The MegaBACE 1000 is an automated machine capable of high-throughput DNA analysis, processing 96 samples in just a few short hours. Applications that are compatible with this system are DNA sequencing, genotyping, and fragment analysis.

The MegaBACE 1000 has 6 arrays of 16 capillaries with an interior diameter of about 100 µm. The system uses high-pressure nitrogen gas to inject the capillaries with Linear Polyacrylamide, a denaturing gel. To load samples, a 96-well plate is loaded into the machine and a current is set up at the tip of each capillary where it comes into contact with the sample. DNA (and other charged particles in the sample) are electro-kinetically injected into the Linear Polyacrylamide and travel the length of the capillary during the course of the run. A typical sequencing run takes about 4 hours while genotyping and fragment analysis takes only a little over 2 hours. All sequencing samples are automatically base-called. After the run, data from all samples are ready to be exported to other types of DNA analysis programs.

Because of the electro-kinetic injection, initial optimization for a specific set of samples is critical. The ratio of labeled DNA to unlabeled DNA and other charged particles plays a large role in the success of any type of analysis. After optimization, the 96-well capacity of the MegaBACE allows the processing of large numbers of samples in a relatively short amount of time.

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