DNA Fragment Analysis

We offer fragment analysis services with our ABI3730 Genetic Analyzer. The 3730 employs an array of 48 capillaries to electrophoretically separate fluorescently labeled DNA fragments.

Fragments in the approximate size range 35bp and 500bp can be sized to within 1 bp resolution. PCR products, generated within this size range can be polymorphic in their lengths (e.g. amplified fragment length polymorphisms, AFLP Analysis or micro-satellite Analysis) or become polymorphic after digestion with certain enzymes (e.g. terminal restriction length polymorphism, T-RFLP).  It is possible to analyze larger fragments using the LIZ1200 marker, please contact us for more information.

The fragments are sized by comparison with a standard size marker, which is loaded with each sample. Usually this is labelled with an 'orange' fluorescent dye, LIZ. We recommend 6FAM, VIC, NED or PET labels for PCR products. Our instrument is calibrated for use with Dye Set DS-33 (filter set G5) and will not work optimally with other dyes. Labeled primers can be purchased from most oligonucleotide producers.

Data Analysis

For data analysis, we use GeneMapper from Applied Biosystems. Additionally PeakScanner is free to download at Thermo Fisher (http://resource.thermofisher.com/page/WE28396_2/) and can do basic sizing and quantitation.