Invitrogen™ E-Gel™ CloneWell™ II Agarose Gels with SYBR Safe, 0.8%

Loading buffer is optional. Samples can be loaded directly into the wells if no buffer is used, or you can dilute them with deionized water or TE buffer. If you want to use a loading buffer, please see the recipes below:

E-Gel agarose gels (including EX)
10 mM Tris-HCl, pH 7.5
1 mM EDTA
0.005% bromophenol blue
0.005% xylene cyanol FF
E-Gel CloneWell II and E-Gel SizeSelect II agarose gels
10 mM Tris-HCl, pH 7.5
1 mM EDTA

Alternatively, you can use 10X BlueJuice Gel Loading Buffer or TrackIt Loading Buffer. Dilute this buffer 50- to 200-fold to obtain optimal results with E-Gel agarose gels.

We offer our E-Editor Software, which can help you align images after a gel run. The E-Editor 2.0 Software is only available for PCs, but the older E-Gel 96 Editor software is still available for the Mac operating system and can align images from E-Gel 96 and E-PAGE 96 agarose gels. However, the original software is not compatible with E-Gel 48 or E-PAGE 48 agarose gels. Please go to www.thermofisher.com and enter "E-Editor software" in the main search to download the E-Editor Software. You can use the E-Gel Imager System for data analysis.

If you do not have enough samples to use all the wells, fill each empty well with the same volume of water as the loaded samples. For E-Gel CloneWell II agarose gels and E-Gel SizeSelect II agarose gels, it is important to add the water according to the respective manual.

Our E-Gel agarose gels can be used for either DNA or RNA separation. RNA separation occurs under non-denaturing or denaturing conditions. Please note, our gels are not QC tested for the presence of RNases. See our suggestions below for running your non-denaturing or denaturing samples:

Non-denaturing conditions
1. Mix RNA sample with 15 µL of RNase-free water.
2. Do not heat. Load the entire sample onto the E-Gel agarose gel.
3. Electrophorese for 30 min.

Denaturing conditions
1. Mix 15 µL of RNA loading buffer with 1-5 µL of RNA (1-5 µg).
2. Heat samples at 65 degrees C for 10 min to denature RNA.
3. Place samples on ice immediately after heating.
4. Load entire sample onto E-Gel agarose gel.
5. Electrophorese for 30 min.

Note:
- The only denaturing agent that is compatible with the E-Gel system is formamide, 50-95%. Heating the sample for 5 min at 65 degrees C should be sufficient for denaturing. Using other denaturing agents like glyoxal, formaldehyde, or urea will result in very poor separation and band morphology on E-Gel agarose gels.
- Additionally, we do not recommend running samples with RNA loading buffer on the same gel as samples loaded with water.
- E-Gel EX Double Comb agarose gels and E-Gel Double Comb agarose gels with SYBR Safe stain have not been tested for use in RNA applications.

We recommend using the E-Gel Opener (Cat. No. G530001) for the SYBR and ethidium bromide E-Gel agarose gels. The E-Gel EX agarose gels, E-Gel SizeSelect agarose gels, and E-Gel GO! agarose gels can be opened with the Gel Knife (Cat. No. EI9010). We do not recommend opening the E-Gel 48 agarose gels or the E-Gel 96 agarose gels.

To create a bufferless system, each E-Gel cassette contains two unique ion exchange matrices that lie between the running gel and the electrodes. The ion exchange matrices provide a buffer-ion reservoir that supplies a continuous flow of Tris, acetate, and dye ions throughout the gel. This patented technology results in a sustained electric field with enhanced buffering capacity. E-Gel gels thus eliminate the need for you to prepare and dispose of liquid buffer, thus saving time and waste.

The E-Gel agarose gel system is a precast bufferless TAE system that uses ion exchange matrices. The gels themselves are enclosed within a semi-UV-transparent cassette. This patented technology results in a sustained electric field with enhanced buffering capacity. E-Gel gels thus eliminate the need for you to prepare and dispose of liquid buffer, thus saving time and waste.

Some institutions and municipalities have approved the disposal of SYBR Safe DNA Gel Stain directly into their waste water systems and regular trash receptacles. However, disposal regulations vary; please contact your safety office or local municipality for disposal guidelines. For more information on environmental testing and safety standards for SYBR Safe stain, please visit our main SYBR Safe informational page, which you can find by searching "SYBR Safe DNA Gel Stain" from the Thermo Fisher Scientific website home page.

Pre-run is no longer necessary for any of our E-Gel agarose gels.

E-Gel agarose gels are routinely used in-house in R&D and manufacturing for RNA analysis with excellent results. However, the gels are not guaranteed to be “RNAse-free”. The manufacturing process is designed to avoid contamination of any type, but not RNAses specifically.

If you do want to try it, any loading buffer that would be used for non-denaturing RNA electrophoresis should be fine for E-Gel agarose gels. Depending on your application, these gels may or may not be suitable for use.

Do not run E-Gel agarose gels longer than 40 min for the single comb gels or longer than 20 min for the double comb gels as longer run times will cause ions to get depleted and will damage the gel. Do not run E-Gel 48 agarose gels longer than 30 min or E-Gel 96 agarose gels longer than 20 min.

All E-Gel gels are labeled with expiration dates.

Potential problems include:
- Loading too much DNA. Do not load more than the recommended amount.

- Samples with a high salt concentration. Samples containing > 50 mM NaCl, 100 mM KCl, 10 mM acetate ions, or 10 mM EDTA will cause loss of resolution.

- Samples may have been diluted in TAE instead of TE or water.

- Samples may have been pre-run; pre-running is not recommended for any of our E-Gel agarose gels.

- Sample was not properly loaded or had a very low volume of sample loaded. Load the recommended sample volume based on the gel type and loading method. For proper band separation, we recommend keeping sample volumes uniform.

- Bubbles may have been introduced while loading the samples. Bubbles will cause band distortion. Load deionized water or TE into any empty wells, and avoid introducing bubbles.

- A longer electrophoresis run time was used. Do not run the gel longer than the recommended time for each gel type. Longer run times cause an increase in the current, resulting in poor band migration or a melted gel. We recommend that you run single comb gels for 25-30 min (double comb gels 15-20 min) for straighter patterns. Do not run single comb gels longer than 40 minutes (20 minutes for double comb), or the gel will be damaged and resolution will be poor.

- Voltage or current too high. This should not be an issue with the E-Gel PowerBase power supply, which is pre-set with the proper conditions. However, researchers using the old E-Gel Base (the one that plugged into a separate power supply) should ensure that they run the gel at 60 to 70 volts (constant voltage) or 40-50 mA (constant current). Do not allow the current to exceed 60 mA.

- For E-Gel 96 Agarose Gels being run on an E-Base device, be sure you are running on the “EG” program rather than the “EP” program designed for E-PAGE gels.

- The gel was not electrophoresed immediately after sample loading (for best results, run gel within 1 min of loading).

- The gel may have been used beyond its expiration date. Check the expiration date.

The agarose used in the 0.8%, 1.2% and 2% E-Gel agarose gels is molecular biology grade, with a normal melting point and less than 0.25% ash content. For the 4% E-Gel agarose gels, we use a special high-resolution agarose.

The E-Gel agarose gel system uses TAE buffer.

The dimensions of a single comb 12 well E-Gel agarose gel are as follows: The cassette itself is 8 cm by 10 cm and 0.6 cm thick. The workable gel area is 7.5 cm by 5.8 cm (from well to bottom). The thickness of the gel is estimated to be 0.4 cm. There are 12 wells and each well is 4 mm wide. The space between the wells is 1 mm.

We do not recommend using the E-Gel Power Snap Electrophoresis Device to image pour-your-own gels.

We do not recommend using the E-Gel Power Snap Electrophoresis Device to run pour-your-own gels.

Yes, both the E-Gel GelCapture Acquisition Software and E-Gel GelQuant Express Analysis Software applications are compatible with Windows 10; however, the E-Gel GelQuant Express Analysis Software will require the purchase of an E-Gel Imager Quantitation USB dongle (Cat. No. 4466610):
https://www.thermofisher.com/order/catalog/product/4466610

Please visit the following link (https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/nucleic-acid-gel-electrophoresis/e-gel-electrophoresis-system/e-gel-imager-system/e-gel-software.html) and follow the instructions to download the software.
Note: Please make sure that you download the correct version of the E-Gel GelCapture Software based on the serial number of your instrument.

Each program on the E-Gel Power Snap Electrophoresis Device is optimized to obtain the best possible results. The device does not offer user-adjustable voltage functionality.

To select the DNA ladder that yields the best resolution for your specific E-Gel, please refer to the table on page 45 of the E-Gel Power Snap Electrophoresis System user guide (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017050_egel_powersnapsystem_UG.pdf).

Follow recommended DNA dilutions and leave the gel to cool down on the bench or for a few minutes in the fridge. Please check troubleshooting tips provided in the manual.

No. Standard safety and hazardous waste disposal procedures should be followed when handling E-Gel EX agarose gels.

E-Gel EX agarose gels separate DNA faster, offer enhanced sensitivity, and provide added flexibility. The stain within the E-Gel EX agarose gels is SYBR Gold II which has similar spectral properties but increased sensitivity compared to SYBR Safe DNA Gel Stain. E-Gel EX agarose gels are especially suited for applications where high sensitivity is critical.

No. E-Gel agarose gels have enough buffering capacity for one run only. Performance will be impaired with multiple runs.