The CHEF Mapper system lets you choose any pulse angle from 0–3,600. This allows you to achieve optimal separation of both chromosomal DNA (Figure 1) and plasmid DNA (Figure 2), with one flexible system.
A, 106° angle; B, 120° angle.
Two-state mode
48 hr run
2 V/cm (67 V), 14°C, 1x TAE
30 min switch time
0.8% chromosomal-grade agarose
Fig. 1, Increased mobility of S. pombe chromosomes using the CHEF Mapper XA system
FIGE mode
180° angle
1x TAE, 14°C
9 V/cm forward
6 V/cm reverse
18 hr run
Switch time 200–800 ms ramp
Forward switch time = reverse time
Lane 1: Bio-Rad lambda HindIII standard (6.6, 9.4, 23.1 kb)
Lane 2: Bio-Rad 8–48 kb size standard (8.3, 8.6, 10.0, 12.2, 15.0, 17.1, 19.4, 22.6, 24.8, 29.9, 33.5, 38.4, 48.5 kb)
Fig. 2, High resolution of 8–48 kb size standard on the CHEF Mapper XA system with asymmetric voltage FIGE.
Accurate sizing of fragments requires an expanded linear range of separation. Switch-time ramps increase the mobility of fragments as a function of molecular weight by gradually changing the switch times during the course of a run. Nonlinear ramps change the rate at which the switch time moves from the specified initial switch time to the specified final switch time. These nonlinear ramps (e.g., concave or convex) have been shown to provide very linear separations from 50–700 kb (Figure 3). Therefore, fragment sizes will be measured more precisely.
Fig. 3. Mobility effects of nonlinear switch time ramps on the CHEF Mapper system. Molecular size vs. migration for linear, concave, and convex ramps. The convex ramp results in the widest linear range.
The multi-state mode of the CHEF Mapper system enhances resolution in selected fragment size ranges. Each vector (angle of pulse) can be assigned its own voltage (field intensity) and its own switch time (duration of pulse). Up to eight different states may be combined into one run to optimize the separation of subsets of fragments in the sample (Figure 4). The application of secondary pulses of defined voltage, duration, angle, and frequency can enhance the separation and resolution of very large DNA molecules (Figure 5). These secondary pulses may release DNA caught in the gel matrix.
A. Two-state mode
24 hr run time, 120° included angle
60 to 120 sec switch-time ramp
6 V/cm, 0.5x TBE at 14°C
1.0% pulsed field Certified agarose
B. Multi-state mode
60 hr run time
State (vector)
1. 90 sec switch time, -60° angle
2. 45 sec switch time, 180° angle
3. 90 sec switch time, 60° angle
4. 90 sec switch time, -60° angle
5. 90 sec switch time, 60° angle
6. 45 sec switch time, 180° angle
7. 90 sec switch time, -60° angle
8. 90 sec switch time, 60° angle
Fig. 4 High-resolution separation with multiple states (vectors). S. cerevisiae chromosomes separated under A, two-state conditions; B, multi-state conditions. Notice separation of the co-migrating chromosomes with multi-state conditions.
Multi-state mode
20 hr run time,
120° included angle
60 to 120 sec switch-time ramp
6 V/cm (200 V), 0.5x TBE at 14°C
1.0% molecular biology Certified agarose
Secondary pulses
6 V/cm (200 V), 0° angle
3 sec switch time
4 pulses/minute
Fig. 5. Increased separation with secondary pulsed-field electrophoresis (SPFE). S. cerevisiae chromosomes separated under A, two state conditions; B, two-state conditions with secondary pulses.