Bio-Rad CHEF Mapper® XA System - Manual (Page 56)

Fig. 9.5. Three gels were run to show the difference In linear and nonlinear ramping. The first was
a linear ramp with a half height of 50%, the second was a nonlinear ramp with a half height of 21%,
and the third was a nonlinear ramp with a half height of 79%. Lambda ladders were separated on a
1% gel with a 6.8 to 54.3 second ramp for 21 hours, at 6 V/cm, in 0.5x TBE chilled at 14 °C.
9.3 Multi State Interrupts
In the multi state mode, the CHEF Mapper system allows the use interrupts during the run.
Interrupts theoretically allow the DNA to disentangle from obstructions in the gel matrix to
reduce band broadening and help larger molecules adjust to sudden changes in the field con-
ditions. Consequently, run times may decrease [Zhang, T., Smith, C. L. and Cantor, C. R.,
Nucleic Acids Res., 19, 1291 (1991)]. Interrupts, or secondary pulses, allow periodic voltage
spikes to occur at a specific angle, duration, and frequency. The interrupt function has the
constraint that the interrupt voltage cannot exceed that of the primary voltage. If the number
of interrupts per cycle is small, higher voltages on the interrupts may be achieved by bypass-
ing this function. The interrupts are then programmed as ordinary vectors in multi state mode
(up to 15 vectors/cycle).
9.4 Pulsed Field Conditions by DNA Size
The table below shows suggested run parameters that can be used for the various DNA
size ranges listed.
DNA DNA DNA DNA
1–100 kb 0.1–2.0 mb 2–4 mb > 4 mb
% Agarose 1.0–1.2% 0.8–1.2% 0.6–1% 0.5–0.8%
Buffer 0.5x TBE 0.5x TBE 1.0x TAE 1.0x TAE
Temperature 14 °C 14 °C 14 °C 14 °C
Voltage 6–9 V/cm 4.5–6 V/cm 2–3 V/cm 1.5–2.5V/cm
Pulse parameters 0.05–10 sec 10–200 sec 200–1,800 sec 10–60 min
Run times 2–15 hr 15–30 hr 24–72 hr 72–144 hr
Angle 0° + 180°, 120° 120° 120°, 106° 106°
52
50% 21% 79%
0.5 0.4 0.3 0.2 0.1 0.0
0
100
200
300
400
500
600
700
a = 0 (50%)
a = 0.357 (21%)
a = -1.357 (79%)
Migration (cm/hr)