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A green method of staining DNA in polyacrylamide gel electrophoresis based on fluorescent copper nanoclusters synthesized in situ

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Abstract

The safety of nucleic acid staining dyes has long been recognized to be a problem. Extensive efforts have been made to search for alternatives to the most popular but toxic staining dye, ethidium bromide (EtBr). However, so far no staining method that can be guaranteed to be sufficiently safe has been developed. In this paper, we report a green staining method of DNA in polyacrylamide gel electrophoresis, where in situ synthesis of DNA-templated fluorescent copper nanoclusters (CuNCs) in the gel is achieved to make the DNA bands visible under UV light. Moreover, a comprehensive study of the performance of this staining method has been conducted and the experimental results show that it has favorable sensitivity, stability, and usability. Meanwhile, in our animal experiments, the two reagents (copper sulfate and ascorbic acid) as well as the synthesized CuNCs have been proven to be non-toxic in contact with skin. In addition, all the reagents employed in this work are readily available and low cost, and the procedure is simple to carry out. Therefore, this novel staining method based on the in situ synthesis DNA-templated fluorescent CuNCs has many potential applications.

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References

  1. Meyers, J. A.; Sanchez, D.; Elwell, L. P.; Falkow, S. Simple agarose gel electrophoretic method for the identification and characterization of plasmid deoxyribonucleic acid. J. Bacteriol. 1976, 127, 1529–1537.

    Google Scholar 

  2. Lee, J. D.; Huang, C. H.; Wang, N. W.; Lu, C. S. Automatic DNA sequencing for electrophoresis gels using image processing algorithms. J. Biomed. Sci. Eng. 2011, 4, 523–528.

    Article  Google Scholar 

  3. Ogier, J. C.; Son, O.; Gruss, A.; Tailliez, P.; Delacroix-Buchet, A. Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis. Appl. Environ. Microb. 2002, 68, 3691–3701.

    Article  Google Scholar 

  4. Rotaru, A.; Dutta, S.; Jentzsch, E.; Gothelf, K.; Mokhir, A. Selective dsDNA-templated formation of copper nanoparticles in solution. Angew. Chem. Int. Edit. 2010, 49, 5665–5667.

    Article  Google Scholar 

  5. Yi, S. H.; Xu, L. C.; Mei, K.; Yang, R. Z.; Huang, D. X. Isolation and identification of age-related DNA methylation markers for forensic age-prediction. Forensic. Sci. Int.: Genet. 2014, 11, 117–125.

    Article  Google Scholar 

  6. Aaij, C.; Borst, P. The gel electrophoresis of DNA. Biochim. Biophys. Acta, Nucleic Acids Protein Synth. 1972, 269, 192–200.

    Article  Google Scholar 

  7. Singer, V. L.; Lawlor, T. E.; Yue, S. Comparison of SYBR (R) green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the salmonella/mammalian microsome reverse mutation assay (ames test). Mutat. Res., Genet. Toxicol. Environ. Mutagen. 1999, 439, 37–47.

    Article  Google Scholar 

  8. Ohta, T.; Tokishita, S.; Yamagata, H. Ethidium bromide and SYBR Green I enhance the genotoxicity of UV-irradiation and chemical mutagens in E-coli. Mutat. Res., Genet. Toxicol. Environ. Mutagen. 2001, 492, 91–97.

    Article  Google Scholar 

  9. Yang, Y. Y.; Chen, S. W. Surface manipulation of the electronic energy of subnanometer-sized gold clusters: An electrochemical and spectroscopic investigation. Nano. Lett. 2003, 3, 75–79.

    Article  Google Scholar 

  10. Peyser, L. A.; Vinson, A. E.; Bartko, A. P.; Dickson, R. M. Photoactivated fluorescence from individual silver nanoclusters. Science. 2001, 291, 103–106.

    Article  Google Scholar 

  11. Hicks, J. F.; Miles, D. T.; Murray, R. W. Quantized doublelayer charging of highly monodisperse metal nanoparticles. J. Am. Chem. Soc. 2002, 124, 13322–13328.

    Article  Google Scholar 

  12. Vosch, T.; Antoku, Y.; Hsiang, J. C.; Richards, C. I.; Gonzalez, J. I.; Dickson, R. M. Strongly emissive individual DNAencapsulated Ag nanoclusters as single-molecule fluorophores. Proc. Natl. Acad. Sci. USA 2007, 104, 12616–12621.

    Article  Google Scholar 

  13. Huang, C. C.; Yang, Z.; Lee, K. H.; Chang, H. T. Synthesis of highly fluorescent gold nanoparticles for sensing Mercury(II). Angew. Chem. Int. Edit. 2007, 46, 6824–6828.

    Article  Google Scholar 

  14. Seeman, N. C. DNA in a material world. Nature 2003, 421, 427–431.

    Article  Google Scholar 

  15. Lin, C. X.; Liu, Y.; Rinker, S.; Yan, H. DNA tile based self-assembly: Building complex nanoarchitectures. ChemPhysChem 2006, 7, 1641–1647.

    Article  Google Scholar 

  16. Lin, C. X.; Liu, Y.; Yan, H. Designer DNA nanoarchitectures. Biochemistry 2009, 48, 1663–1674.

    Article  Google Scholar 

  17. Sharma, J.; Yeh, H. C.; Yoo, H.; Werner, J. H.; Martinez, J. S. A complementary palette of fluorescent silver nanoclusters. Chem. Commun. 2010, 46, 3280–3282.

    Article  Google Scholar 

  18. Rotaru, A.; Dutta, S.; Jentzch, E.; Gothelf, K.; Mokhir, A. Selective dsDNA-templated formation of copper nanoparticles in solution. Angew. Chem. Int. Ed. 2010, 49, 5665–5667.

    Article  Google Scholar 

  19. Petty, J. T.; Zheng, J.; Hud, N. V.; Dickson, R. M. DNAtemplated Ag nanocluster formation. J. Am. Chem. Soc. 2004, 126, 5207–5212.

    Article  Google Scholar 

  20. Liu, G. Y.; Shao, Y.; Ma, K.; Cui, Q. H.; Wu, F.; Xu, S. J. Synthesis of DNA-templated fluorescent gold nanoclusters. Gold Bull. 2012, 45, 69–74.

    Article  Google Scholar 

  21. Monson, C. F.; Woolley, A. T. DNA-templated construction of copper nanowires. Nano lett. 2003, 3, 359–363.

    Article  Google Scholar 

  22. Qing, Z. H.; He, X. X.; He, D. G.; Wang, K. M.; Xu, F. Z.; Qing, T. P.; Yang, X. Poly(thymine)-templated selective formation of fluorescent copper nanoparticles. Angew. Chem. Int. Edit. 2013, 52, 9719–9722.

    Article  Google Scholar 

  23. Liu, G. Y.; Shao, Y.; Peng, J.; Dai, W.; Liu, L. L.; Xu, S. J.; Wu, F.; Wu, X. H. Highly thymine-dependent formation of fluorescent copper nanoparticles templated by ss-DNA. Nanotechnology 2013, 24, 345502.

    Article  Google Scholar 

  24. Zhang, L. L.; Zhao, J. J.; Duan, M.; Zhang, H.; Jiang, J. H.; Yu, R. Inhibition of dsDNA-templated copper nanoparticles by pyrophosphate as a label-free fluorescent strategy for alkaline phosphatase assay. Anal. Chem. 2013, 85, 3797–3801.

    Article  Google Scholar 

  25. Xu, F. Z.; Shi, H.; He, X. X.; Wang, K.; He, D. G.; Guo, Q.; Qing, Z. H.; Yan, L. A.; Ye, X. S.; Li, D. et al. Concatemeric dsDNA-templated copper nanoparticles strategy with improved sensitivity and stability based on rolling circle replication and its application in microRNA detection. Anal. Chem. 2014, 86, 6976–6982.

    Article  Google Scholar 

  26. Chen, J. H.; Liu, J.; Fang, Z. Y.; Zeng, L. W. Random dsDNA-templated formation of copper nanoparticles as novel fluorescence probes for label-free lead ions detection. Chem. Commun. 2012, 48, 1057–1059.

    Article  Google Scholar 

  27. Pacioni, N. L.; Filippenko, V.; Presseau, N.; Scaiano, J. C. Oxidation of copper nanoparticles in water: Mechanistic insights revealed by oxygen uptake and spectroscopic methods. Dalton Trans. 2013, 42, 5832–5838.

    Article  Google Scholar 

  28. Chen, T. S.; Zeng, S. Q.; Zhou, W.; Luo, Q. M. A. Quantitative theory model of a photobleaching mechanism. Chinese Phys. Lett. 2003, 20, 1940–1943.

    Article  Google Scholar 

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Correspondence to Genxi Li.

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Zhu, X., Shi, H., Shen, Y. et al. A green method of staining DNA in polyacrylamide gel electrophoresis based on fluorescent copper nanoclusters synthesized in situ . Nano Res. 8, 2714–2720 (2015). https://doi.org/10.1007/s12274-015-0778-y

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  • DOI: https://doi.org/10.1007/s12274-015-0778-y

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