Pulsed Field Gel Electrophoresis
ProtocolBulletin 6229

Optimizing Sample Resolution
Switch Time and Switch Time Ramping
Switch time is the critical parameter in achieving the best
pulsed field gel electrophoresis (PFGE) resolution. It is thelength of time the electrical field is pulsed in a single direction.
For example, a 60 sec switch time means that the electricalfield will be pulsed in one direction for 60 sec and thenswitched to the other direction for 60 sec.
The switch time is generally shorter for samples with small
DNA fragments and longer for samples with large DNAfragments. Samples with a wide range of DNA fragment sizes,
for example the Saccharomyces cerevisiae chromosomes,
can be resolved by changing the switch time over the courseof the run. This is referred to as switch time ramping because
the switch time will “ramp up” from a short switch time to alonger one.
The ramp of the switch time can be linear, that is, increasing
in exact increments over the course of a run, or nonlinear, sothat the user can concentrate the switch times on the largest
or smallest regions as necessary to achieve better resolution.
The nonlinear switch time ramping expands the linear rangeof fragment separation to 50–700 kb, yielding more precise
fragment size measurements.
The nonlinear ramp is described by how much of the run time
has elapsed by the time the user has ramped up to 50%of the final switch time. In a 21% nonlinear gradient, only 21%of the total run time would have elapsed even though theuser has already achieved 50% of the final switch time.
Choosing a nonlinear ramp <50%, results in greater separationof larger DNA fragments and compression of smaller DNAfragments. Choosing a nonlinear ramp >50%, results ingreater separation of smaller DNA fragments and compressionof larger DNA fragments.

45 sec60 sec90 secEffect of switch time on sample resolution. As the switch time increases,
the larger DNA fragments move farther into the gel during the same time period.
The brackets indicate the same region of the lane for each gel. The sizes of thefragments in this region become larger as the switch time increases.

Pulse/Reorientation Angle
Angle is an important factor in achieving optimal resolution,most protocols are optimized for the 120° angle.
Separations of larger sizes of DNA, such as chromosomal
DNA, are greatly improved by the use of a smaller included
angle (106°). Using a smaller included angle for large DNA
fragments (over 1 Mb in size) results in a 50% savings in runtime. As the angle is decreased, the resolution of the largest
fragments generally improves and the smaller fragments
become crowded.

Field A

Voltage Gradient
The voltage gradient describes the strength of the electricalfield and is represented as V/cm, where the total voltage
is divided over the distance between two electrodes.
Since that distance in a CHEF gel box is approximately
33 cm, a 200 V run is approximately 6 V/cm. Most CHEF
protocols are optimized for 6 V/cm gel runs.
Typically, the best resolution of chromosomal-sized DNA
fragments (>3 Mb) is achieved when using low-voltage
gradients, 1.5–3 V/cm, combined with a narrow angle ofelectrophoresis.
High resolution of DNA fragments up to 250 kb can beachieved by using high-voltage gradients at 9 V/cm.
This voltage can be combined with a narrow angle ofelectrophoresis to resolve samples in very short run times,
4 hr or less.

Field B

Reorientation
angle

Note: Voltage alone will not improve resolution. Switch times
must also be adjusted to produce the best results.

2.2 Mb
1.6

120°

105°

100°
Pulse angle

96°

94°

Effects of different pulse angles on sample resolution. The space between
the largest two fragments increased with the smaller angle, but the remaining
14 fragments became compressed. If the total analysis was in the range ofthese largest two fragments, then the user may choose a smaller pulse angle.

3 V/cm for
60 hr

6 V/cm for
30 hr

9 V/cm for
20 hr

Effect of voltage gradient on sample resolution. The lines identify thelargest resolved fragment in each gel and the position of that fragment in
the next gel. The 3 V/cm gel separated ~400 kb fragments, the 6 V/cm gel
separated up to 850 kb fragments, and the 9 V/cm gel separated up to1.2 Mb fragments in the same V-hr. All gels used the same switch times.
The resolution of the gel is diminished even though the range is greater in the9 V/cm gel. Switch times must also be adjusted to produce better resolution.

© 2011 Bio-Rad Laboratories, Inc.

Bulletin 6229

Buffer Type, Concentration, and Temperature
Buffer TypeIn general, the lower the ionic strength of the buffer,
the faster the run. The run time advantage of low ionicstrength buffer must be weighed against the limited
buffering capacities of dilute buffers and the loss ofresolution due to buffer breakdown.
The two buffers most frequently used for PFGE are
0.5× TBE buffer (Tris-Borate-EDTA) and 1.0x TAE buffer(Tris-Acetate-EDTA). 1× TAE buffer is very useful whenseparating megabase-sized DNA fragments (>3 Mb).
0.5× TBE is the most commonly used buffer. It is usefulfor most separations up to megabase-sized DNA and does
not need to be changed, even over multi-day runs.
Buffer Temperature

Buffer recirculating during the electrophoresis run can bechilled to as low as 4°C or not chilled at all.
Buffer temperature will affect run time. The warmer thebuffer temperature, the faster the run. Resolution decreases
as the temperature increases.

1.0× TAE

0.5× TBE
1.0× TAE
Size, kb

Buffer temperatures at room temperature will decrease therun time by approximately 50% when compared to chillingto 14°C, but the resolution loss will be so great it might not
be worth the time savings. Buffer temperatures at 4°C will
provide the sharpest resolution but at a greatly increased runtime. Generally, buffer is cooled to between 12 and 15°C andthis is the best compromise between run time and resolution.

0.5× TBE

Velocity, cm/hr
Effects of buffer on sample resolution. Fragments of all sizes migrate
farther, with a greater velocity, in the TAE gel than the TBE gel. The TAE
buffer is lower in ionic strength (40 mM buffering agent) than the TBE buffer(90 mM buffering agent).

© 2011 Bio-Rad Laboratories, Inc.

Bulletin 6229

Agarose Type and Concentration
Agarose type affects both sample migration and ease ofhandling for PFGE gels. Agaroses for PFGE must be very
pure, have a high tensile strength, and have a minimumof charged contaminants (usually described by the low
electroendosmosis [EEO] or [Mr] agarose).
Generally, 0.8–1% agarose is ideal for PFGE separations up
to 3 Mb and 0.5–0.9% is useful for the range above 3 Mb.
As the agarose concentration decreases, the DNA migrates
faster, a larger range of DNA can be resolved on one gel, theDNA is less well resolved, and the gel becomes more difficult
to handle.
Bio-Rad agaroses are available specifically for PFGE thatprovide superior resolution (pulsed field Certified™ agarose)and decrease run time while maintaining good resolution(Certified megabase agarose).
Run Time
Several strategies may be employed to minimize or extend runtime. In general, it is best to optimize for the shortest run timethat allows clear sample resolution. This will maximize theefficiency of PFGE-related experiments.
It is possible to resume a run after staining the gel if it appears
that the separation is not complete. This is not generally
recommended because the ethidium bromide in the staining
solution will migrate in the reverse direction of the DNA,retarding its progress.
If necessary, it is safe to leave the gel for several hours after
run completion because the DNA is too large to diffuse out(>10 kb) and the presence of EDTA in the buffer and the coolbuffer will inhibit nucleases.

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