Fragment Analysis | Macrogen Europe

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Fragment analysis encompasses a wide variety of genotyping, DNA profiling and mutation detection techniques for medical, environmental, and agricultural research.

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Fragment analysis is used for checking amplified fragments' size only. Since PCR amplification is not available through this service, fluorescently labeled PCR products should be supplied as microsatellite analysis (VNTRs) samples.

Fragment analysis is technique with a wide range of applications and these include, genotyping, SNP analysis and micro-satellite marker analysis. Similarly to Sanger sequencing, this method is highly accurate and cost-effective, making it a reliable method to carry out its various applications. This is a technique that incorporates florescent tags with PCR and capillary electrophoresis. These florescent tags are known as fluorophores and are attached to the primer that amplifies the 5’ end.

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These are the steps we follow to perform fragment analysis:

The primers are designed in the usual way, i.e. with amplification at the 3’ and 5’ end. However, a fluorophore protein is attached at the 5’ end. When searching for fragments of different sizes, different coloured fluorophores are used for each size of fragment.
For example, a blue fluorophore may be used to amplify fragments of 300bp and then a yellow fluorophore may be used for amplification of fragments of 600bp.
DNA extraction is then carried out on your sample of interest, it is very important that this is done well as the quality of the sample can affect the results.
CR is carried out using the fluorophore-tagged primers and will result in fragments of different sizes.
These fragments are then separated using capillary electrophoresis where they will be separated by their length, due to smaller fragments travelling quicker through the matrix.
Once separated, a laser is used to excite the attached fluorophore and the reflected light indicates its colour. This then gives us the size information and allows us to distinguish between the fragments.

What is fragment analysis? How can you benefit from it?

Understanding all aspect of sequencing is essential for your projects. Now, you can go to our section Learn with Macrogen Europe to learn more about sequencing topics.

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