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Molecular Biology Shared Resource
Dartmouth College
HB 7650
Remsen Building (Room 243)
Hanover, NH 03755-3526
Phone: 603-650-6546
Fax: 603-650-1129

DNA Fragment Analysis

Fragment analysis (Genotyping) can be preformed on DNA fragments that have fluorescent labels. Using a labeled primer with PCR amplification is a common method used to incorporate these labels. The Molecular Biology Core lab is already set to run multiple fluorescent dye sets.

6-FAM, VIC, NED, PET, LIZ (for ABI Dye Set G5, DS-33)

6-FAM, HEX, NED, ROX (for ABI Dye Set D, DS-30)

Other fluorescent dye sets are possible. Please contact the Core Facility for more information.

Setting up your reactions

Post PCR reaction mircosatellites should be visible on a gel as a strong band. For capillary electrophoresis analysis samples need to be diluted down to a working concentration. Our recommended starting point would be about 1 in 50 dilution of the PCR product. Add 1ul of this dilution to 10ul of Hi-Di Formamide (ABI# 4311320), along with 0.25ul of your selected size standard (we recommend ABI GS500 LIZ ABI# 4322682 or GS500 ROX ABI #401734 for the Dye set listed above) for a total reaction volume of 10.25ul for each sample.

The amount of the mircosatellite product used for each reaction may need to be further optimized. With too much product the signals can be saturated preventing the software from reading some of the fragments or the size standard signals. Too little product and fragments may not be detected above the background. Adjustments will need to be made based on the amount PCR product generated. Multiple amplicons generated in a single reaction may need to be more dilute while a single amplicon may need to be less dilute.

The reactions need to be set up in an approved 96 well plate (ABI cat# N8010560 or similar plate) before you give them to the core. Samples are run by the sequencer by every other column on the plate, so set up samples by filling all the odd number wells first  (column 1A through H followed 3,5,7, 9 and 11 A through H. Then fill all the even numbered columns 2,4,6,8,10, 12, A through H. See Instructions for submitting samples in 96 well plates for more information.

 Sample Processing and Data analysis

 Samples are processed 48 at a time for each run, which takes less than 1 hour to finish. Once all the samples are complete the raw data is posted on the CCOP's for you to retrieve by using your Molecular Biology CCOP’s account. For basic analysis and viewing of the data we recommend the “Peak Scanner” software, which is free software that can be down loaded from the ABI web site. Peak Scanner identifies peaks and fragment sizes up to 1200bp in size from ABI capillary electrophoresis assays. The software allows you to annotate data with labeling, simultaneous viewing of raw and analyzed data, and allows the organization of the sample files into projects. For more complex analysis we offer access to ABI Vairant Reporter and GeneMapper software.  Other options are available but most are not free. For more information contact us.

 For More Information on Fragment analysis go to our Down load page and select the DNA Fragment Analysis by Capillary Electrophoresis User Guide from Life Technologies.


Last Updated: 3/4/14