Detection and discrimination of maintenance and de novo CpG methylation events using MethylBreak

William Hsu, Augustus T. Mercado, George Hsiao, Jui Ming Yeh, Chung Yung Chen

Research output: Contribution to journalArticlepeer-review


Understanding the principles governing the establishment and maintenance activities of DNA methyltransferases (DNMTs) can help in the development of predictive biomarkers associated with genetic disorders and diseases. A detection system was developed that distinguishes and quantifies methylation events using methylation-sensitive endonucleases and molecular beacon technology. MethylBreak (MB) is a 22-mer oligonucleotide with one hemimethylated and two unmethylated CpG sites, which are also recognition sites for Sau96I and SacII, and is attached to a fluorophore and a quencher. Maintenance methylation was quantified by fluorescence emission due to the digestion of SacII when the hemimethylated CpG site is methylated, which inhibits Sau96I cleavage. The signal difference between SacII digestion of both MB substrate and maintenance methylated MB corresponds to de novo methylation event. Our technology successfully discriminated and measured both methylation activities at different concentrations of MB and achieved a high correlation coefficient of R2=0.997. Additionally, MB was effectively applied to normal and cancer cell lines and in the analysis of enzymatic kinetics and RNA inhibition of recombinant human DNMT1.

Original languageEnglish
Pages (from-to)658-663
Number of pages6
JournalBiosensors and Bioelectronics
Publication statusPublished - May 15 2017


  • de novo methylation
  • DNA methyltransferases
  • Maintenance methylation
  • Methylation-sensitive endonucleases
  • MethylBreak
  • Molecular beacon

ASJC Scopus subject areas

  • Biotechnology
  • Biophysics
  • Biomedical Engineering
  • Electrochemistry


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