Bio-Rad CHEF Mapper® XA System - Manual (Page 36)

Calibration Factor: Adjusts calculated run time by the fraction entered. Press ENTER for
default of 1.0 (NC = no change).
When you press ENTER after entering the calibration factor, the screen displays:
The auto algorithm will indicate the buffer type and concentration, buffer temperature, and
agarose type and concentration for the run. The auto algorithm requires that for DNA < 2.5
mb, 0.5x TBE at 14 °C, in a 1.0% PFC agarose gel be used. For DNA > 2.5 mb the buffer must
be 1.0x TAE at 14 °C, with a gel of 0.8% PFC agarose. Press ENTER. The screen display
indicates one of the following run conditions:
• For DNA between 1 kb and 50 kb, FIGE will be implemented. See Section 4.3.
• For DNA smaller than 2.5 mb, the two state operating mode will be implemented.
See Section 4.4.
• For DNA larger than 2.5 mb, the multi state operating mode will be implemented.
See Section 4.5.
You can change any of the auto algorithm parameters from the original screen or the edit
modes. To change any entry, move the cursor to the parameter you want to change using the
cursor arrows. Press CLR ENTRY, enter the value and dimension, and press ENTER. To
edit the run parameter screens during or after electrophoresis, see Section 4.9.
Pressing ENTER moves the cursor through the display screens to the final screen:
A program is in memory - Please enter another command. The CHEF Mapper system is
programmed and ready to start. After positioning the gel in the electrophoresis chamber and
closing the lid, press START RUN to begin electrophoresis.
5.2 Applications
The auto algorithm simplifies pulsed field electrophoresis. Optimized running conditions
are derived from extensive data stored in the CHEF Mapper system’s microprocessor and
implemented with a few key strokes. Sometimes, however, one or more fine-tuning modifi-
cations of the run parameters must be made to achieve a separation. For example:
• For DNA larger than 2 mb, run times can be hundreds of hours, because the auto algorithm
sets run conditions so that the smallest DNA to be separated will migrate approximately
9 cm from the origin. It is not always necessary to have the smallest DNA fragment,
particularly fragments over 2 mb, migrate the full 9 cm. Adequate resolution can often be
obtained when the smallest DNA moves only part of the way through the gel. Decreasing
the run time parameter will shorten the migration distances of the DNAs in the gel while
maintaining all other relevant parameter settings.
Molecular Weight:
Low____
Molecular weight Low [ ]
Calibration Factor [ ]
32