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Related Experiment Video

Updated: Jun 12, 2026

Methyl-binding DNA capture Sequencing for Patient Tissues
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Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Direct DNA methylation profiling using methyl binding domain proteins.

Yinni Yu1, Steve Blair, David Gillespie

  • 1Department of Bioengineering, University of Utah, 72 South Central Campus Drive, Room 2750, Salt Lake City, Utah 84112, USA.

Analytical Chemistry
|May 29, 2010
PubMed
Summary
This summary is machine-generated.

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This study introduces a novel microarray assay for directly detecting methylated DNA. The method utilizes a recombinant methyl binding domain (MBD) protein, achieving 97.5% accuracy in identifying methylated CpG sites.

Area of Science:

  • Epigenetics and Molecular Biology
  • Biotechnology and Biosensing

Background:

  • DNA methylation, particularly at CpG islands in promoter regions, is a key epigenetic mechanism involved in gene silencing and a known precursor to cancer development.
  • Methyl-binding domain (MBD) proteins naturally bind to methylated CpG dinucleotides (mCpG), recruiting chromatin modifiers to repress transcription.
  • Conventional detection methods for methylated DNA require complex procedures like bisulfite treatment or immunoprecipitation.

Purpose of the Study:

  • To develop and validate a direct, microarray-based assay for detecting methylated DNA.
  • To evaluate the performance of a recombinant 1xMBD-GFP protein in recognizing and quantifying methylated CpG sequences.
  • To assess the accuracy and selectivity of the novel assay for identifying methylated CpG loci.

Main Methods:

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Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
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Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients

Published on: June 16, 2017

Methylated DNA Immunoprecipitation
21:24

Methylated DNA Immunoprecipitation

Published on: January 2, 2009

Related Experiment Videos

Last Updated: Jun 12, 2026

Methyl-binding DNA capture Sequencing for Patient Tissues
08:40

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
13:21

Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients

Published on: June 16, 2017

Methylated DNA Immunoprecipitation
21:24

Methylated DNA Immunoprecipitation

Published on: January 2, 2009

  • Development of a direct microarray assay utilizing surface-bound methylated probes.
  • Employment of recombinant 1xMBD-GFP protein to detect hemimethylation and symmetric methylation of CpG sequences in hybridized double-stranded DNA.
  • Characterization of binding affinity and selectivity using surface plasmon resonance (SPR) and fitting skew normal probability density functions to quantify accuracy.

Main Results:

  • The recombinant 1xMBD-GFP protein demonstrated specific binding to methylated CpG sequences, with greater affinity for symmetric methylation motifs.
  • Dissociation constants (K(D)) for symmetric mCpG ranged from 106 to 870 nM, significantly lower than for nonsymmetrical motifs (>2 μM).
  • The assay achieved an estimated accuracy of 97.5% in identifying methylated CpG loci, with binding selectivity between 4 and 30.

Conclusions:

  • A direct microarray-based assay using surface-bound probes and a recombinant MBD protein is a feasible method for detecting methylated DNA.
  • The developed assay shows high accuracy and selectivity for identifying symmetric methylated CpG sites, offering a promising alternative to conventional methods.
  • Further optimization of probe design and surface density can potentially enhance the assay's performance for methylated DNA detection.