MSMSA (Methylation Sensitive Mobility Shift Assay)
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 like bisulfite sequencing primers (ie: designed to regions without CpGs) using Methyl Primer Express Software, so that PCR amplification is not dependent on methylation status.
Experimental Workflow: Find the Products You Need for Every Step
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Step 1:
DNA Extraction -
Step 2:
Bisulfite Conversion -
Step 3:
Primer Design & Amplification -
Step 4:
Prepare samples for Fragment Analysis Run -
Step 5:
Electrophoresis -
Step 6:
Analyze Data
Click the arrows above to view products
Step 1: DNA Extraction
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.
Products for Step 1: DNA Extraction
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MELT™ Total Nucleic Acid Isolation System
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Stop homogenizing tissue samples. With the MELT Total RNA Isolation System, tissue samples are quickly and easily lysed in MELT solution. The RNA in the resulting lysate is stable for days at room temperature or longer at lower temperatures. Isolate the RNA using magnetic bead-based separation technology.
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RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Tissues
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Extract total RNA or DNA from formalin- or paraformalin-fixed, paraffin-embedded (FFPE) tissues. This kit enables the molecular analysis of archived tissue samples at both the genomic and gene expression levels. With this kit, nucleic acid is obtained that is suitable for qRT-PCR, mutation screening, and microarray analyses.
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NucPrep® DNA Chemistry for Tissues
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Starter kit for DNA isolation from animal and plant tissues and cells, etc., using NucPrep® Chemistry.
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MagMAX™ Express Magnetic Particle Processor
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MagMAX™ Express magnetic particle processors are ideal for researchers who want to automate their MagMAX sample preparation kits. The MagMAX Express platform is the premier automated platform to meet your throughput needs.
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MagMAX™ Express-96 Magnetic Particle Processors
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MagMAX™ Express magnetic particle processors are ideal for researchers who want to automate their MagMAX sample preparation kits. The MagMAX Express platform is the premier automated platform to meet your throughput needs.
Step 2: Bisulfite Conversion
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.
Products for Step 2: Bisulfite Conversion
- methylSEQr™ Bisulfite Conversion Kit
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The methylSEQr™ Bisulfite Conversion Kit converts non-methylated cytosines (C) in your DNA sample to uracil (U). This kit is an initial step in a multi-step workflow that enables you to determine which cytosines in your sample are methylated by comparing the sequences of treated vs. non-treated DNA.
Step 3: Primer Design & Amplification
Design high quality PCR primers for methylation mapping experiments. Simply cut and paste in your region of interest. The tool searches for CpG islands and simulates bisulfite modification of DNA in silico. Perform PCR using dye labeled primers to amplify region of interest.
Products for Step 3: Primer Design & Amplification
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Methyl Primer Express® Software v1.0
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This free software enables you to design high quality PCR primers for methylation mapping experiments. Simply cut and paste in your region of interest. The tool searches for CpG islands and simulates bisulfite modification of DNA in silico. Applied Biosystems supplies all the tools you need to complete methylation mapping experiments.
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GeneAmp® Gold RNA PCR Reagent Kit and Core Kit
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The GeneAmp® Gold RNA PCR Reagent Kit has been optimized to combine reverse transcription using MultiScribe™ Reverse Transcriptase, with highly sensitive and specific amplification using AmpliTaq Gold® DNA Polymerase.
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Custom Oligo Synthesis - Unlabeled Oligo
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We offer a portfolio of fluorescent dyes for gene expression studies, 5’ nuclease assays, PCR, fragment analysis, and genotyping. When you know the exact sequence of a fluorescent labeled probe or primer, we can synthesize it for you.
Step 4: Prepare samples for Fragment Analysis Run
Add aliquot of PCR reaction to size standard and Hi-Di Formamide mix; heat denature and proceed with electrophoresis.
Products for Step 4: Prepare samples for Fragment Analysis Run
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Hi-Di™ Formamide
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Highly deionized formamide used to resuspend samples before electrokinetic injection in capillary electrophoresis systems.
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GeneScan™ Size Standards
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GeneScan™ Size Standards are fluorescently-labeled DNA fragments required for performing fragment analysis and genotyping applications on our capillary electrophoresis platforms.
Step 5: Electrophoresis
During capillary electrophoresis, the products of the PCR reaction are injected electrokinetically into capillaries filled with polymer. High voltage is applied so that the negatively charged DNA fragments move through the polymer in the capillaries toward the positive electrode.
Products for Step 5: Electrophoresis
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3500 Genetic Analyzer
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The 3500 8-capillary platform can run a wide variety of applications—including de novo sequencing and resequencing (mutational profiling)—as well as microsatellite analysis, MLPA™, LOH, MLST, AFLP® and SNP validation or screening. The majority of applications can be run on a single polymer and capillary array.
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3500xl Genetic Analyzer
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The 3500xL 24-capillary platform can run a wide variety of applications, including de novo sequencing and resequencing (mutational profiling), as well as microsatellite analysis, MLPA™, LOH, MLST, AFLP® and SNP validation or screening. The majority of applications can be run on a single polymer and capillary array.
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3730 DNA Analyzer
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The 48-capillary 3730 DNA Analyzer is the Gold Standard in medium-to-high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample. This is upgradeable to 96 capillaries.
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3730xl DNA Analyzer
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The 96-capillary 3730xl DNA Analyzer is the Gold Standard for high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample.
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3130 Genetic Analyzer
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Applied Biosystems 3130 Genetic Analyzer is the latest generation of 4-capillary electrophoresis instruments for the low to medium throughput laboratories. The system offers industry-leading performance, plus sophisticated automation capabilities allowing you to save time, reduce costs and increase productivity.
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3130xl Genetic Analyzer
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Applied Biosystems 3130xl Genetic Analyzer is the latest generation of 16-capillary electrophoresis instruments for the medium throughput laboratories.
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310 Genetic Analyzer
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The ABI PRISM® 310 Genetic Analyzer is an automated single-capillary genetic analyzer designed for a wide range of sequencing and fragment analysis applications.
Step 6: Analyze Data
Explore presence of methylation-specific peaks (fragments) with GeneMapper or PeakScanner software.
Products for Step 6: Analyze Data
- GeneMapper® Software
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GeneMapper is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems.
- Peak Scanner™ Software
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Use this free software to perform DNA fragment analysis; separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments.
Training Courses
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