GeneCopoeia MAK-GCM-30 User Guide

MethylAffinityTM Methylated DNA Enrichment Kit
For rapid purification and enrichment of methylated DNA

Cat.No.MAK-GCM-30 (30 reactions)

User Manual

GeneCopoeia, Inc.
9620 Medical Center Drive, #101
Rockville, MD 20850
USA

301-762-0888
866-360-9531

[e-mail]
www.genecopoeia.com

© 2010 GeneCopoeia, Inc.

MethylAffinityTM Methylated DNA Enrichment Kit User Manual

USER MANUAL

MethylAffinityTM Methylated DNA Enrichment Kit

I. Introduction
II. Advantages and Protocol Overview
III. Kit Components and Storage
IV. DNA Preparation and Fragmentation
V. Methylated DNA Enrichment Procedure
VI. References
VII. Limited Use License and Warranty

I. Introduction

DNA methylation in mammals is involved in many cellular processes and is responsible for gene
silencing by recruitment of transcriptional repression complexes. It plays a critical role in
development. However, massive methylation of the promoter regions has been frequently
observed in cancer, which can cause transcription repression of tumor suppressor and DNA
repair genes.

MethylAffinityTM Methylated DNA Enrichment Kit provides a GCM™-bead-based method for quick
enrichment of methylated DNA fragments from whole genome1. The enriched sample improves
the performance of downstream analysis, such as RT-PCR, microarray and sequencing, for
methylation status and location studies.

GCM™ recombinant protein is designed based on the functional domain of methyl binding
domain (MBD) proteins2. It binds specifically to double-stranded DNA (e.g.genomic DNA)
containing methylated CpG dinucleotides, unlike methylated DNA antibodies which can only bind
to single-stranded DNA.

Compared to wild-type MBD proteins, GCM™ has much stronger affinity for methylated DNA and
minimal affinity for non-methylated DNA, which makes the binding more specific. The affinity for
GCM™ is proportional to the density of methylated CpG dinucleotides contained in the DNA
fragment.

II. Advantages and Protocol Overview
Fewer steps and less time

In MethylAffinityTM Methylated DNA Enrichment Kit, GCM™ is provided as immobilized GCM™
magenta beads. GCM™ was cross-linked to GeneCopoeia's proprietary magenta beads through
strong non-covalent binding. The immobilized GCM™ beads significantly simplify the protocol.
Starting from fragmented DNA samples, the whole procedure can be completed in less than 2
hours (see Protocol Overview).

Highly Sensitive

The genetically engineered GCM™ has much higher affinity than the wild type MBD. The GCM™
beads are able to isolate DNA fragments which contain only a few of methylated CpG
dinucleotides and can be used to enrich methylated DNA from nanograms of genomic DNA
sample.

Easy to handle

The magenta color of the GCM™ beads makes the pellet very easy to spot, which greatly
reduces the risk of incidental beads loss.

2