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CHEF Genomic DNA Plug Kits

Instruction Manual

Catalog Numbers
170-3591
170-3592
170-3593

For Technical Service

Call Your Local Bio-Rad Office or
in the U.S. Call 1-800-4BIORAD
(1-800-424-6723)
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Table of Contents
Section 1 Introduction......................................................1
1.1 Kit Components ..........................................................2
Section 2 Preparation of Agarose Embedded
Mammalian DNA ............................................3
Section 3 Preparation of Agarose Embedded
Bacterial DNA ..................................................5
Section 4 Preparation of Agarose
Embedded Yeast DNA ....................................8
Section 5 Restriction Enzyme Digestion of Plugs ........11
Section 6 References ......................................................12
Section 7 Additional Reagents for Pulsed Field
Electrophoresis ..............................................13
Section 8 Instruments for Pulsed Field
Electrophoresis ..............................................13
Section 9 Appendix ........................................................14
9.1 Solutions....................................................................14
9.2 Agarose Concentrations ............................................15
9.3 Hemocytometer Usage ..............................................16
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Section 1
Introduction
Pulsed-Field Gel Electrophoresis (PFGE) allows the
separation of DNA ranging in size from a few kilobase pairs
to 10 megabase pairs. Because of the large size of these
molecules, simple pipetting mechanically shears the DNA
resulting in unacceptable quality for PFGE separations. This
has necessitated procedures for lysis of whole cells embedded
in agarose, allowing purification of chromosome-sized DNA
without shearing.
The most important and difficult task in preparing cells
for embedding in agarose is to obtain the proper cell
concentration. Although optical density is frequently used to
determine cell concentration, it is not reliable. Different
strains, plasmid content, and growth media all contribute to
the actual cell number achieved for a particular optical
density. Variation in cell number will cause the amount of
DNA per agarose plug to vary, leading to over- and or under-
loading of the sample. To eliminate the need to generate a
growth curve for each strain, a hemocytometer is the most
reproducible method for achieving the proper cell
concentration for different types of cells, bacteria, yeast, and
fungi. Detailed instructions for the use of a hemocytometer
are given in the Appendix.

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1.1 Kit Components 170-3593 CHEF Yeast Genomic DNA Plug Kit, contains Cell
Suspension Buffer, 12 ml; >600 U/ml Proteinase K,
The CHEF Genomic DNA Plug Kits are designed to 1.3 ml; Proteinase K Reaction Buffer, 30 ml;
produce 100 sample plugs of agarose embedded DNA with 2% CleanCut Agarose, 12 ml; 10x Wash Buffer, 60 ml;
5000 U/ml Lyticase, 1.6 ml; Lyticase Buffer, 30 ml,
the quality necessary for PFGE separations. All kits consist 50 well disposable plug mold, 2; Screened Cap, 1
of a core module, which contains all the buffers and
proteinase solutions. This core module is the only component
supplied with the mammalian DNA kit. Other kits contain Section 2
additional modules with lysis buffers specific to that cell Preparation of Agarose Embedded
type. For example, the bacterial kit contains lysozyme and its Mammalian DNA
reaction buffer necessary to digest the outer cell membrane of
lysozyme-sensitive bacteria; the yeast module contains Reagents and Equipment Needed
lyticase and its reaction buffer necessary to digest the cell Sterile transfer pipettes
walls of most yeast. Each of the disposable plug molds 50 °C water bath
provided contains 50 wells which are 1.5 mm thick and 5 mm PMSF stock solution see Appendix
wide and hold 85 µl of volume. It is also possible to use the Hemocytometer see Appendix
10 well reusable sample plug mold (170-3622). Each of the Microscope
wells in the reusable mold are 1 cm wide and 1.5 cm thick 2, 5, 50 ml sterile plastic tubes
and hold 300 µl of volume.
1. Prepare a cell suspension in isotonic saline or tissue
Catalog culture medium without fetal bovine serum. Count the
Number Product Description
cells and remove 5 x 107 cells for each ml of agarose
170-3591 CHEF Mammalian Genomic DNA Plug Kit, contains plugs to be made (use 100 µl/plug for disposable mold or
Cell Suspension Buffer, 12 ml; >600 U/ml Proteinase K,
1.3 ml; Proteinase K Reaction Buffer, 30 ml;
300 µ l/plug for reusable mold) and place on ice.
2% CleanCut™ Agarose, 12 ml; 10x Wash Buffer, 60 ml, See Appendix for hemocytometer usage.
50 well disposable plug mold, 2; Screened Cap, 1 2. Melt the 2% CleanCut agarose solution using a
170-3592 CHEF Bacterial Genomic DNA Plug Kit, contains microwave and equilibrate the solution to 50 °C in a
Cell Suspension Buffer, 12 ml; >600 U/ml Proteinase K,
1.3 ml; Proteinase K Reaction Buffer, 30 ml;
water bath.
2% CleanCut Agarose, 12 ml; 10x Wash Buffer, 60 ml;
25 mg/ml Lysozyme, 1.6 ml; Lysozyme Buffer, 30 ml,
50 well disposable plug mold, 2; Screened Cap, 1

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3. Calculate the amount of Cell Suspension Buffer 7. Wash the plugs four times in 1x Wash Buffer, 1 hour each
and CleanCut agarose necessary (see Section 9.2). For a at room temperature with gentle agitation (for each plug,
final concentration of 0.75% agarose use 0.63 ml of Cell use 1 ml of 1x Wash Buffer). Prepare the Wash Buffer by
Suspension Buffer per ml of agarose plugs. Use 0.37 ml diluting the 10x stock (1:10) with sterile ddH2O. If the
of 2% CleanCut agarose per ml of agarose plugs. plugs are to be used in subsequent enzyme reactions, it is
4. Centrifuge the cell suspension at 1,000 x g for 5 minutes advisable to wash the plugs in 1 mM PMSF during the
at 4 °C. Resuspend the cells in the volume of Cell second or third wash to inactivate residual Proteinase K.
Suspension Buffer calculated above and equilibrate the See Appendix for PMSF stock solution.
cell suspension to 50 °C. Note: For washing a few plugs, use a 2 or 5 ml sterile tube.
5. Combine the calculated volume of 2% CleanCut agarose 8. Store the plugs at 4 °C in 1x Wash Buffer. The plugs
with the cell suspension and mix gently, but thoroughly. should be stable for 3 months.
Keeping the cell/agarose mixture at 50 °C, transfer the
mixture to plug molds using sterile transfer pipettes Section 3
(Bio-Rad's disposable transfer pipettes, catalog 223-9524,
are recommended). Allow the agarose to solidify. This
Preparation of Agarose Embedded
step can be expedited by placing the molds at 4 °C for
Bacterial DNA
10–15 minutes, which also adds strength to the agarose
for removal from the mold. Reagents and Equipment Needed
6. Using a 50 ml conical centrifuge tube, add 100 µ l of Sterile transfer pipettes
Proteinase K stock to 2.5 ml of Proteinase K Reaction 50 °C water bath
Buffer for each ml of agarose plugs. Push the solidified Grams Crystal Violet (Difco)
agarose plugs into the 50 ml centrifuge tube containing Microscope
the Proteinase K solution. Incubate the plugs overnight at PMSF stock solution see Appendix
50 °C without agitation. Hemocytometer see Appendix
Note: Various cell lines have been incubated up to 4 days 2, 5, 50 ml sterile plastic tubes
in Proteinase K without detrimental effects to the quality 1. Inoculate a bacterial culture into 50 ml of LB Broth or
of DNA. appropriate media and grow with agitation to an O.D.600
Note: For processing a few plugs, use a 2 or 5 ml tube. of 0.8–1.0 at the appropriate temperature. See appendix
for LB Broth.

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2. When the desired O.D.600 is reached, add chloramphenicol of Cell Suspension Buffer calculated above and equilibrate
to a final concentration of 180 µ g/ml and continue the cell suspension to 50 °C.
incubation up to 1 hour while performing step 3. 7. Combine the calculated volume of 2% CleanCut agarose
Note: Chloramphenicol is used to synchronize ongoing with the cell suspension and mix gently, but thoroughly.
rounds of chromosomal replication and inhibit further Keeping the cell/agarose mixture at 50 °C, transfer the
rounds of replication. This step is optional, but regions near mixture to plug molds using sterile transfer pipettes
the replication terminus might be under-represented. In (Bio-Rad's disposable transfer pipettes, catalog 223-9524,
addition, chloramphenicol will alter the morphology of the are recommended). Allow the agarose to solidify. This
cells over time causing the appearance of a mixed culture; step can be expedited by placing the molds at 4 °C for
therefore proceed as quickly as possible with step 3. 10–15 minutes, which also adds strength to the agarose
3. Make a twenty-fold dilution of the above bacterial for removal from the mold.
suspension using 1 ml bacteria, 1 ml Gram Crystal 8. Push the solidified agarose plugs into a 50 ml conical
Violet, and 18 ml saline or PBS. Place a small amount of centrifuge tube containing lysozyme solution. Prepare
the bacterial suspension on a hemocytometer and count at lysozyme solution by adding 100 µl of Lysozyme stock
400x power. See Appendix on hemocytometer usage. to 2.5 ml of Lysozyme Buffer for each 1 ml of agarose
4. Melt the 2% CleanCut agarose solution using a plugs. Incubate the plugs for 2 hours at 37 °C.
microwave or hot water bath and equilibrate the solution Note: For processing a few plugs, use a 2 or 5 ml tube.
to 50 °C in a water bath. 9. Remove the lysozyme solution and rinse the plugs with
5. Calculate the amount of Cell Suspension Buffer and sterile water. Add 2.5 ml of Proteinase K Reaction Buffer
CleanCut agarose necessary (see Section 9.2). For a final for each ml of agarose plugs, followed by 100 µ l of
concentration of 1% agarose use 0.5 ml of Cell Suspension Proteinase K stock. Incubate the plugs overnight at 50 °C
Buffer per ml of agarose plugs (use 100 µ l/plug for without agitation.
disposable mold or 300 µl/plug for reusable mold). Use Note: Various cell lines have been incubated up to 4 days
0.5 ml of 2% CleanCut agarose per ml of agarose plugs. in Proteinase K without detrimental effects to the quality
6. Remove 5 x 108 cells for each ml of agarose plugs to be of DNA.
made. Centrifuge for 3 minutes in a microcentrifuge. If the
volume is too large, spin at 10,000 x g for 5 min at 4 °C in
an appropriate size tube. Resuspend the cells in the volume

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10. Wash the plugs four times in 1x Wash Buffer, 1 hour each 1. Inoculate a single colony into 50 to 100 ml YPD broth or
at room temperature with gentle agitation (for each plug, appropriate media. Grow with agitation to an O.D.600 of
use 1 ml of 1x Wash Buffer). Prepare the Wash Buffer by >1.0 at the appropriate temperature for your strain.
diluting the 10x stock (1:10) with sterile ddH2O. If the See Appendix for YPD broth.
plugs are to be used in subsequent enzyme reactions, it is 2. When the desired O.D.600 is reached, centrifuge the cells
advisable to wash the plugs in 1 mM PMSF during the at 5,000 x g, 10 min, 4 °C. Pour off the supernatant and
second or third wash to inactivate residual Proteinase K. resuspend in 10 ml cold 50 mM EDTA, pH 8.
See Appendix for PMSF stock solution. 3. Determine the cell concentration by adding 10 µl of cells
Note: For washing a few plugs, use a 2 or 5 ml sterile tube. to 990 µ l of water. Place the yeast suspension on a
11. Store the plugs at 4 °C in 1x Wash Buffer. The plugs hemocytometer and count at 400x power. See Appendix
should be stable for 3 months. on hemocytometer usage.
4. Heat the 2% CleanCut agarose solution using a
Section 4 microwave and equilibrate the solution to 50 °C in a
Preparation of Agarose Embedded water bath.
Yeast DNA 5. Calculate the amount of Cell Suspension Buffer and
CleanCut agarose necessary (see Section 9.2). For a
Reagents and Equipment Needed final concentration of 0.75% agarose use 0.63 ml of
Cell Suspension Buffer per ml of agarose plugs (use
50 mM EDTA, pH 8 100 µ l/plug for disposable mold or 300 µ l/plug for
Sterile transfer pipettes reusable mold). Use 0.37 ml of 2% CleanCut agarose
50 °C water bath per ml of agarose plugs to be made.
Microscope
6. Remove 6 x 108 cells for each ml of plugs to be made.
PMSF stock solution see Appendix
Centrifuge in a microfuge for 3 minutes if volumes are
Hemocytometer see Appendix
small, otherwise centrifuge the cells at 5,000 x g, for
2, 5, 50 ml sterile plastic tubes 10 minutes at 4 °C. Resuspend the cells in the volume of
Cell Suspension Buffer calculated above and equilibrate
to 50 °C.

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7. Just prior to mixing the cells with agarose, add 30 µl of Note: Various cell lines have been incubated up to 4 days
the Lyticase stock, for each ml of plugs to be made, to the in Proteinase K without detrimental effects to the quality
cell suspension. of DNA.
Note: It is recommended that Lyticase be added imme- 11. Wash the plugs four times in 1x Wash Buffer, 1 hour each
diately prior to imbedding the cells in agarose. It has been at room temperature with gentle agitation (for each plug,
found that certain strains do not give acceptable DNA use 1 ml of 1x Wash Buffer). Prepare the Wash Buffer by
when Lyticase is allowed to diffuse into the agarose plug. diluting the 10x stock (1:10) with sterile ddH2O. If the
8. Combine the calculated volume of 2% CleanCut agarose plugs are to be used in subsequent enzyme reactions, it is
with the cell suspension and mix gently, but thoroughly. advisable to wash the plugs in 1 mM PMSF during the
Keeping the cell/agarose mixture at 50 °C, transfer the second or third wash to inactivate residual Proteinase K.
mixture to plug molds using sterile transfer pipettes See Appendix for PMSF stock solution.
(Bio-Rad's disposable transfer pipettes, catalog 223-9524, Note: For washing a few plugs, use a 2 or 5 ml sterile tube.
are recommended). Allow the agarose to solidify. This 12. Store the plugs at 4 °C. The plugs should be stable for
step can be expedited by placing the molds at 4 °C for 3 months.
10–15 minutes, which also adds strength to the agarose
for removal from the mold.
Section 5
9. Push the solidified agarose plugs into a 50 ml conical
centrifuge tube containing Lyticase solution. Prepare
Restriction Enzyme
Lyticase solution by adding 85 µl of Lyticase stock to
Digestion of Plugs
2.5 ml of Lyticase Buffer for each 1 ml of plugs. Incubate 1. Place one plug per digest in a sterile 1.5 ml microcentrifuge
the plugs for 2 hours at 37 °C. tube. Wash once for 1 hour in 1 ml 0.1x Wash Buffer
Note: For processing a few plugs, use a 2 or 5 ml tube. (1:100 dilution of 10x stock Wash Buffer) Use 1 ml 0.1x
10. Remove the lyticase solution and rinse the plugs with Wash Buffer per plug. Decant and resuspend in a sufficient
sterile water. Add 2.5 ml of Proteinase K Reaction Buffer amount of fresh 0.1x Wash Buffer to cover the plugs. This
for each ml of agarose plugs, followed by 100 µ l of last wash reduces the EDTA concentration, allowing faster
Proteinase K stock. Incubate the plugs overnight at 50 °C buffer equilibration with restriction enzyme buffers.
without agitation.

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2. Aspirate the Wash Buffer and add 1 ml of the appropriate Section 7

1x restriction enzyme buffer for about 1 hour with gentle Additional Reagents for
agitation at room temperature. Aspirate off the buffer and Pulsed Field Electrophoresis
add 0.3 ml of fresh 1x enzyme buffer. Add the restriction
enzyme (30–50 U per 100 µl plug) and incubate overnight Catalog
at the appropriate temperature. Number Product Description
162-0137 Pulsed Field Certified Agarose, 100 g
3. After overnight digestion, remove the buffer and incubate
in 1 ml of 1x Wash Buffer for approximately 30 minutes 162-0135 Chromosomal Grade Agarose, 25 g
with gentle agitation. 170-3594 CleanCut Agarose, 2%, 12 ml
170-3624 DNA Size Standards, 5 kb ladder
4. Optional: Remove the Wash Buffer and equilibrate the
170-3605 DNA Size Standards, Yeast chromosomal
plug in the appropriate concentration of gel running
buffer, i.e. 0.5x TBE, 1.0x TAE, etc. 170-3633 DNA Size Standards, S. pombe chromosomes
170-3635 DNA Size Standards, lambda ladder
5. Load 1⁄4 to 1⁄3 of a plug per well (this is approximately 50 µg
162-0196 Zeta-Probe® GT Nylon Membrane, roll, 30 cm x 3.3 m
DNA) and adjust the volume if necessary on subsequent
161-0733 10x TBE Buffers, 1 liter
gels. In addition, always load appropriate size standards.

Section 6 Section 8
References Instruments for Pulsed Field
Electrophoresis
1. Smith, C. L., Klco, S. R. and Cantor, C. R., Genome Analysis,
Chapter 3, K. Davis ed., IRL Press Ltd., Oxford, England (1988). Catalog
2. Smith, C. L. and Cantor, C. R., Methods in Enzymology, 155, Number Product Description
449–467 (1988). 170-3612 CHEF-DR® II System
170-3695 CHEF-DR III System
170-3670 CHEF Mapper® XA Chiller System
170-3654 Cooling Module
165-5031 GS GeneLinker® UV Chamber

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Section 9 9.2 Agarose Concentrations

Appendix Various agarose plug percentages are reported in the
literature. The most common final concentration is 0.5%, but
9.1 Solutions the softness of these plugs makes them difficult to keep intact
and handle. We have found that 0.75% to 1% agarose greatly
PMSF, 100 mM Add 0.174 g to 10 ml of 100%
(phenylmethanesulfonyl isopropanol. Store at room tem- enhances the strength of the plug without interfering with the
fluoride) perature. migration of the DNA out of the plug. These kits contain a 2%
CleanCut agarose solution, which when mixed with differing
A stock solution of 100 mM in amounts of Cell Suspension Buffer, will give agarose
100% isopropanol is stable at
room temp for 1 year. PMSF is concentrations ranging from 0.5 to 1%. This allows the option
not stable in aqueous solutions. of using a different final concentration of agarose if desired.
Activity lasts approximately 30 to
50 min at room temperature at pH
7.5-8. Desired Agarose CleanCut Agarose Cell Suspension
Concentration 2%* Buffer*
LB Per liter:
10 g Bacto Tryptone
5 g Bacto Yeast Extract
10 g NaCl 1% (0.5)vol. = ____ (0.5)vol. = ____
pH 7
YPD Per liter:
20 g Bacto Peptone 0.75% (0.375)vol. = ____ (0.625)vol. = ____
10 g Bacto Yeast Extract
20 g dextrose (glucose)
0.5% (0.25)vol. = ____ (0.75)vol. = ____

* Vol. is the total volume of plugs to be made at 75 µl/plug, i.e. for 5 ml

of plugs at 0.75% final agarose concentration, add (0.375)5 ml = 1.9 ml
of 2% agarose solution to (0.625)5 ml = 3.4 ml of cell suspension.

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9.3 Hemocytometer Usage A. Mammalian or Tissue Culture Cells:

A hemocytometer is usually divided into nine large Because of the large size, tissue culture cells can be
squares (Figure 1). Each large square is 1 x 10-4 cm2 or 0.1 counted at 100x power. Count 10 of the large squares, five on
mm3, two such squares are shown the figure with darkened each side of the hemocytometer. Determine the average cells
borders (A&B). The large circle around the center square (B) per square using the equations below:
represents your field of view at 100x power (10x objective Cells Counted
lens, 10x eye piece). The center square is subdivided into 25 = Average Cells per Square
Number of Center Squares
smaller squares. The smaller circle in the center square (C)
represents your field of view at 400x power (40x objective Average Cells per square × Dilution Factor × 104 = Cells per ml.
lens, 10x eye piece). These 25 center squares are further Use the following ratio to determine how many ml of cell
divided into 16 squares. suspension to use to achieve the desired cell concentration for
the plugs.
5 x 107 cells desired
× ml of plugs to be made = ml of cell suspension
actual cell concentration to use.

For Example: 500 cells in 10 squares = average of

B 50 cells /square x 5 (dilution factor) x 104 = 2.5 x 106 cells per
ml. For 1 ml of plugs you need 1 ml x (5 x 107) cells final
C
concentration divided by 2.5 x 106 actual cells concentration =
20 ml of cell suspension is required to make 1 ml of agarose
plugs.

A B. Bacteria and Yeast Cells:

Count five to ten of the 25 center squares, at 400x power,
to get a representative sample of your cell suspension. You
should have approximately 25 to 75 cells per square. The
Fig. 1. Hemocytometer grid. cells should be relatively free of clumps. Bacteria which
naturally chain or grow in clusters are relatively easy to count

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and do not have to be dispersed by chemical or enzymatic

methods. The Grams Crystal Violet aids in the visualization
of bacteria.
Use the equations below to determine the cell
concentration:

Cells Counted
= Average Cells per Square
Number of Squares

Average Cells per square × 25 Squares × Dilution Factor × 104 = Cells per ml

desired cell concentration

× ml of plugs to be made = ml of cell suspension
actual cell concentration to use.

For example: 300 bacteria in 5 squares = average of

60 bacteria/square x 25 (squares) x 20 (dilution factor, yeast
use 100 for dilution factor) x 104 = 3 x 108 bacteria per ml.
For 5 ml of plugs you need 5 ml x (5 x 108) cells final
concentration ÷ (3 x 108) actual cells concentration = 8.33 ml
of cell suspension is required.
Bio-Rad
For yeast use 6 x 10 8 cells per ml for the final Laboratories
concentration (see page 9).
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