MSMSA is a DNA fragment analysis application used to assess the degree of methylation present in a given amplicon.

Samples from a fragment analysis assay can also be used in a downstream sequencing step, making this application ideal for screening. The assay primers are designed in regions that don’t contain CpGs using Methyl Primer Express® Software, so that PCR amplification is not dependent on methylation status.

Step-by-Step Guide to Methylation Sensitive Mobility Shift Assay

DNA Purification kit

DNA extraction is a critical first step in the experimental workflow of DNA Sequencing and Fragment analysis. The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.

Recommended Products: DNA Isolation


The methylSEQr™ Bisulfite Conversion Kit converts non-methylated cytosines (C) in the DNA sample to uracil (U). Methylated cytosines remain unchanged. Comparing the sequences of treated vs. non-treated DNA and detection of converted cytosines (now apparent as T base) determine which cytosines in the sample are methylated in CpG dinucleotides.

Recommended Products: Perform Bisulfate Conversion

Which Kits are Right for You?


Design high quality PCR primers for methylation mapping experiments. Simply cut and paste in your region of interest in the primer design software. The tool searches for CpG islands and simulates bisulfite modification of DNA in silico. Perform PCR to amplify region of interest.

Recommended Products: Perform PCR

Fragment Analysis sizing graph image.

Add aliquot of PCR product to size standard and Hi-Di Formamide mix; heat denature and proceed with electrophoresis.

Recommended Products: Prepare Sample for Analysis

Sizing Information

To learn more about our GeneScan Size standards used in sizing experiments please see our table below.

When DNA fragments are labeled with: Choose a size standards labeled with: Recommended Size Standard Possible Applications Other Kits and Products
dR110, dR6G, dTAMRA™, dROX (Dye Set DS-02 - Filter E5) LIZ®
Microsatellite, LOH, ISSR, Chimerism, ISSR, RFLP, T-RFLP, MSMSA
5-FAM™, HEX™, NED™ (Dye Set DS-30 - Filter D) ROX™ GeneScan™ 500 ROX™ Size Standard Custom Fragment Analysis Custom Labeled Primer
6-FAM™, VIC®, NED™ (Dye Set DS-31 - Filter D**) ROX™ GeneScan™ 500 ROX™ Size Standard

Custom Fragment Analysis

Custom Labeled Primer
5-FAM™, JOE, NED™ (Dye Set DS-32 - Filter F) ROX™ GeneScan™ 500 ROX™ Size Standard
Microsatellite (Forensic)
6-FAM™, VIC®, NED™, PET® (Dye Set DS-33 - Filter G5) LIZ® GeneScan™ 600 LIZ Size Standard v2.0
Microsatellite (Forensic)
Custom Fragment Analysis
Capillary Electrophoresis

During capillary electrophoresis, the products of the PCR are injected electrokinetically into capillaries filled with polymer. High voltage is applied so that the fluorescent DNA fragments are separated by size and are detected by a laser/camera system.

Which Electrophoresis Instrument (Genetic Analyzer) Is Right for You?

Number of Capillaries 96 48 24 8 16 4 1
Compatible Applications:
(S) Supported; (A) AB Demonstrated; (C) Customer Demonstrated; (N) Not Supported
Methylation S S S S S S C

Analyze the MSMSA profile.

Which Data Analysis Software Is Right for You?

Highlighted products for Methylation Sensitive Mobility Shift Assay:

Verti Thermal Cycler

3500 Series Genetic Analyzers

GeneMapper® Software

Visistat reference component