978-922-1832
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BluePippin Operations Manual 460013 Rev F
1-2
1.2 How the System Works
The BluePippin systems use pre-cast and disposable agarose gel cassettes. DNA
fractions are collected by electro-elution into a buffer-filled well using a branched
channel configuration with switching electrodes. The timing of switching is determined
by measuring the rate of DNA migration with optical detection of labelled markers. The
position of the detectors beneath the gel cassette is shown in the schematic below.
1.3 Collection Strategies
Collection timing (start, duration, and end) is based on the factory calibration
settings provided with a cassette definition file, and the user-input size range settings
in software.
Note: The agarose gel matrix does not contain intercalating dyes or gel stains, sample DNA
is not viewable or monitored.
Size Selections can be undertaken using one of the following strategies:
•
Labeled internal standards
–Fluorescein labeled DNA internal standards are
added to samples, and run ahead of the input sample. The rates of migration of
the internal standards are used to determine the collection timing within the
sample lane. Up to 5 samples may be run per cassette.
Note: The DNA sequence of internal standards may be found at
www.sagescience.com/support
, on the BluePippin resources pa
ge in the “Casssette
Guides” section.
•
Labeled external marker
– The fluorescein labeled DNA marker is loaded in a
single dedicated sample lane during a run. The rates of migration of the markers
are used to determine the collection timing for the remaining sample lanes.
•
Timed runs
– The beginning and end time of elution (size selection) is set by the
user. Neither internal standards or external markers are used.
Gel Cassette Schematic
Close-up of the collection well
Sample Well