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A methylation-stimulated DNA machine: an autonomous isothermal route to methyltransferase activity and inhibition analysis

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Abstract

The operation of DNA nanomachines is generally triggered by either conformational changes of DNA nanostructure or external environmental stimuli. In the present study, we demonstrate an alternative driving force, DNA methylation, to stimulate DNA machine operation. DNA methylation changes neither DNA sequence and conformation nor external environment, however, blocks its cleavage by corresponding methylation-sensitive restriction endonuclease. We thus designed a strand displacement amplification DNA machine, which could be stimulated upon DNA methylation and then autonomously generates accumulated amounts of peroxidase-mimicking DNAzyme signaling machine products in an isothermal manner. The machine product DNAzyme could catalyze the H2O2-mediated oxidation of 2,2′-azino-bis(3-ethylbenzo thiazoline-6-sulfonic acid) (ABTS2−) to a colored product ABTS·−. This methylation-stimulated DNA machine was further used as a colorimetric assay for analysis of methyltransferases activities and screening of methylation inhibitors. As compared with classical methylation assay, this facile isothermal DNA machine avoids the introduction of methylation-specific polymerase chain reaction and radioactive labels, which might be employed as an effective tool for DNA methylation analysis.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (20873175, 21075128, and 20725516), Shanghai Municipal Commission for Science and Technology (0952 nm0460, 10QA1408200), Ministry of Health (2009ZX10004-301), and Ministry of Science and Technology (2007CB936000 and 2007AA06A406).

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Authors and Affiliations

  1. Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China

    Changfeng Zhu, Yanqin Wen, Hongzhen Peng, Yao He, Qing Huang, Di Li & Chunhai Fan

  2. School of Chemistry and Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China

    Yitao Long

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  1. Changfeng Zhu
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  2. Yanqin Wen
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  3. Hongzhen Peng
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  4. Yitao Long
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  5. Yao He
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  6. Qing Huang
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  7. Di Li
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  8. Chunhai Fan
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Correspondence to Di Li.

Additional information

Published in the special issue Analytical and Bioanalytical Science in China with Guest Editors Lihua Zhang, Qiankun Zhuang, and Yukui Zhang.

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Zhu, C., Wen, Y., Peng, H. et al. A methylation-stimulated DNA machine: an autonomous isothermal route to methyltransferase activity and inhibition analysis. Anal Bioanal Chem 399, 3459–3464 (2011). https://doi.org/10.1007/s00216-010-4137-2

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  • DOI: https://doi.org/10.1007/s00216-010-4137-2

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