GeneGelRed^TM Nucleic Acid Gel Stain

GeneGelRed is the best nucleic acid gel stains by combining sensitivity, safety and stability. It represents a new generation of fluorescent nucleic acid dye designed to replace the highly toxic ethidium bromide (EB) for staining dsDNA, ssDNA or RNA in agarose gels or polyacrylamide gels. It is far more sensitive than EB without requiring a destaining step.Since GeneGelRed and EB have virtually the same spectra, you can directly replace EB with GeneGelRed without changing the instrument setting used for EtBr.

GeneGelRed is highly sensitive either as precast gel stains or post gel stains. It can be used to stain dsDNA, ssDNA or RNA in agarose gels via either precast or post gel staining. To stain dsDNA, ssDNA or RNA in polyacrylamide gels, post gel staining is required.

GeneGelRed is compatible with downstream DNA manipulations such as restriction digest, sequencing, and cloning.

Nucleic acid dyes are inherently hazardous because of their potential to cause DNA mutation.

GeneGelRed is unable to cross cell membranes, thus denying the opportunity for them to interact with intracellular DNA. Extensive tests, including those by third party labs have confirmed that GeneGelRed is noncytotoxic, nonmutagenic and nonhazardous for disposal.

1. Safer than EB: nonmutagenic and noncytotoxic proved by Ames and other tests.

2. Easy disposal: Passed environmental safety tests for direct disposal down the drain or in regular trash.

3. Ultra-sensitive: Much more sensitive than EtBr and other EtBr alternatives.

4. Extremely stable: Available in water, stable at room temperature for long-term storage and microwavable.

5. Simple to use: Very simple procedures for precast or post-electrophoresis gel staining.

6. Perfect Compatibility with a standard UV transilluminator ore a Gel Reader: Replaces EtBr with no optical setting change.

7. Flexible for different downstream applications: Gel purification, restriction digest, sequencing and cloning.

1. For more information please refer to GeneGelRed^TM Nucleic Acid Gel Stain User Manual

1. Why do you offer GeneGelRed in DMSO or water?

Answer

The water formulation is a newer and improved product compared to the stock in DMSO. We recommend using dyes in water to avoid the potential hazards of handling DMSO, which can be absorbed through the skin. We continue to offer dyes in DMSO because some users do not wish to alter their established laboratory protocols. Based on internal testing, both formulations perform similarly.

2. What instruments can be used to detect GeneGelRed?

Answer

GeneGelRed is compatible with a standard UV transilluminator (302 or 312 nm).

3. What emission filters are suitable for use with GeneGelRed?

Answer

Use the ethidium bromide filter for GeneGelRed; use a SYBR^® Green or yellow filter for GelGreensup^®. Alternatively, a long-pass yellow filter can be used with both GeneGelRed. Please review the emission spectra for GeneGelRed for more specific wavelengths.

4. How safe is GeneGelRed?

Answer

In AMES and related tests, GeneGelRed^® was shown to be much safer alternatives to EtBr and SYBR dyes. Nevertheless, please exercise safe laboratory practices when using these reagents.

5. How should I dispose of GeneGelRed?

Answer

GeneGelRed passed the EPA regulated Title 22 test. Some facilities have approved the disposal of GeneGelRed directly down the drain. However, because regulations vary, please contact your safety office for local disposal guidelines. Please review the GeneGelRed safety report for more detailed information.

6. How do I use GeneGelRed?

Answer

GeneGelRed^® can be added to agarose during gel casting at a final concentration of 1X, or they can be used for post-electrophoresis gel staining at a final concentration of 3X in water.

7. Why am I seeing smeared or smiling DNA band(s) or discrepant DNA migration?

Answer

Many customers use GeneGelRed precast gels for convenience. However, because GeneGelRed is high affinity dyes designed to be larger dyes to improve their safety, they can affect the migration of DNA in precast gels. Some samples, such as restriction digested DNA may migrate abnormally in GeneGelRed precast gels.

Tip #1: Load less DNA

Smearing and smiling in GeneGelRed precast gels most often caused by overloading of DNA. If you see band migration shifts or smearing and smiling, try reducing the amount of DNA loaded. The recommended loading amount for ladders and samples of known concentration is 50-200 ng/lane. For samples of unknown concentration, try loading one half or one third of the usual amount of DNA. This usually solves band migration problems.

Tip #2: Try the post-staining protocol

To avoid any interference the dye may have on DNA migration, we recommend using the post-staining protocol. If your application requires loading more than the recommended amount of DNA, use the post-staining protocol. While we recommend post-staining gels for 30 minutes, you may be able see bands in as little as five minutes, depending on how much DNA is present. Post-staining solutions can be reused.

8. Why do I see weak fluorescence, decreased dye performance over time, or a film of dye remaining on the gel after post-staining?

Answer

There are a few possibilities: The dye may have precipitated out of solution. Heat the GeneGelRed solution to 45-50°C for two minutes and vortex to dissolve. Store dye at room temperature to avoid precipitation. If you are seeing high background staining of the gel, the agarose that you are using may be of low quality. Contaminants in the agarose may bind to the dye, resulting in increased background.

9. Can I make GeneGelRed gels ahead of time and store them for later use?

Answer

Yes. You can store precast GeneGelRed gels for up to a week. We recommend storing gels at room temperature in the dark. Do not store the gels at 4°C, because this will lead to dye precipitation and poor performance.

10. How much GeneGelRed do I need to use? How many gels can I run with a vial of GeneGelRed?

Answer

A 0.5 mL vial of GeneGelRed can be used to prepare 100 minigels (50 mL each) using the precast protocol, or for post-electrophoresis staining of 33 minigels in 50 mL staining solution per gel. Post-staining solution also can be re-used for staining 2 or more gels.

11. What is the stability of GeneGelRed in molten agarose?

Answer

We do not recommend storing GeneGelRed in molten agarose for more than a few days.

12. Do GeneGelRed need to be used in the dark?

Answer

GeneGelRed is a stable dye. You can use it in room light. However, we recommend storage of the dye in the dark between uses.

13. Can GeneGelRed post-staining solution be reused?

Answer

Yes. However, if the sensitivity decreases, use a fresh solution of the dye.

14. Does post-staining require a de-staining step?

Answer

No, but de-staining with water can be performed if background is high.

15. What DNA ladders and loading buffers can I use with GeneGelRed?

Answer

We have tested a variety of DNA ladders from different suppliers with GeneGelRed with good results. Similarly, any common DNA loading buffers can be used. Band migration problems or smearing or smiling DNA bands are most commonly caused by overloading of ladder. If you are experiencing band migration problems with your ladder, please try reducing the amount of ladder you load. We recommend loading 50-200 ng ladder per lane for GeneGelRed precast gels.

16. Can I reuse a GeneGelRed precast gel after running samples?

Answer

No. We do not recommend reusing GeneGelRed gels after electrophoresis because the staining intensity can be decreased with sequential electrophoresis.

17. Can I re-melt a GeneGelRed gel and cast again?

Answer

Yes, but it may be necessary to add some more dye to the re-melted gel for the best signal.

18. Is GeneGelRed compatible with downstream applications such as cloning, ligation and sequencing?

Answer

Yes. We recommend Qiagen or Zymoclean™ gel extraction kits or phenol-chloroform extraction to remove the dye from DNA.

19. Can I use GeneGelRed to stain ssDNA or RNA?

Answer

GeneGelRed can be used to stain both ssDNA and RNA. Titration assays using a fluorescence microplate reader showed that the fluorescence signal of GeneGelRed bound to ssDNA and RNA is about half that of GeneGelRed bound to dsDNA.

20. What is the lower detection limit of GeneGelRed?

Answer

GeneGelRed is ultra-sensitive dyes. Some users have reported being able to detect bands containing less than 0.1 ng DNA. However, the sensitivity of the staining will depend on the instrument capability and exposure settings.

21. What is the binding mechanism of GeneGelRed?

Answer

GeneGelRed binds DNA exclusively by intercalation (Characterizing the interaction between DNA and GelRed fluorescent stain.).

22. In which direction does GeneGelRed migrate?

Answer

GeneGelRed do not migrate through the gel as easily as ethidium bromide. It is not necessary to add additional dye to the running buffer, and the gel will be stained more homogenously than a gel stained with ethidium bromide.

23. Can GeneGelRed be used for Southern or Northern blotting?

Answer

GeneGelRed has been validated for Southern blotting. We recommend using the post-staining protocol for blotting applications.

24. Can GeneGelRed be used in formaldehyde based RNA gels?

Answer

Yes, customers have reported using GeneGelRed in glyoxal and formaldehyde agarose gels for precast staining of RNA.

25. Can I use GeneGelRed in polyacrylamide, DGGE, EMSA or PFGE (pulse-field) gels?

Answer

Yes. Please use the post-staining procedure for DGGE and EMSA gels. For PFGE gels, the pre-cast or post-staining protocol may be used.

26. Can GeneGelRed be used for Comet Assay?

Answer

Yes, GeneGelRed can be used for Comet assay.

27. Is GeneGelRed compatible with alkaline gel running buffer (30mM NaOH, 1mM EDTA)?

Answer

Yes, GeneGelRed is compatible with alkaline running buffer.

28. Can GeneGelRed be used for cesium chloride gradient purification of DNA?

Answer

Customers have reported using GeneGelRed in cesium gradients. To extract GeneGelRed from DNA after cesium banding, we recommend adding SDS to a final concentration of 0.1% before butanol extraction. Alternatively, chloroform can be used instead of butanol for extraction.

29. What purification protocols are recommended to remove GeneGelRed after staining?

Answer

Customers report good results using ZymoClean™ Gel DNA Recovery Kit from Zymo Research, GenElute™ Agarose Spin Column from Sigma, PureLink® Quick Gel Extraction kit from Life Technologies, illustra GFX PCR DNA and Gel Band Purification kit from GE Healthcare, High Pure PCR Product Purification Kit from Roche Applied Sciences, and GenJET gel extraction kit from Thermo Scientific.

30. Can I use GeneGelRed to detect ssDNA in a precast gel?

Answer

Yes, see Ana. Biochem. doi>>.

31. Can GeneGelRed be used in Loop-mediated Isothermal Amplification Assay?

Answer

Yes, see Virol J. 2012, 9, 110.

32. Can GeneGelRed be used to stain DNA in acrylamide gels?

Answer

Yes, use the post-staining protocol for polyacrylamide gels. For polyacrylamide gels containing 3.5-10% acrylamide, typical staining time is 30 minutes to 1 hour with gels of higher acrylamide content requiring longer staining time.,

33. My product was accidentally left out at room temperature or exposed to light. Is it ruined?

Answer

Most of our products are stable at room temperature for many days, so in all likelihood the product will still work just fine. To be on the safe side, we recommend performing a small scale positive control experiment to confirm that the product still works for your application before processing a large number of samples or precious samples.