Instructions are provided below for using the E-Gel CloneWell pre-cast agarose gels with the E-Gel iBase™ Power System.


Store the gels and iBase at room temperature. Do not allow the temperature to drop below 4°C or rise above 40°C. Do not expose the gels unnecessarily to light.

Kit Contents

Each package of E-Gel CloneWell 0.8 % SYBR Safe pre-cast agarose gels contains 18 E-Gel CloneWell 0.8 % SYBR Safe cassettes.

Product Description

E-Gel CloneWell pre-cast agarose gels provide a novel way to purify DNA bands. E-Gel CloneWell offers the following advantages:

  • No purification necessary for downstream applications such as cloning
  • Contains the safer and environmentally friendly SYBR Safe DNA gel stain, enabling you to view the bands with a blue light transilluminator (such as Invitrogen’s Safe Imager blue light transilluminator, cat. no. S37102), minimizing DNA damage
  • Supplied as precast 0.8 % agarose gel in the familiar E-Gel format, allowing fast, safe, consistent, and high-resolution separation of small and large DNA fragments.
  • Eliminates the need to prepare agarose gels and buffers, and stain gels.

E-Gel CloneWell Features

The E-Gel CloneWell precast agarose gels have the following features:

  • Two rows of wells: the top row to load your sample, the bottom row to retrieve your DNA (collection well).
  • A reference line just above the second row to help you time the exact moment of DNA retrieval
  • A small middle well to load a molecular weight marker

General Guidelines

For best results with E-Gel CloneWell agarose gels, follow these guidelines:

  • Use the recommended DNA amount and sample volume to prepare samples.
  • Keep all sample volumes uniform and load deionized water in empty wells.
  • Load gel within 15 minutes after opening the pouch; run immediately after loading.
  • Use a blue-light transilluminator (such as Safe Imager) to visualize DNA.
  • Monitor the band of interest carefully as it migrates near the second row of wells. It may be difficult to see low amounts of DNA in the well.


Prepare Samples

  • Load 500-700 ng of total sample; load 50-200 ng DNA per band, though 20-400 ng per band is acceptable. Higher amounts require two fractions.
  • Load 20-25 μl total sample volume per well. Lower volumes may result in poor band shape. Excess sample may cause well to well contamination.
  • You may prepare DNA samples in deionized water or preferably in loading buffer; do not use a tracking dye to avoid masking the bands.
  • Dilute high salt samples (certain restriction enzyme and PCR buffers) 2- to 20-fold as described in the E-Gel Technical Guide before loading.

Load E-Gel CloneWell

  1. Plug the E-Gel iBase into an electrical outlet using the adapter plug on the base.

  2. Remove the gel from the package and insert gel (with the comb in place) into the base by sliding the gel into the two electrode connections on the iBase. Make sure that the two electrodes on the right side of the cassette are in contact with the two contacts on the iBase. The Thermo Fisher logo should be located at the bottom of the base. Press firmly at the top and bottom to seat the gel in the base. A steady, red light illuminates on the base if the gel is correctly inserted.

  3. Pre-run the gel (with the comb in place) by selecting the program PRE-RUN 2 min and pressing the Go button on the iBase. The red light changes to a green light indicating the start of a 2-minute pre-run. At the end of the pre-run, the current automatically shuts off.

  4. Remove combs. Load 20-25 μl prepared sample into well 1-8 of the top row.

  5. Load 5-10 μl DNA Molecular Weight Marker into the small middle well of the top row (marked M).

  6. Load 25 μl water into any remaining empty wells in the top row.

  7. Load 25-30 μl water into wells 1-8 of the bottom row, and 5-10 μl water in the middle well of the bottom row.

Estimate Run Time

Refer to the Run Time table to the right to estimate run times of your fragments to the reference line, and from the reference line to the collection well.

Same bands in different wells may migrate differently; DNA fragment sizes, amounts and salt content may also slightly affect the migration rates. The run times indicated are estimates; monitor your gel occasionally during the run.

Band Size
Run Time to
Reference Time
From Ref. Line to
Collection Well
200 bp14-18 minutes1-2 minutes
400 bp15-19 minutes1-2 minutes
800 bp17-21 minutes1-2 minutes
1000 bp19-23 minutes1-2 minutes
2000 bp21-25 minutes1.5-2.5 minutes
3000 bp24-28 minutes1.5-2.5 minutes
4000 bp28-32 minutes2-3 minutes
6000 bp32-36 minutes2-3 minutes

Run E-Gel CloneWell

  1. Place the E-Gel iBase Power System over a blue light transilluminator. Use the orange cover or orange goggles to view the bands and to avoid overexposure of your eyes to blue light.

  2. Select the Run CloneWell program and enter the estimated Run time to Reference Line as listed in the above table (refer to the iBase Power System manual for instructions). Press the Go button on the iBase to run your band of interest to reach the printed reference line just above the bottom row of wells. The red light turns to a green light indicating the start of the run.

  3. Monitor your gel occasionally during the run. If your band of interest reaches the reference line, press the Go button to stop the run. Continue with Step 5.

  4. At the end of the run, the iBase stops after the entered run time and displays a flashing red light and beeps rapidly. If your band did not reach the reference line, run the gel for a few more minutes until the band reaches the line.

  5. Once the band reaches the reference line, refill the bottom row again with sterile water until the well is full (some pre-filled water is lost during the run).

  6. Press the Go button to run the gel for the time listed in the above table until the band enters the collection well. During this period, monitor the run over a Safe Imager™. At the end of this run, you may see the band of your interest migrating into the well. We recommend monitoring the run in a darkened room for optimal results. Small DNA amounts and low molecular weight bands may be difficult to view inside the well.

  7. Collect DNA from the well using a pipette. Be careful not to perforate the agarose bottom of the collection well. Some residual DNA will remain visible underneath the well due to migration in the garose bottom. Proceed to your application using collected DNA without any further purification. If your band of interest overruns the collection well and re-enters the gel, use the REVERSE E-Gel program of the iBase Power System to run the band backwards into the collection well (see the iBase Power System manual for instructions).

  8. You may continue to collect more DNA bands from the same well (be sure to fill more water into the second row) or from other wells.


For photographing gels, use the SYBR Safe photographic filter (S37100) or SYPRO™ photographic filter (S6656). Photograph E-Gel CloneWell using Polaroid™ 667 black-and-white print film, or image using a CCD camera or a laser-based scanner. Refer to E-Gel Technical Guide to determine the optimal filter sets to use, or contact the instrument manufacturer for advice.


No currentCassette improperly inserted or is defectiveRemove the gel cassette and re-insert the cassette correctly, or try using a fresh cassette.
Poor resolution or smearing of bandsSample overloadedDo not load more than 200 ng of DNA per band.
 High salt samplesDilute your samples as described in the E-Gel Technical Guide.
 Aberrant pre-run stepBe sure to pre-run the gel but do not exceed 2 minutes.
 Sample not loaded properly or low sample volume loadedDo not introduce bubbles while loading samples. For proper resolution, keep all sample volumes uniform and load water into empty wells. Use Two-Step Loading (see E-Gel Technical Guide for details).
Melted gelIncreased current due to longer run timesDo not run the gel longer than 40 minutes.
Sample leaking from wellsWells damaged during comb removalBe sure to remove the comb gently without damaging the wells.
 Sample is overloadedLoad the recommended sample volume per well. Use Two-Step Loading (see E-Gel Technical Guide for details).
High background, suboptimal, or no imageNo filters or wrong filter setRefer to E-Gel Technical Guide to determine the optimal filter sets to use, or contact the instrument manufacturer for advice.
 Photographic settings not optimalOptimize settings of your system for E-Gel CloneWell empirically. You may need to increase the exposure time or gain setting.
Stripes visible on imageNo IR coating on camera lense.Use IR blocking filter or emission filter with IR coating.
Band of interest below collection wellRun time too long.Use the REVERSE program of the iBase™ Power System to run the band backwards into the collection well (see the iBase™ Power System manual)
Low volume for collectionMissed refilling waterRefill the second row with sterile water until the well is full prior to running your band of interest into the collection well.
Low yieldBand is too bigCollect DNA from the well in two or more fractions. Be sure to load the recommended DNA amount.


SYBR Safe DNA gel stain shows no or very low mutagenic activity when tested by an independent, licensed testing laboratory, and this stain is not classified as hazardous waste under U.S. Federal regulations. Many institutions and have approved safe disposal of SYBR Safe into their waste water systems. As disposal regulations vary, contact your safety office or local municipality for appropriate SYBR Safe disposal in your community.

251044W        11-Nov-2008

For Research Use Only. Not for use in diagnostic procedures.