Abstract
This protocol describes a homogeneous, convenient and sensitive DNA methylation detection method, using an optically amplifying cationic conjugated polymer (CCP, poly((1,4-phenylene)-2,7-[9,9-bis(6′-N,N,N-trimethyl ammonium)-hexyl fluorene] dibromide)). Genomic DNA from cancer cells is pretreated with a methylation-sensitive restriction endonuclease, followed by PCR amplification in the presence of fluorescein-labeled dNTP and Taq polymerase. The PCR only occurs for methylated DNA. DNA methylation of the gene sequence of interest is detected as a result of the fluorescence resonance energy transfer (FRET) between CCP and fluorescein that is incorporated into DNA. The methylated statuses of the p16, HPP1 and GALR2 promoters of five cancer cell lines (HT29, HepG2, A498, HL60 and M17) were assayed to provide an association study between the cancers and susceptibility genes, which shows great potential for early cancer diagnosis. This protocol simplifies previously available procedures by avoiding the need for primer labeling, isolation or purification steps, and sophisticated instruments. The assay takes about 20 h to obtain the methylated statuses of cancer cells.
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Acknowledgements
We are grateful to the National Natural Science Foundation of China (Nos. 90913014 and 20725308) and to the Major Research Plan of China (No. 2006CB932102).
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F.F. conducted experiments and data analysis, and wrote the paper; L.L. conducted experiments and data analysis; S.W. designed experiments, performed data analysis and wrote the paper.
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Feng, F., Liu, L. & Wang, S. Fluorescent conjugated polymer-based FRET technique for detection of DNA methylation of cancer cells. Nat Protoc 5, 1255–1264 (2010). https://doi.org/10.1038/nprot.2010.79
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DOI: https://doi.org/10.1038/nprot.2010.79
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