Stain

Type/mode of action

Supplier

Sensitivity

Cost (ex VAT)

Comments

Azure A

Thiazin dye.

Binds ionically to DNA and RNA.

Numerous suppliers e.g., Sigma-Aldrich

Also supplied by the NCBE as a solution.

Slightly better than methylene blue, but with far less background staining.

Typical price of powder: GBP 35 for 25 g.

From the NCBE, 50 ml of a 2 x concentrate costs GBP 7.20

Stains DNA and RNA.

About a third of the price of the similar Azure B!

NCBE suggests using 0.04% (w/v) in 20% ethanol to stain the gel after running it.

Destaining is not required.

Bleaches in stong sunlight, although gels can be kept for several months without fading in the dark.

BlueView (TM)

Proprietary product, provided as a powder for dissolution in either TBE and TAE buffers, which are also included as 10x concentrates.

Sigma-Aldrich

Cat No. T8935 (TBE buffer)
Cat No. T9060 (TAE buffer)

Manufacturers claim that it is able to detect <250 ng of DNA, which is not much of a claim! We could detect 40 ng of DNA.

GBP 32 for 1 litre of 10x solution.

Used in both the gel and running buffers.

Should be stored in a glass bottle as plastic lifts away the stain.

Does not detect RNA.

This product is probably Nile blue sulphate.

CarolinaBLU (TM)

Proprietary product, supplied in two bottles at two

Carolina Biological.

Cat No. WW-21-7300

Similar to that of methylene blue, but with far less background staining.

USD 6.90 for 30 ml of the gel and running buffer concentrate, plus 250 ml of the 1x gel-staining solution.

About 120 µl of the concentrate is required for each 30 ml of agarose.

The suppliers recommend using a low concentration of this dye in the gel and buffer during running (which shows the bands very faintly), then post-electrophoresis staining with a greater concentration of dye.

Methylene blue (trihydrate)

Thiazin dye.

Binds ionically to DNA and RNA.

Numerous suppliers e.g., Sigma-Aldrich

Not very sensitive. With luck, about 40 ng of DNA is the smallest amount that can be detected after destaining, although at least 80-100 ng is usually required to produce a clear band.

Typical price of powder: GBP 15 for 25 g.

0.025% (w/v) in water is usually recommended.

Can be used to detect both DNA and RNA.

Requires prolonged destaining (overnight) with a small volume of warm tap water to remove background. Excessive destaining can wash out the bands, however.

Bleaches in sunlight, and fades through oxidation.

Nile blue sulphate

Mode of action uncertain, but probably intercalates within DNA double helix.

Numerous suppliers e.g., Sigma-Aldrich

Allows about 40 ng of DNA to be seen while running gels. If these are allowed to dry, it is claimed that a mere 4 ng can be detected, although we have not seen this ourselves.

Typical price of powder: GBP 40 for 25 g.

Also known as Nile blue A. Used in gel and running buffer.

1-3 µg per ml of buffer is suggested. Concentrations of > 3 µg per ml severely reduce migration of DNA and hence the resolution of the gel.

Only stains DNA.

Thought to be non-toxic.

Brilliant cresyl blue

Thiazin dye.

Binds ionically to DNA and RNA.

Numerous suppliers e.g., Sigma-Aldrich

About 40 ng in our experience. See 'Comments'

Typical price of powder: GBP 40 for 25 g.

Use 0.04% (w/v) in 20% ethanol to stain the gel after running it.

 

Santillán Torres and Ponce-Noyoia claim that 25 ng of DNA can be detected with this stain. However, we were disappointed by a lower-than-expected sensitivity plus heavy background staining.

 

Oddly, a 40-year-old sample of the stain gave good results, suggesting that their results were due to an oxidation product of brilliant cresyl blue.

Crystal violet

Intercalates within DNA double helix.

Numerous suppliers e.g., Sigma-Aldrich

>=100 ng.

Typical price: GBP 7 for 25 g.

A mutagen.

Not worth using unless you have a special reason for doing so. Less sensitive than several safer stains.