Introduction—E-Gel® Electrophoresis System

The E-Gel® agarose gel electrophoresis system is a complete bufferless system for agarose gel electrophoresis of DNA samples.

The major components of the system are:

  • E-Gel® pre-cast agarose gels
  • E-Gel® PowerBase™ v.4. or Mother E-Base™


E-Gel® pre-cast agarose gels are self-contained gels that include electrodes packaged inside a dry, disposable, UV-transparent cassette. The E-Gel® agarose gels run in a specially designed device that is a base and power supply combined into one device. They either contain SYBR Safe™ DNA gel stain, ethidium bromide, or no DNA gel stain.
 
Advantages of E-Gel®
Using E-Gel® agarose gels for electrophoresis of DNA samples offer the following advantages:

  • Provides fast, safe, consistent, high-resolution electrophoresis
  • Eliminates the need to prepare agarose gels and buffers, and to stain gels
  • Compatible with most commercially available robotic systems for high-throughput agarose gel electrophoresis
  • Available in a variety of agarose percentages, well formats, and throughput to suit your applications
  • Offered with SYBR Safe™ DNA gel stain, a safer, more environmentally friendly alternative to ethidium bromide 


Available DNA Gel Stains
E-Gel® agarose gels come in three formats for staining your DNA:

  • Regular E-Gel® agarose gels contain the standard DNA gel stain ethidium bromide
  • E-Gel® with SYBR Safe™ contains SYBR Safe™ DNA gel stain, which is not classified as hazardous waste under U.S. Federal regulations, and improves cloning efficiency when using blue light for imaging
  • Clear E-Gel® does not contain a DNA gel stain, and is intended for custom staining or for analyzing fragments coupled to a fluorescent label.


Advantages of SYBR Safe™
SYBR Safe™ DNA gel stain offers the following advantages:

  • SYBR Safe™ DNA gel stain is not classified as hazardous waste under U.S. Federal regulations and meets the requirements of the Clean Water Act and the National Pollutant Discharge Elimination System regulations.
  • SYBR Safe™ DNA gel stain does not cause mutations, chromosomal aberrations, or transformations in appropriate mammalian test systems, in contrast to ethidium bromide which is a strong mutagen.
  • A single oral administration of SYBR Safe™ DNA gel stain produces no signs of mortality or toxicity at a limit dose of 5000 mg/kg.
  • Visualizing E-Gel® with SYBR Safe™ using blue light transilluminators dramatically reduces DNA damage that lowers cloning efficiency.
  • For details on SYBR Safe™ DNA gel stain.


Throughput Formats
Two types of E-Gel® agarose electrophoresis systems are available from Invitrogen based on your throughput requirements.

  • Low-Throughput E-Gel® Electrophoresis System
  • Medium/High-Throughput E-Gel® Electrophoresis System


Low-Throughput E-Gel Electrophoresis System
The Low-Throughput E-Gel® Electrophoresis System is designed for electrophoresis of 12-16 DNA samples per gel. For details on this system, see page 5.The system consists of the following components:

  • E-Gel® with SYBR Safe™, E-Gel® single comb, double comb, and Clear E-Gel® pre-cast agarose gels
  • Gels are available in a variety of well formats and percentages. Choose an appropriate gel based on your application. (see table).
  • E-Gel® PowerBase™ v.4
  • The E-Gel® PowerBase™ v.4 is a base and a power supply in one device. The E-Gel® PowerBase™ connects directly to an electrical outlet using the adapter supplied with the base.•E-Gel®Opener
  • The E-Gel®Opener is an easy-to-use device specifically designed to open any E-Gel® single comb, double comb, or Clear E-Gels®

 

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Low-Throughput E-Gel® Electrophoresis System

System Components
The Low-Throughput E-Gel® Electrophoresis System consists of the following components:

  • E-Gel® with SYBR Safe™, E-Gel® single comb, double comb, and Clear E-Gel® pre-cast agarose gels  
  • E-Gel® PowerBase™ v.4
  • E-Gel® Opener


Note:   The E-Gel® Base previously available from Invitrogen can be used for electrophoresis of E-Gel® with SYBR Safe™, E-Gel® single comb, double comb, and Clear E-Gel® agarose gels.

Applications
E-Gel® agarose gels are suitable for analyzing:

  • PCR products
  • Restriction digests
  • RT-PCR reactions

 
When to Use E-Gel® With SYBR Safe™
E-Gel® with SYBR Safe™ contains SYBR Safe™ DNA gel stain instead of ethidium bromide. Use E-Gel® with SYBR Safe™ for these reasons:
If you want to minimize your hazardous waste, since SYBR Safe™ DNA gel stain is not classified as such under U.S. Federal regulations.

  • If you want to protect yourself or your co-workers, because E-Gel® with SYBR Safe™ eliminates the use of the strong mutagen ethidium bromide and reduces UV exposure.
  • If you want to maximize cloning efficiency, since E-Gel® with SYBR Safe™ dramatically reduces DNA damage if using blue light transilluminators.   


When to Use Clear E-Gel®
Clear E-Gel® agarose gels do not contain ethidium bromide in the gels and are ideal for the following applications:

  • Post-staining gels with sensitive stains such as SYBR® Green I or II, or SYBR® Gold.
  • Analyze DNA fragments pre-labeled with fluorescein, Texas Red® or Alexa Fluor®
  • Perform downstream applications with DNA in which ethidium bromide may interfere
  • Determine accurate size and form of the DNA band (most DNA staining dyes intercalate into the DNA and change molecular weight and form of the DNA)
  • Stain only one lane of the gel and then excise a specific band or size range in the remaining gel for cloning purposes thereby avoiding UV exposure to the DNA resulting in a significant increase in the cloning efficiency.


E-Gel® Single Comb and Double Comb Gels
The E-Gel® single comb and double comb gels are bufferless gels containing electrodes embedded in the agarose matrix. Each gel contains an ion generating system (TAE buffer system), a pH balancing system, and ethidium bromide for DNA staining and is packaged inside an UV-transparent cassette.
 
To create a patented bufferless system, each E-Gel® single comb and double comb cassette contains two ion exchange matrices (IEMs) that are in contact with the gel and electrodes. The IEMs supply a continuous flow of ions through out the gel resulting in a sustained electric field required for running the gel (see figure below).
 
Clear E-Gel® agarose gels are single comb gels that do not contain any nucleic acid stain in the agarose.

E-Gel® PowerBase™
The E-Gel® PowerBase™ Version 4 is an easy-to-use, automated device specifically designed to simplify electrophoresis of single comb or double comb E-Gel® agarose gels from Life Technologies. The E-Gel® PowerBase™ is a base and a power supply all in one device.
 
The operation of the E-Gel® PowerBase™ v. 4 is controlled by two buttons on top of the base. The left button is for a double comb run and right button is for a single comb run (see the label on the unit). To select different electrophoresis runs for the PowerBase™, do one of the following.

  • Press and release the button OR
  • Press and hold the button


E-Gel® Base
The E-Gel® Base previously available from Invitrogen connects to a power supply and is used for electrophoresis of E-Gel® single comb, double comb, and Clear E-Gel® agarose gels.

E-Gel® Opener
The E-Gel® Opener is an easy-to-use device specifically designed to open any E-Gel® single comb, double comb, or Clear E-Gels® for excision of DNA fragments or for blotting. 

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Materials

Product Specifications

E-Gel® Single Comb and Double Comb Gel Specifications
The E-Gel® cassette is 8 cm x 10 cm and 0.6 cm thick. The thickness of the E-Gel® gel is 3 mm and the volume of the gel is 20 ml.

  • Single comb gel—Each well is 4.1 mm wide and the space between wells is 1 mm. The running distance is 5.8 cm. Each gel contains 12 lanes.
  • Double comb gel—The sample well is 4.6 mm wide and the marker well is 2.8 mm wide. The running distance from each comb is 2.9 cm. Each gel contains two rows of 8 sample wells and 2 marker wells (M). The wells of the double comb gel are compatible for loading with a multichannel pipettor.


E-Gel® 48 Gel Specifications
Each E-Gel® 48 gel contains 48 sample wells and 4 marker wells (M). 

Cassette Size:13.5 cm (l) x 10.8 cm (w) x 0.67 cm (thick)
Gel Thickness:3.7 mm
Gel Volume:50 ml
Gel Percentage:1%, 2%, and 4%
Well Depth:3 mm
Dimensions of the Well:3.6 mm (l) x 2.2 mm (w)
Running Distance: (one well to the next)32 mm
Space between Well Center:4.5 mm



E-Gel® 96 Gel Specifications
Each E-Gel®  96 gel contains 96 sample wells and 8 marker wells (M).

Cassette Size:13.5 cm (l) x 10.8 cm (w) x 0.67 cm (thick)
Gel Thickness:3.7 mm
Gel Volume:50 ml
Gel Percentage:1% and 2%
Well Depth:3 mm
Well Opening3.8 mm x 1.8 mm
Well Bottom3.3 mm x 1.1 mm
Running Distance: (one well to the next)16 mm
Space between Wells:9 mm

The wells of the E-Gel® 96 cassette are compatible with a multichannel pipettor or 8, 12, or 96-tip robotic loading devices.



E-Base™ Specifications
The specifications for Mother E-Base™ and Daughter E-Base™ are listed below.

Dimensions:14.6 cm x 15 cm x 5.3 cm
Weight:Mother E-Base™- 370 g
Daughter E-Base™- 271 g
Safety:Double Insulation, UL listed, and CE certified
Temperature:Ambient 15°C to 40°C
Built-in Features:Digital time display (00-99 minutes), alarm, light LED                                          

The SBS (Society for Biomolecules Screening) standard 96-well plate format of the E-Base™ fits on most robotic platforms allowing the loading and °electrophoresis of gels on the E-Base™ directly on the robot.


 
E-Gel® PowerBase™ v.4 Specifications

The specifications for E-Gel® PowerBase™ V.4 are listed below.

Dimensions:12.5 cm x 13 cm x 13.5 cm
Weight:1.19 lbs (540 g) with adapter
Safety:UL listed and CE certified
Temperature:Ambient 15°C to 40°C
Built-in Features:Alarm, light LED


 
E-Gel® PowerBase™ Adapter Specifications
The E-Gel® PowerBase™ v.4 is designed for use with an adapter included with the PowerBase™. Use only UL Listed Class 2 Direct Plug-in Adapter included with the PowerBase™. Input and Output supplied by the adapter are shown in the table below.

 
CountryInputOutput
U.S. and Canada
110-120 V AC, 60 Hz
12 V DC, 880 mA
Europe
220-240 V AC, 50 Hz
12 V DC, 880 mA

 


E-Gel® Base Specifications
The specifications for E-Gel® Base are listed below:

  • Dimensions:                           12.5 x 13 x 3.5 cm
  • Weight:                                     3.18 oz. (90 g)
  • Temperature:                          Ambient 15C to 40°C

 

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Sample Preparation for E-Gel®

Introduction
For optimal results, follow the guidelines for preparing your DNA sample as described in this section.
 
Materials Needed

  • DNA sample
  • Loading buffer (optional)
  • Molecular weight markers


Amount of DNA
Use 20-100 ng DNA per band for samples containing one unique band, or up to 500 ng per lane for samples containing multiple bands. If you are unsure how much to use, test a range of concentrations to determine the optimal concentration for your particular sample. Excess DNA will cause poor resolution.
 
Loading Method
The DNA samples are loaded in E-Gel® agarose gels using the One-Step Loading or Two-Step Loading method.
 
The One-Step Loading method is routinely used to load E-Gel® agarose gels.
The Two-Step Loading method is used to load E-Gel® agarose gels, if the One-Step Loading method produces fuzzy or indistinct bands, or the gel was removed from its plastic pouch for more than 30 minutes

Prepare loading buffer and sample volumes based on the loading method as described below.

Total Sample Volume
The recommended total sample volume for each gel type is listed in the table below.
 
Note:   For best results, keep all sample volumes uniform. If you do not have enough samples to load all wells of the gel, load an equal volume of deionized water (E-Gel®) or buffer containing the same salt concentration as samples (E-Gel® 48/96 gels) into any empty wells.

Gel Type
One-Step Loading
Two-Step Loading
E-Gel® single comb gel
20 µl
10 µl
E-Gel® double comb gel
20 µl
10 µl
Clear E-Gel®
20 µl
10 µl


Loading Buffer
Loading buffer is optional for One-Step Loading method but is required for the Two-Step Loading method for E-Gels.
 
You can load your samples directly into the wells, if no loading buffer is used. If you are using loading buffer, mix the required amount of DNA with the loading buffer.
 
We recommend using a loading buffer with the following formulation:

  • For One-Step Loading method, use a loading buffer that yields a final concentration of 10 mM Tris-HCl, pH 7.5; 1 mM EDTA; 0.005% bromophenol blue; 0.005% xylene cyanol FF.
  • For Two-Step Loading method, use a loading buffer that yields a final concentration of 10% glycerol (or 6% Ficoll 400) 10 mM Tris-HCl, pH 7.5; 1 mM EDTA; 0.005% bromophenol blue; 0.005% xylene cyanol FF


If you are using 10X BlueJuice™ Gel Loading Buffer or TrackIt™ Loading Buffer available from Invitrogen, dilute this buffer 50-to 200-fold to obtain optimal results with E-Gel® agarose gels. For Two-Step loading with 10X BlueJuice™ Gel Loading Buffer or TrackIt™ Loading Buffer dilute this buffer 50- to 200-fold and add 10% glycerol.
 
High Salt Samples
Important:
To obtain the best results, prepare your high salt samples as described below.
 
Samples containing > 50 mM NaCl, 100 mM KCl, 10 mM acetate ions, or 10 mM EDTA (i.e. certain restriction enzyme and PCR buffers) will cause loss of resolution on E-Gel® agarose gels. Dilute samples 2- to 20-fold as described:

  • Restriction Digests—Digest 500 ng-1 µg of DNA in 20 µl final volume. Use 1 µl (for samples >1 kb) or 5-10 µl (for samples <1 kb) and dilute as described below.
  • PCR Samples—Use 1-5 µl of a 50 µl reaction and dilute as described below.

 

One-Step Loading
Two-Step Loading
Dilute samples with the loading buffer, deionized water, or TE to a final volume of 20 µl
Dilute samples with glycerol loading buffer, glycerol in deionized water, or glycerol in TE buffer to obtain a final glycerol concentration of 10% in a final sample volume of 10 µl


Preparing Samples
Prepare your samples based on the loading method used as described below: 

 
One-Step Loading
Two-Step Loading
Total Sample Volume
Add deionized water to the required amount of DNA to bring the total sample volume to 20 µl.
Mix the required amount of DNA with a glycerol loading buffer (see below) to obtain a final glycerol concentration of 10% in a total sample volume of 10 µl.
When loading into the gel, first load 10 µl of deionized water directly into each well and then add 10 µl of sample containing 10% glycerol.
Loading Buffer
Optional: Instead of water, you may use a loading buffer that yields a final concentration of 10 mM Tris-HCl, 1 mM EDTA, pH 7.5; 0.005% bromophenol blue; and 0.005% xylene cyanol FF.
To use 10X BlueJuiceTrackIt™ Loading Buffer, dilute this buffer 50- to 200-fold to obtain the optimal dye concentration.
Prepare a loading buffer that yields a final concentration of 10% glycerol (or 6% Ficoll 400), 10 mM Tris-HCl, pH 8.1; 1 mM EDTA, pH 7.5; 0.005% bromophenol blue; 0.005% xylene cyanol FF.
To use 10X BlueJuiceTrackIt™ Loading Buffer vii, dilute this buffer 50- to 200-fold and then add glycerol to a final concentration of 10% in the sample.


DNA Molecular Weight Markers
We recommend using the following DNA molecular weight markers for different types of E-Gel® agarose gels to obtain good resolution.
 
Note:   Supercoiled DNA molecular weight markers may produce a slightly fuzzy pattern when run on E-Gel® agarose gels containing ethidium bromide. Consider using Clear E-Gel® agarose gels and post-staining with ethidium bromide.

 

Product
Markers
Catalog no.
Amount Used
Single comb E-Gel® gels
0.8%
TrackIt 1 Kb Plus DNA Ladder
10488-085
Load 100-250 ng markers in a volume of 20 µl.
 
1 Kb Plus DNA Ladder
10787-018
 
500 bp DNA Ladder
10594-018
 
High DNA Mass Ladder
10496-016
 
E-Gel® High Range DNA Marker
12352-019
1.2%
TrackIt 100 bp DNA Ladder
10488-058
 
TrackIt 1 Kb Plus DNA Ladder
10488-085
 
100 bp DNA Ladder
15628-019
 
1 Kb Plus DNA Ladder
10787-018
 
High DNA Mass Ladder
10496-016
 
E-Gel® High Range DNA Marker
12352-019
2%
TrackIt 25 bp DNA Ladder
10488-022
 
TrackIt 50 bp DNA Ladder
10488-043
 
25 bp DNA Ladder
10597-011
 
50 bp DNA Ladder
10416-014
 
100 bp DNA Ladder
15628-019
 
Low DNA Mass Ladder
10068-013
 
E-Gel® Low Range Quantitative DNA Marker
12373-031
4%
TrackIt 10 bp DNA Ladder
10488-019
 
TrackIt 25 bp DNA Ladder
10488-022
 
TrackIt 50 bp DNA Ladder
10488-043
 
TrackIt 1 Kb Plus DNA Ladder
10488-085
 
10 bp DNA Ladder
10821-014
 
25 bp DNA Ladder
10597-011
 
50 bp DNA Ladder
10416-014

 

Product
Markers
Catalog no.
Amount Used
Double comb E-Gel® gels
0.8%
Low DNA Mass Ladder
10068-013
Load 100-250 ng markers in a volume of 10 µl in marker well.
 
High DNA Mass Ladder
10496-016
 
 
E-Gel® High Range DNA Marker
12352-019
 
2%
TrackIt 1 Kb Plus DNA Ladder
10488-085
 
 
TrackIt 50 bp DNA Ladder
10488-043
 
 
E-Gel® Low Range Quantitative DNA Marker
12373-031
 
Clear E-Gel®
1.2%
TrackIt 100 bp DNA Ladder
10488-058
Load 100-250 ng markers in a volume of 20 µl.
 
TrackIt 1 Kb Plus DNA Ladder
10488-085
 
 
100 bp DNA Ladder
15628-019
 
 
1 Kb Plus DNA Ladder
10787-018
 
 
High DNA Mass Ladder
10496-016
 
 
E-Gel® High Range DNA Marker
12352-019
 

Loading Single Comb and Double Comb Gels

Introductio
After you have prepared your samples, you are ready to proceed with electrophoresis. Instructions are provided below to load and run E-Gel® single comb, double comb gels, and Clear E-Gel® gels using the E-Gel® PowerBase™ v.4.
 
For details on using the E-Gel® agarose gels with the E-Gel® Base. The total run times are:

  • 30–33 minutes for single-comb/Clear E-Gel® gels
  • 15–17 minutes for double-comb gels


Pre-running E-Gel® with SYBR Safe™
You must first pre-run the E-Gel® with SYBR Safe™ agarose gel for 2 minutes with the comb in place before loading your samples to ensure proper resolution of your DNA fragments.
 
Each E-Gel® cassette is supplied individually wrapped and ready for use. To set up and use an E-Gel® with SYBR Safe™ gel, follow the instructions below:

  1. Plug the E-Gel® PowerBase™ v.4 into an electrical outlet using the adapter plug.
  2. Open the package containing the gel and insert the gel (with the comb in place) into the apparatus right edge first. Press firmly at the top and bottom to seat the gel in the base. You should hear a snap when it is in place. The Invitrogen logo should be located at the bottom of the base, close to the positive pole. See the diagram below. A steady, red light will illuminate when the E-Gel® gel is correctly inserted (Ready Mode).
  3. Press and hold either button until the red light turns to a flashing green light. This indicates that the 2-minute pre-run has started.
  4. At the end of the pre-run, current will automatically shut off. The flashing green light will change to a flashing red light and the PowerBase™ will beep rapidly.
  5. Press and release either button to stop the beeping (you will hear only one beep). The light will change from a flashing red light to a steady red light.

 
Method of Loading Samples
The E-Gel® agarose gels are designed for loading samples manually or using a multichannel pipettor. We recommend the following methods of sample loading based on the gel type:
 
Gel Type                                                Method of Loading
 
E-Gel® single comb/Clear E-Gel®         Manual
E-Gel® double comb                             Manual or multichannel pipettor
 
Loading E-Gel®
All wells in the gel must contain sample or water. Avoid introducing bubbles while loading, as bubbles will cause bands to distort.

  1. Remove the comb from the E-Gel® gel using both hands to lift the comb gently by rolling the comb slowly towards you. Be careful to pull the comb straight up from both sides. Do not bend the comb. Remove any excess fluid using a pipette.
  2. Load samples into the wells using the One-Step Loading or Two-Step Loading method.
  3. The One-Step Loading method is routinely used to load E-Gel® single comb and double comb gels. Use the Two-Step Loading method, if the One-Step Loading method produces fuzzy or indistinct bands, or the gel was removed from its plastic pouch for more than 30 minutes.

    • One-Step Loading Method: Load 20 µl of sample into each well(page 38 for sample preparation). Load 20 µl of water into any remaining empty wells.
    • Two-Step Loading Method: First load 10 µl of deionized water into each well (including sample and empty wells). Do not premix with sample. Then load 10 µl of sample containing 10% glycerol into each sample well.

Load 100-250 ng of the appropriate molecular weight markers.

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Running Single Comb and Double Comb Gels

Electrophoresis of E-Gels®

  1. Choose between a 30-minute run for single-comb gels and a 15-minute run for double-comb gels on the E-Gel® PowerBase™ v.4. For the 30-minute run, press and release the 30-min button to start the 30-minute electrophoresis run. The light will change to a steady green light.
    For the 15-minute run, press and release the 15-min button. A steady blue light appears to indicate the beginning of the 15-minute run.
    Note:   The actual running time of the E-Gel® gel may vary between 15-17 minutes for double-comb gels and 30-33 minutes for single-comb gels.
  2. Current through the E-Gel® gel automatically shuts off at the end of each run. The E-Gel® PowerBase™ v.4 signals the end of the run with a flashing red light and rapid beeping.
  3. Press and release either button to stop the beeping. The light will turn to a steady red light.
  4. At the end of the run, remove the gel cassette from the power unit and analyze your results using a UV transilluminator. For Clear E-Gels®, open the gel cassette as described below and proceed to staining the gel (see below).

E-Gel® agarose gels can only be used once. Do not re-use them.
 
Staining Clear E-Gel®
Clear E-Gel® gels are suitable for post-staining DNA bands using a wide variety of DNA stains including SYBR® Green I or II, or SYBR ® Gold.
 
To open the Clear E-Gel® cassette for staining, see next page. General guidelines are given below for post-staining DNA on Clear E-Gel® gels using a stain of choice. For details, follow the manufacturer’s recommendations.

  • For optimal staining sensitivity, make sure the pH of the staining solution is between pH 7.0-8.0.
  • Use TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) or TAE (40 mM Tris-acetate, 1 mM EDTA, pH 8) buffer to dilute the stain. 
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Opening an E-Gel® Single Comb and Double Comb Cassette

Introduction
The E-Gel® Opener is an easy-to-use device specifically designed to open any E-Gel® single comb or double comb gels for excision of DNA fragments or for blotting.
 
Do not use the E-Gel® Opener to open the E-Gel® 48 or 96 cassettes. The E-Gel® 48 or 96 cassette cannot be opened.
 
Description of Opener
The E-Gel® Opener consists of an anodized aluminum platform housing two recessed steel blades, one which is stationary and one which is movable. The blades are brought into contact with the E-Gel® cassette by turning the large knob clockwise.

  • Before using the E-Gel® Opener for the first time, we recommend that you practice opening a few used E-Gels® to familiarize yourself with the process. Practice on E-Gels® that will not be used further for preparative purposes.
  • Electrophoresis must be complete before opening the E-Gel®. We recommend that you place the E-Gel® on the transilluminator and photograph the gel before proceeding further. If you plan to isolate DNA from the E-Gel®, we recommend that you open the gel and excise the gel fragment immediately after electrophoresis as bands will diffuse within 20 minutes. If you plan to blot the gel, keep your blotting apparatus ready before opening the gel.

The blades on the E-Gel® Opener are extremely sharp. Do not insert your fingers into the area housing the blades! Pick up the E-Gel® Opener by holding the large knob only (see Figure 1 above). Exercise caution when handling and cleaning the E-Gel ® Opener. Dispose of blades in a needle disposal container or a Sharps disposal box.
 
Procedure
The following section provides instructions to open an E-Gel® cassette. Before beginning, you should wear safety goggles and gloves.

  1. Place the E-Gel® Opener on a flat surface, with the knob extending off the edge of the laboratory bench and facing the user. Set the E-Gel® Opener to its widest open position by turning the knob counterclockwise.
  2. Insert the E-Gel® into the E-Gel® Opener so that two opposing sides of the gel cassette are aligned with the blades. Position the E-Gel® such that the two sides fit into the grooves housing the blades.
  3. Turn the knob steadily clockwise to bring the blades in contact with the E-Gel® cassette. As the knob is tightened, you will hear a series of pops. Continue to turn the knob until the resistance increases. Stop turning the knob as soon as the E-Gel® cassette begins to lift off the surface of the platform. Two sides of the E-Gel ®will now be unsealed. Note: Once you observe the E-Gel® cassette begins to lift off the surface of the platform, do not continue to tighten the knob as you will damage the E-Gel®.
  4. Unscrew the knob and remove the E-Gel®. The E-Gel® cassette fits snugly in the recessed groove, and you may have to carefully work the cassette from the housing. Turn the E-Gel® 90° and re-insert the gel cassette into the Opener so that the two remaining sealed sides can be opened.
  5. Repeat Step 2 to open the remaining two sides of the E-Gel®. Stop turning the knob when you see the top of the E-Gel® cassette begins to lift off the gel.
  6. Unscrew the knob and carefully remove the E-Gel® cassette. The 4 sides of the cassette should be unsealed. If not, repeat Steps 2-5 as necessary. Remove the E-Gel® and set the opened cassette on your bench.
  7. If you plan to blot the gel, do not pick up the gel from the cassette. Lift off the top of the gel cassette. Place the blotting membrane on the gel and pick up the cassette with the gel and membrane. Flip the gel and membrane out of the cassette onto your gloved hand and then flip the gel and the membrane directly onto your wet blotting paper.   If you plan to purify DNA from the gel, lift off the top of the gel cassette and excise the gel fragment. Transfer the gel slice to a microcentrifuge tube.
  8. After using the opened E-Gel®, discard it as hazardous waste.

 
Cleaning and Storage
After use, clean the E-Gel® Opener with mild detergent and water to remove excess agarose, ethidium bromide, and plastic from the platform. Use a squirt bottle and wipe the platform dry with a clean tissue. Do not insert your fingers into the area housing the blades, and do not immerse the E-Gel® Opener in water as the blades may rust. Store the E-Gel® Opener at room temperature.

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Troubleshooting

Problem Cause Solution
No currentCopper contacts in the base are damaged due to improper useMake sure the copper contacts in the base are intact.
 Expired or defective gel cassetteUse fresh gel cassette. Use properly stored gels before the specified expiration date. 
 E-Gel® cassette is not inserted properly into a baseRemove cassette and reinsert; a steady red light illuminates on the base when the cassette is correctly inserted and power is on.
 Incorrect adapter usedUse only UL Listed Class 2 Direct Plug-in Adapter included with the E-Gel® PowerBase™.
Poor resolution or smearing of bandsSample is overloadedLoad 20-100 ng of sample DNA per band. Less DNA is required since E-Gel ® agarose gels are thinner.
 High salt concentrationDilute your high-salt samples as described.
 Very low volume of sample loaded or sample was not loaded properlyAvoid introducing bubbles while loading the samples. Bubbles will cause band distortion.

Load the recommended sample volume based on the gel type and loading method.

For proper band separation, we recommend keeping sample volumes uniform. Load deionized water or TE into any empty wells.
 Gel was not electrophoresed immediately after sample loadingFor best results, run the gel within 15 minutes of sample loading.

If you cannot run the gel immediately after sample loading, use the Two-Step Loading method.
 Expired gel usedUse properly stored gels before the expiration date.
 Longer electrophoresis run time or high current during the runLonger run times cause an increase in the current, resulting in poor band migration or a melted gel. Do not run the gel longer than recommended time for each gel type.
Sample leaking from the wellsSample is overloadedLoad the recommended sample volume per well.
 Wells damaged during comb removalRemove the comb gently without damaging the wells.
Failure Mode indicated by a steady red light and continuous rapid beepingDefective cassetteDisconnect the base and replace gel cassette with a fresh gel cassette. Press and release the power button to return to Ready Mode
 Cold cassette or improper operating conditions.Use a cassette stored at room temperature. Avoid storing gel cassettes at 4°C. Use E-Gel ® PowerBase™ and E-Gel ® Base at room temperature (20-25°C).
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