C. L.; Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994, 22, 990–2997.

    Google Scholar 

  13. Cokus, S. J.; Feng, S. H.; Zhang, X. Y.; Chen, Z. G.; Merriman, B.; Haudenschild, C. D.; Pradhan, S.; Nelson, S. F.; Pellegrini, M.; Jacobsen, S. E. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452, 15–219.

    Article  Google Scholar 

  14. Le, T.; Kim, K. P; Fan, G. P.; Faull, K. F. A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal. Biochem. 2011, 412, 03–209.

    Article  Google Scholar 

  15. Globisch, D.; Münzel, M.; Müller, M.; Michalakis, S.; Wagner, M.; Koch, S.; Brückl, T.; Biel, M.; Carell, T. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 2010, 5–e15367.

    Google Scholar 

  16. Ito, S.; Shen, L.; Dai, Q.; Wu, S. C.; Collins, L. B.; Swenberg, J. A.; He, C.; Zhang, Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333, 300–1303.

    Article  Google Scholar 

  17. 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, 8–72.

    Article  Google Scholar 

  18. 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, 94–397.

    Article  Google Scholar 

  19. Szwagierczak, A.; Bultmann, S.; Schmidt, C. S.; Spada, F.; Leonhardt, H. Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res. 2010, 38. e181.

    Google Scholar 

  20. Terragni, J.; Bitinaite, J.; Zheng, Y.; Pradhan, S. Biochemical characterization of recombinant ß-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes. Biochemistry 2012, 51, 009–1019.

    Google Scholar 

  21. Kinney, S. M.; Chin, H. G.; Vaisvila, R.; Bitinaite, J.; Zheng, Y.; Estève, P. O.; Feng, S. H.; Stroud, H.; Jacobsen, S. E.; Pradhan, S. Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes. J. Biol. Chem. 2011, 286, 4685–24693.

    Article  Google Scholar 

  22. Höbartner, C. Enzymatic labeling of 5-hydroxymethylcytosine in DNA. Angew. Chem., Int. Ed. 2011. 50, 4268–4270

    Google Scholar 

  23. Harris. P. J. F. Carbon Nanotubes and Related Structures: New Materials for the Twenty-First Century; Cambridge University Press: Cambridge, 2001.

    Google Scholar 

  24. Dai, H. J. Carbon nanotubes: Opportunities and challenges. Surf. Sci. 2002, 500, 18–241.

    Article  Google Scholar 

  25. Katz, E.; Willner, I. Biomolecule functionalized carbon nanotubes: Applications in nanobioelectronics. ChemPhysChem 2004, 5, 084–1104.

    Google Scholar 

  26. Daniel, S.; Rao, T. P.; Rao, K. S.; Rani, S. U.; Naidu, G. R. K.; Lee, H. Y.; Kawai, T. A review of DNA functionalized/ grafted carbon nanotubes and their characterization. Sens. Act. B 2007, 122, 72–682.

    Article  Google Scholar 

  27. Drouvalakis, K. A.; Bangsaruntip, S.; Wolfgang, H.; Kozar, L. G.; Utz, P. J.; Dai, H. J. Peptide-coated nanotube-based biosensor for the detection of disease-specific autoantibodies in human serum. Biosens. Bioelectron. 2008, 23, 413–1421.

  28. Shim, M.; Kam, N. W. S.; Chen, R.; Li, Y. M.; Dai, H. J. Functionalization of carbon nanotubes for biocompatibility and biomolecular recognition. Nano Lett. 2002, 2, 85–288.

    Article  Google Scholar 

  29. Javey, A.; Guo, J.; Wang, Q.; Lundstrom, M.; Dai, H. J. Ballistic carbon nanotube field-effect transistors. Nature 2003, 424, 54–657.

    Article  Google Scholar 

  30. Byon, H. R.; Choi, H. C. Network single-walled carbon nanotube-field effect transistors (SWNT-FETs) with increased Schottky contact area for highly sensitive biosensor applications. J. Am. Chem. Soc. 2006, 128, 188–2189.

    Article  Google Scholar 

  31. Chen, R. J.; Bangsaruntip, S.; Drouvalakis, K. A.; Kam, N. W. S.; Shim, M.; Li, Y. M.; Kim, W.; Utz, P. J.; Dai, H. J. Noncovalent functionalization of carbon nanotubes for highly specific electronic biosensors. Proc. Natl. Acad. Sci. USA 2003, 100, 984–4989.

    Google Scholar 

  32. Li, C.; Curreli, M.; Lin, H.; Lei, B.; Ishikawa, F. N.; Datar, R.; Cote, R. J.; Thompson, M. E.; Zhou, C. W. Complementary detection of prostate-specific antigen using In2O3 nanowires and carbon nanotubes. J. Am. Chem. Soc. 2005, 127, 2484–12485.

    Google Scholar 

  33. Park, D. W.; Kim, Y. H.; Kim, B. S.; So, H. M.; Won, K.; Lee, J. O; Kong, K. J.; Chang, H. Detection of tumor markers using single-walled carbon nanotube field effect transistors. J. Nanosci. Nanotechnol. 2006, 6, 499–3502.

    Article  Google Scholar 

  34. Takeda, S.; Sbagyo, A.; Sakoda, Y.; Ishii, A.; Sawamura, M.; Sueoka, K.; Kida, H.; Mukasa, K.; Matsumoto, K. Application of carbon nanotubes for detecting anti-hemagglutinins based on antigen-antibody interaction. Biosens. Bioelectron. 2005, 21, 01–205.

    Article  Google Scholar 

  35. Veetil, J. V.; Ye, K. M. Development of immunosensors using carbon nanotubes. Biotechnol. Prog. 2007, 23, 17–531.

    Google Scholar 

  36. Liu, Z.; Zhao, J. W.; Xu, W. Y.; Qian, L.; Nie, S. H.; Cui, Z. Effect of surface wettability properties on the electrical properties of printed carbon nanotube thin-film transistors on SiO2/Si substrates. ACS Appl. Mater. Interfaces 2014, 6, 997–10004.

    Google Scholar 

  37. Maehashi, K.; Katsura, T.; Kerman, K.; Takamura, Y.; Matsumoto, K.; Tamiya, E. Label-free protein biosensor based on aptamer-modified carbon nanotube field-effect transistors. Anal. Chem. 2007, 79, 82–787.

  38. Wang, C.; Zhang, J. L.; Ryu, K.; Badmaev, A.; De Arco, L. G.; Zhou, C. W. Wafer-scale fabrication of separated carbon nanotube thin-film transistors for display applications. Nano Lett. 2009, 9, 285–4291.

  39. Tsang, S. C.; Davis, J. J.; Green, M. L. H.; Hill, H. A. O.; Leung, Y. C.; Sadler, P. J. Immobilization of small proteins in carbon nanotubes: High-resolution transmission electron microscopy study and catalytic activity. J. Chem. Soc., Chem. Commun. 1995, 1803–1804.

  40. Tsang, S. C.; Guo, Z. J.; Chen, Y. K.; Green, M. L. H.; Hill, H. A. O.; Hambley, T. W.; Sadler, P. J. Immobilization of platinated and iodinated oligonucleotides on carbon nanotubes. Angew. Chem., Int. Ed. 1997, 36, 198–2200.

    Article  Google Scholar 

  41. Guo, Z. J.; Sadler, P. J.; Tsang, S. C. Immobilization and visualization of DNA and proteins on carbon nanotubes. Adv. Mater. 1998, 10, 01–703.

    Google Scholar 

  42. Balavoine, F.; Schultz, P.; Richard, C.; Mallouh, V.; Ebbeson, T. W.; Mioskowski, C. Helical crystallization of proteins on carbon nanotubes: A first step towards the development of new biosensors. Angew. Chem., Int. Ed. 1999, 38, 912–1915.

    Article  Google Scholar 

  43. Chen, R. J.; Zhang, Y. G.; Wang, D. W.; Dai, H. J. Noncovalent sidewall functionalization of single-walled carbon nanotubes for protein immobilization. J. Am. Chem. Soc. 2001, 123, 838–3839.

    Google Scholar 

  44. Lee, C. S.; Baker, S. E.; Marcus, M. S.; Yang, W. S.; Eriksson, M. A.; Hamers, R. J. Electrically addressable biomolecular functionalization of carbon nanotube and carbon nanofiber electrodes. Nano Lett. 2004, 4, 713–1716.

    Article  Google Scholar 

  45. Hermanson, G. T. Bioconjugate Techniques; Academic Press: San Diego, 1996.

    Google Scholar 

  46. Thordarson, P.; Atkin, R.; Kalle, W. H. J; Warr, G. G.; Braet, F. Developments in using scanning probe microscopy to study molecules on surfaces—From thin films and singlemolecule conductivity to drug-living cell interactions. ChemInform 2006, 37. DOI: 10.1002/chin.200639277.

    Google Scholar 

  47. Katz, E. Application of bifunctional reagents for immobilization of proteins on a carbon electrode surface: Oriented immobilization of photosynthetic reaction centers. J. Electroanal. Chem. 1994, 365, 57–164.

    Article  Google Scholar 

  48. Jaegfeldt, H.; Kuwana, T.; Johansson, G. Electrochemical stability of catechols with a pyrene side chain strongly adsorbed on graphite electrodes for catalytic oxidation of dihydronicotinamide adenine dinucleotide. J. Am. Chem. Soc. 1983, 105, 805–1814.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Chemical Biology & Biotechnology, Peking University, Shenzhen, 518055, China

    Fang Yuan & Zigang Li

  2. School of Electronic and Computer Engineering, Peking University, Shenzhen, 518055, China

    Yanyan Deng & Min Zhang

  3. Shenzhen Thin Film Transistor and Advanced Display Lab, Shenzhen, 518055, China

    Yanyan Deng & Min Zhang

  4. Shenzhen Second People’s Hospital, Shenzhen, 518035, China

    Wenyu Zhou

Authors
  1. Fang Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yanyan Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenyu Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Min Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zigang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Wenyu Zhou, Min Zhang or Zigang Li.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yuan, F., Deng, Y., Zhou, W. et al. A simple and novel method for the quantitative detection of 5-hydroxymethylcytosine using carbon nanotube field-effect transistors. Nano Res. 9, 1701–1708 (2016). https://doi.org/10.1007/s12274-016-1064-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12274-016-1064-3

Keywords

Search

Navigation