Bio-Rad CHEF Mapper® XA System - Manual (Page 37)

Note: Always edit the run time before pressing START RUN. After the run has started,
it is not possible to enter a new run time.
• Enter the low and high DNA size just outside the DNA size range to be optimized. For
example, to optimize the separation of DNA in the size range of 200 kb and 500 kb, enter
150 kb as the low DNA size and 550 kb as the high DNA size.
Important! When you are entering extremely wide size ranges in the auto algorithm (or its
counterpart in the interactive program disc), there is likely to be a band inversion in the mid
range of the gel. For example, a low size of 1 kb and a high of 6 mb results in a mobility
reversal somewhere in the 200–500 kb range.
Section 6
The Interactive Algorithm
6.1 Introduction
The PC based interactive algorithm allows greater flexibility in setting run conditions
than the auto algorithm in the CHEF Mapper system. It has two operating modes, fully
automated and semi-automated. The former exactly duplicates the auto algorithm embedded
in the CHEF Mapper system. It assumes standard 0.5x TBE, 1% PFC (low EEO) agarose,
and 14 °C. The interactive algorithm (semi-automated) allows you to vary the buffer type
and concentration, agarose type and concentration, and buffer temperature. As with the auto
algorithm, the lowest and highest fragment sizes are entered. The software then computes the
optimized operating parameters. Both of these algorithms are under the algorithm menu, with
a toggle to get from one mode to the other.
Both forms of the algorithm permit you to edit or change the calculated parameters before
electrophoresis, and to employ nonlinear switch-time ramps, although these are not used in the
calculations. The semi-automated mode also permits the use of interrupt pulses (see Section 9.3).
You may bypass either of these primary operating modes, and manually set up parame-
ters in FIGE, two state, and multi state program menus. Nonlinear switch-time ramping is
permitted in all three modes, but interrupt pulses are allowed only in the multi state mode.
The results calculated by the fully automated and semi-automated programs will specify
FIGE, two state, or multi state, depending on the fragment range. The software automatically
selects the appropriate mode according to the following rules:
• If the largest fragment is < 50 kb, a FIGE routine will result. The smallest fragment will
be placed 9 cm from the well, or about 1 cm from the bottom of a standard gel.
• If the largest fragment is < 2,500 kb, a two state mode is selected. If the largest fragment
is < 2,500 kb and the smallest fragment is > 2,000 kb, either two state or multi state mode
is used.
• If the smallest fragment is < to 2,000 kb, and the largest fragment is > 2,500, multi state
(2 block) is used.
All routines are subject to an upper limit of 6,000 kb. When the smallest fragment is
> 2,000 kb, the separation time is such that high resolution occurs within 3 days, but the
fragment is not necessarily placed 9 cm from the well. The algorithms also have an effective
lower limit of 1 kb.
All data files may be saved on hard disk or floppy disk, or printed out.
All of the functions are easily accessed from the pull down menus across the top of the screen.
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