BIO-RAD 170-3612 through 170-3729 Instruction Manual
Summary
Essential guide for operating the CHEF-DR II Pulsed Field Electrophoresis System. This comprehensive manual is designed for laboratory professionals and molecular biologists performing advanced DNA analysis. It covers everything from safety standards and component setup to detailed procedures for various sample preparations, including mammalian, bacterial, and yeast genomic DNA. Use this resource to master gel casting, buffer circulation, and precise, reliable pulsed field electrophoresis results in a bio-safe environment.
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CHEF-DR® II Pulsed Field Electrophoresis Systems
Instruction Manual and Applications Guide
Catalog Numbers 170-3612 through 170-3729
For Technical Service Call Your Local Bio-Rad Office or in the U.S. Call 1-800-4BIORAD (1-800-424-6723)
Page Summary Contents For BIO-RAD 170-3612 through 170-3729 Instruction Manual
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CHEF-DR® II Pulsed Field Electrophoresis Systems Instruction Manual and Applications Guide Catalog Numbers 170-3612 through 170-3729 For Technical Service Call Your Local Bio-Rad Office or in the U.S....
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Warranty The CHEF-DR II control module, drive module, chamber, variable speed pump, and accessories are warranted against defects in materials and workmanship for 1 year. If any defects occur in the i...
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Table of Contents Section 1 Introduction ..................................................................................................1 1.1 Safety ...................................................
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Section 1 General Information 1.1 Safety The CHEF-DR II system uses high voltage and current and should be operated with care at all times. The safety interlocks are for your protection and should not...
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1.3 Specifications These specifications pertain to the complete CHEF-DR II system. A system including the Model 1000 Mini Chiller is also available. CHEF-DR II Specifications Drive Module Dimensions 2...
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Accessories included Variable speed pump 120 V, ground isolated. Flow rate 0.75 liter/min, typical Casting stand 14 cm x 13 cm Comb 10 well comb and comb holder Tygon tubing 365 cm Sample plug mold 10...
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Figure 1.1 A shows the relative potentials of each electrode pair when the + 60° vector (indicated by the arrow) is activated. Net field vector is from NW to SE. The highest poten- tials are found alo...
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and high voltage to the electrophoresis cell is disrupted. The lid also contains a mount at the upper right for an external temperature probe, which monitors buffer temperature in the cham- ber, and r...
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Model 1000 Mini Chiller The Model 1000 Mini Chiller is a stand alone, portable refrigerated apparatus specifi- cally designed for use with the CHEF-DR II system. Electrophoresis buffer is circulated b...
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Connect the set of black and red cables from the left set of jacks on the control module labeled POWER SUPPLY (- and +) to the left set of jacks on the drive module labeled FROM POWER SUPPLY. Connect ...
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2.3 CHEF-DR II Operation This section describes general operation. See Sections 3 and 4 for sample preparation, gel casting, gel running, and staining. In the following sections capitalized words refe...
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Block Adjust from 1-2 Blocks. Block 1 is run first, then Block 2. A run time of 0 will disable a Block. Initial Sw. Time Press BLOCK and VOLTS/CM simultaneously. Adjust from 0.1 second-65,000 seconds ...
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Volts/cm This will display the set voltage gradient for 3 seconds after which the remaining time for the current Block in progress will be displayed. Actual Current This will display the actual curren...
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Section 3 Sample Preparation 3.1 Agarose Blocks Standard procedures for DNA preparation do not yield intact, high molecular weight DNA molecules. Large DNA molecules (chromosome-sized) are so fragile ...
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4. Combine the cell suspension with an equal volume of 2% Clean Cut agarose and mix gen- tly but thoroughly. Keeping the cell/agarose mixture at 50 °C, transfer the mixture to plug molds using sterile...
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5. Remove 5 x 108 cells for each ml of agarose plugs to be made. Centrifuge for three min- utes in a microcentrifuge. If the volume is too large, spin at 10,000 x g for 5 minutes at 4 °C in an appropr...
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3.5 Preparation of Agarose Embedded Yeast DNA The buffers, enzymes, and agarose found in the following procedure are provided in the CHEF Yeast Genomic DNA Plug Kit (catalog number 170-3593; see Secti...
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12. Maintain the plugs in 1x Wash Buffer for long term storage. However , for subsequent restriction digestion, the EDTA concentration must be lowered. Wash the plugs to be restricted for 30 minutes i...
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3.8 Hemocytometer Usage A hemocytometer is usually divided into nine large squares (Figure 3.1). Each large square is 1 x 10-4 cm2 or 0.1 mm3, one such square (A) is shown in the figure with darkened ...
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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....
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Example Calculations: Mammalian: (A) (6 x 109 bp)(660 g/mole) = 6.547 x 10-12 g DNA/cell 6.02 x 1023 bp/mole (B) (6.578 x 10-12 g/cell)(5 x 107 cells/ml) = (3.289 x 10-4 g DNA/ml)(1x106 µg/g) - 329 mg...
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Yeast: (A) (1.5 x 107 bp)(660 g/mole) = 1.644 x 10-14 g DNA/cell 6.02 x 1023 bp/mole (B) (1.644 x 10-14 g DNA/cell)(6 x 108 cells/ml) = (9.876 x 10-6 g DNA/ml)(1x106 µg/g) = 9.876 µg DNA/ml (C) (9.876...
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4. Place the comb holder (with attached comb) into one of the two positioning slots on each side of the casting stand. Check that the bottom of the comb is at least 2 mm above the sur- face of the pla...
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Buffer Voltage Current Concentration Gradient Range 0.5x TBE (at 14 ˚C) 2 V/cm 30-40 m A 0.5x TBE (at 14 ˚C) 3 V/cm 50-60 m A 0.5x TBE (at 14 ˚C) 6 V/cm 110-120 m A 1.0x TAE (at 14 ˚C) 2 V/cm 80-90 m ...
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4.4 DNA Size Standards Bio-Rad recommends running standards in each gel to allow the sizes of unknown sam- ples to be determine and to verify the electrophoresis conditions. Figure 4.2 shows four Bio-...
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4.6 Separations at Room Temperature Electrophoresis may be conducted at room temperature, without a chiller, but the buffer should not be allowed to exceed 30 °C. It is important to maintain the tempe...
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There are several agarose types that allow easy handling of low concentration gels. These agaroses, in the concentration range of 0.5-0.8%, can be used to decrease the run time on sep- aration of larg...
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very large DNA (>3 mb) cannot be resolved on the gel and the field strength needs to be reduced. Moreover, some large DNA molecules will not enter the gels at high field strengths. Therefore, in se...
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5.4 Blotting Megabase DNAs† Southern Blot Transfer Pulsed field electrophoresis has become a powerful technique for physical mapping of genes in various organisms. In order to determine the chromosoma...
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6. Carefully remove the paper towel and blotting papers. Remove the membrane together with the gel, turn over the membrane and gel, lay them gel side up, and mark the location of the wells and the ori...
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6. The DNA is transferred from the back of the gel (the side opposite the wells) onto the membrane because irregularities in the surface of the gel frequently occur during solidi- fication of these hi...
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5. Hansenula wingei Size Range: 1-3.1 mb Agarose: 0.8% Molecular Biology Certified Buffer: 1.0x TAE Temperature: 14 °C Switch Time: 250-900 seconds Run Time: 50 hours Voltage Gradient: 3 V/cm 6. Schiz...
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6.2 Fuses If the DC current during a run exceeds 500 m A entering the electrophoresis cell, the 0.5 ampere FB (fast blow) fuse will blow on the front panel of the drive module. Replace the fuse by uns...
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Problem Solution Gel floats away 1. Pump flow rate is too high. Adjust with Variable Speed pump No or low buffer flow 1. Look for kink in tubing 2. Check Model 1000 Mini Chiller; buffer in the heat ex...
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Section 8 References 8.1 Applications in Pulsed Field Electrophoresis The following are references in pulsed field electrophoresis, primarily from 1987-1989. The list surveys a wide area of applicatio...
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CHEF 13, 20, 26, 28, 30, 31, 36, 37, 39, 42, 45, 56, 57, 58, 61, Application Reference Numbers Chromosome rearrangements 127, 141, 147, 166 Circular DNA 8, 75, 78, 79, 104, 118, 159, 160, 163, 164, 19...
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TAFE 51, 62, 63, 132, 148, 179 Theory 15, 22, 44, 48, 76, 81, 100, 101, 117, 126, 129, 130, Application Reference Numbers Two-D PFG 10, 203 Virus 15, 145 Visualization of DNA 154, 168 (microscope) Yea...
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29. Chou, H. S., Nelson, C. A., Godambe, S. A., Chaplin, D. D. and Loh, D. Y., Science, 238, 545-547 (1987). 30. Chu, G., Electrophoresis, 10, 290-295 (1989). 31. Chu, G., Vollrath, D. and Davis, R., ...
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65. Gejman, P.V., Sitaram, N., Hsieh, W-T., Gelernter, J. and Gershon, E. S., Applied and Theoret. Electrophor., 1, 29-34 (1988). 66. Gemmill, R. M., Coyle-Morris, J. F., Mc Peek, F. D., Ware-Uribe, L...
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100. Lalande, M., Noolandi, J., Turmel, C., Brousseau, R., Rousseau, J. and Slater, G. W., Nucleic Acids Res., 16, 5427-5437 (1988). 101. Lalande, M., Noolandi, J., Turmel, C., Rousseau, J. and Slater...
Manual Details
| Brand | Bio-Rad |
|---|---|
| Pages | 46 |
| File Size | 223.65 KB |
| Published | May 16, 2026 |
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Frequently Asked Questions
What safety standards does this instrument meet?
It is designed and certified to meet IEC1010-1 safety standards.
What solvents should not be used with the CHEF-DR II chamber?
Chlorinated hydrocarbons, aromatic hydrocarbons (toluene, benzene), or acetone are incompatible.
If I need technical service, what information must I provide?
You must inform Bio-Rad of the model and serial number of your instrument.
What happens if the instrument is altered by a third party?
Alteration voids both the manufacturer’s warranty and the IEC1010-1 safety certification.