CHEF Mapper® XA System



Introduction to Pulsed Field Gel Electrophoresis
CHEF Mapper XA Experimental Results

Left, two-state mode, 24 hr run, 120° included angle
60–120 sec switch-time ramp
6 V/cm, 0.5x TBE, 14°C
1.0% pulsed field certified agarose

Right, multistate mode, 60 hr run
State (pulse angle):
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

Multistate mode, 20 hr run, 120° included angle
60–120 sec switch-time ramp
6 V/cm (200 V), 0.5x TBE, 14°C
1.0% Certified™ molecular biology agarose

Secondary pulses
6 V/cm (200 V), 0° angle
3 sec switch time
4 pulses/min

High-resolution separation with multiple states (pulse angles). S. cerevisiae chromosomes separated under two-state conditions (left) and under multistate conditions (right). Notice separation of the comigrating chromosomes under multistate conditions.

Increased separation with secondary pulsed field electrophoresis. S. cerevisiae chromosomes separated under two-state conditions (left) and under two-state conditions with secondary pulses (right).

PFGE Standards Selection Guide
5 kb Ladder 8–48 kb Ladder Lambda Ladder S. cerevisiae
Chromosomal DNA
H. wingei
Chromosomal DNA
S. pombe
Chromosomal DNA
Comparison of Pulsed Field Standards
  Range Contents Amount Number of Applications
5 kb ladder 4.9–120 kb Concatemers of pBR328 20 µg in 200 µl 20–25
8–48 kb ladder 8.3–48.5 kb Mixed digest of phage λ 25 µg in 125 µl 125
Lambda (λ) ladder 0.05–1 Mb Concatemers of phage λcl857Sam7 5 agarose blocks 25–40
S. cerevisiae 0.225–2.2 Mb Saccharomyces cerevisiae chromosomal DNA 5 agarose blocks 25–40
H. wingei 1–3.1 Mb Hansenula wingei chromosomal DNA 5 agarose blocks 25–40
S. pombe 3.5–5.7 Mb Schizosaccharomyces pombe chromosomal DNA 5 agarose blocks 25–40


Certified Agarose Selection Guide
25 g 161-3100 161-3103
161-3106   161-3111 161-3113 162-0137
100 g             162-0138
125 g 161-3101 161-3104 161-3107   161-3112 161-3114  
500 g 161-3102 161-3105       161-3115  
Analytical Separation
≥1,000 bp          
≤1,000 bp          
20–800 bp            
1 kb–2 Mb          
1 kb–5 Mb            
Preparative Separation
Quantum Prep methods      
Low-melt methods          
Agarose methods          
In-gel applications          
Other Applications
Postpreparative enzymatic treatments    
Tissue/cell culture            
Pulsed field sample preparation          
Nonlinear Switch and Mobility

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 CHEF Mapper® XA system incorporates patented FIGE and AFIGE* technologies for superior resolution in the range of 100 bp to 10 Mb, in addition to the features of the CHEF-DR® II and the CHEF-DR III systems. The CHEF Mapper XA system also includes algorithms for deriving separation conditions. This system is ideal for both the PFGE novice and the seasoned expert.

Each CHEF Mapper XA system is supplied with a power module, embedded auto-algorithm for protocol optimization, interactive algorithm program disk, electrophoresis cell, cooling module, variable-speed pump, and accessory kit.

The CHEF Mapper XA system offers two ways to optimize your separations. The unique auto-algorithm can automatically select optimal separation conditions, integrating 11 key variables and implementing starting separation conditions. Protocols can be refined using the Windows operating system-based interactive algorithm, which lets you specify several run variables simultaneously to derive optimal separation protocols.

Busy laboratories need equipment that can store and readily access key separation conditions. The CHEF Mapper XA system can store up to 99 programs.

Application Versatility
The CHEF Mapper XA system is the most flexible of the PFGE units. The CHEF Mapper XA system achieves higher resolution with greater speed and accuracy than any other PFGE system, making it ideal for all PFGE applications. The CHEF Mapper XA system lets you choose any pulse angle from 0 to 360°, which allows optimal separation of both chromosomal and plasmid DNA with one system. Accurate sizing of fragments requires an expanded linear range of separation. Switch-time ramps increase the mobility of fragments by gradually changing the switch times during the course of a run. Nonlinear (for example, concave or convex) ramps change the switch-time increments from the start to the end of a run. These nonlinear ramps separate fragments linearly from 50 to 700 kb, yielding more precise fragment size measurements. The multistate mode of the CHEF Mapper XA 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 can be combined into one run to optimize the separation of subsets of fragments in the sample. The application of secondary pulses of defined voltage, duration, angle, and frequency can enhance the separation and resolution of very large DNA molecules by releasing DNA caught in the gel matrix.

* U.S. patent 5,549,796.

Power Module  
Dimensions (W x D x H) 55.9 x 34.5 x 30 cm
Construction Aluminum chassis
Weight 16 kg (35.3 lb)
Power supply 350 V maximum, to allow maximum gradient of 9 V/cm, continuously adjustable; built in
Maximum current 0.5 A
Allowable voltage gradients 0.6–9 V/cm, in 0.1 V/cm increments
Battery back-up All parameters in memory, up to 3 hr of interruption
Delayed start Up to 72 hr
Electrode potentials Dynamically regulated (feedback adjustment) +/- 0.5% F.S.
Program storage 20 average size protocols
Display Fluorescent, 2 lines x 40 characters per line, alphanumeric
Operating temperature 50°F (10°C) to 90°F (32°C); 30–80% humidity
Storage temperature 32°F (0°C) to 140°F (60°C); 10–90% humidity
Switching Functions  
Switching range 50 ms to 18 hr
Switch angle variable 0–360° (all electronic switching) in 0.5° increments
Multistate vector switching Up to 15 vectors per pulse cycle, each definable by angle, voltage, and duration
Switch time ramps Linear, concave, or convex using hyperbolic function
Secondary pulses Defined by voltage, frequency, angle, and duration
Field inversion (FIGE) Available with asymmetric forward, reverse voltages
Maximum program blocks 8, with automatic execution
Maximum run time 999 hr per block
Fuses 3 A Slow-Blow; two each for AC line input
Electrophoresis Cell  
Dimensions (W x D x H) 44.2 x 50.3 x 11.4 cm, horizontal format
Construction Cover: vacuum-formed polycarbonate, base: injection-molded polycarbonate
Lid Safety interlocked
Weight 10.2 kg (22.5 lb)
Electrodes 24, platinum (0.02" diameter)
Temperature monitoring Via precision temperature probe mounted in base of cell
Accessories Included  
Variable speed oscillating pump 120 V, ground isolated; flow rate 1 liter/min, typical
Casting stand 14 x 13 cm
Comb 15-well comb and comb holder
Tygon tubing 365 cm
Disposable sample plug mold 50 slot
Yeast DNA standard S. cerevisiae YNN295
Chromosomal grade agarose 5 g
Pulsed field Certified agarose 5 g
Leveling bubble 1
Cooling Module (optional)  
Weight 14 kg (30.9 lb)
Construction Aluminum
Dimensions (W x L x H) 23 x 42 x 24 cm
Cooling capacity 75 W of input power at 14°C
Operating range 5–25°C
Total system weight 41.7 kg (91.9 lb)

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CHEF Mapper XA Chiller System

120 V, complete PFGE system, includes cooling module, pump, tubing, S. cerevisiae DNA size standard, 5 g pulsed field Certified agarose, 5 g pulsed field Certified megabase agarose

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Number Description Options
M1703650 Instruction Manual, CHEF Mapper® XA, Rev E Click to download
5901 Pulsed Field Gel Electrophoresis Brochure, Rev B Click to download [ Add to Cart (Free) ]
1906 CHEF Mapper Pulsed Field Electrophoresis System Product Information Sheet Click to download
1637 CHEF Mapper™ and CHEF Mapper XA System Specifications Click to download
4006187 Instruction Manual, CHEF Mapper ROM Upgrade Kit (Y2K), Rev A Click to download
4000066 Instruction Manual, Cooling Module, Rev C Click to download
1659 Extending the Upper Limits of Pulsed Field DNA Electrophoresis Using Programmed Voltage Gradients Bulletin Click to download
1753 Preparation and Restriction Digestion of Escherichia coli Chromosomal DNA in Agarose Plugs for Use in PFGE Bulletin, Rev A Click to download
1589 Preparation and Separation of Mammalian DNA by Pulsed Field Gel Electrophoresis Bulletin, Rev A Click to download
1624 Model 1000 Mini Chiller Product Information Sheet Click to download
9204213 Instruction Manual, CHEF Variable Speed Pump, Rev B Click to download
LIT526 Instruction Manual, Standard Casting Stand Combination Comb Holder Wide/Long Combination Casting Stand Click to download
6228 Using Pulsed Field Gel Electrophoresis Standards, Rev A Click to download