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Related Experiment Video

Updated: Feb 17, 2026

DNA Methylation: Bisulphite Modification and Analysis
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Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes.

Dinh Diep1, Nongluk Plongthongkum1, Kun Zhang2

  • 1Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, Mail code 0412, La Jolla, CA, 92093, USA.

Methods in Molecular Biology (Clifton, N.J.)
|December 11, 2017
PubMed
Summary

Bisulfite padlock probes (BSPP) enable precise DNA methylation quantification across many genomic regions. This method streamlines sample processing for efficient, targeted epigenomic analysis.

Keywords:
CaptureDNA methylation quantificationEpigeneticsMultiplexingPadlock

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Genomics

Background:

  • DNA methylation is crucial for mammalian genome regulation.
  • Accurate quantification of methylation patterns is essential for understanding various biological processes and diseases.
  • Existing methods can be limited in scalability and flexibility for targeted methylation analysis.

Purpose of the Study:

  • To introduce Bisulfite Padlock Probes (BSPP) as a novel method for targeted DNA methylation quantification.
  • To highlight the advantages of BSPP in terms of resolution, flexibility, and efficiency.
  • To demonstrate the applicability of BSPP in diverse research settings.

Main Methods:

  • BSPP utilizes padlock probes for targeted capture of specific genomic regions.
  • Methylcytosine modification is analyzed at single-base resolution.
  • A streamlined, three-enzymatic-step protocol converts samples into multiplexed sequencing libraries.
  • Conventional library preparation steps are omitted.

Main Results:

  • BSPP allows simultaneous characterization of methylation levels in numerous targeted regions.
  • The method offers flexible capture of hundreds to hundreds of thousands of genomic loci in single-tube reactions.
  • Efficient processing of large sample numbers is achieved with minimal enzymatic steps.

Conclusions:

  • BSPP provides a powerful and efficient tool for targeted DNA methylation analysis in mammalian genomes.
  • The technique is suitable for clinical studies, cell line screening, and deep sequencing of low-abundance regions.
  • BSPP offers a scalable and flexible approach to epigenomic research.