Electrophoresis Stains

Errday I'm stainin'

Option 0: Ethidium Bromide

• Cost of product: essentially nothing
• Cost of disposal: £125 per 60 litres. Therefore minimum cost with 50ml gels is 125 / (60000 / 50) = £0.104 a gel
• Cost, total: 10p per gel, perhaps more realistically 15p-20p per per gel (since we'll want to put other stuff in the bins).

Option 1: SafeWhite

• Info: http://nbsbio.co.uk/product.asp?pID=6241&cID=71
• Cost of product: £40 for 1ml. 2ul per reaction, therefore 40 / (1000 / 2) = £0.08 a reaction
• Cost, total: 8p per reaction, assuming 4 reactions per gel = 32p per gel.
• Other considerations: must be refrigerated (4C).

Option 2: SafeWhite in bulk

• Info: http://nbsbio.co.uk/product.asp?pID=12207&cID=71
• Cost of product: £175 for 5ml. 2ul per reaction, therefore 175 / (5000 / 2) = £0.07 a sample
• Cost, total: 7p per reaction, assuming 4 reactions per gel = 28p per gel.
• Other considerations: As above.

Option 3: SYBR Green

• Info: http://www.sigmaaldrich.com/catalog/product/sial/s9430?lang=en&region=GB
• Cost of product: £242 for 0.5ml, produces 5 litres of staining solution. Assume 100ml of solution per gel = 50 gels = £4.84 a gel.
• Cost, total: £4.84 per gel.
• Other considerations: must be frozen (-20C); must be used as a post-stain (20-40 minutes after electrophoresis has finished). Apparently just as hazardous as EtBr: datasheet claims that staining solution can be poured through activated charcoal which "may then be disposed of as hazardous waste".

Option 4: SYBR Green, re-use of staining solution

• Info: As above.
• Cost of product: As above, but staining solution can be refrigerated and re-used "three to four times". This reduces the cost by 4.
• Cost, total: £1.20 per gel.
• Other considerations: Re-using the staining solution seems like a pain. Even with re-use, this is expensive stuff. We would have to re-use each solution 40 times in order to get in the same league as the other stains (and that doesn't take disposal into account).

Option 5: SYBR Green as part of a readymix

• Info: http://www.sigmaaldrich.com/catalog/product/sigma/s4438?lang=en&region=GB
• Cost of product: £96.60 for 100 reactions, so £0.96 per gel, BUT Taq readymix itself costs around £100 for 100 reactions, so it is essentially free.
• Cost, total: Free -- unless the small amount of SYBR Green present in the readymix qualifies the whole gel as hazardous waste (seems unlikely)
• Other considerations: can't use it to visualise ladders.

Option 6: GelGreen or GelRed

• Info: http://www.bioscience.co.uk/product~88488 (for example)
• GelGreen and GelRed cost roughly the same amount and have the same protocols.
• Cost of product: £81 for 0.5ml, 5ul per 50ml gel, so 81 / (500 / 5) = £0.81 per gel
• Cost, total: 81p per gel.

Option 7: Methylene blue

• Info: About £4.95 for 100ml. See eg http://cgi.ebay.com.au/ws/eBayISAPI.dll?ViewItem&item=220367085167&ssPageName=ADME:L:OU:AU:1123#ht_1288wt_1085
• Cost of product: 1ml in 100ml of water for post-staining. So £0.0495 per gel. Or, 0.1ml in 100ml of water, for £0.00495 per gel
• Cost, total: 5p per gel, or 0.5p per gel.
• Other considerations: About 100 times less sensitive than EtBr (100ng DNA at most sensitive, some reports put it at no less than 500ng => won't be able to see the ladder). Post-staining is annoying.

Option 8: SYBR Safe

• Info: https://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/DNA-RNA-Purification-Analysis/Nucleic-Acid-Gel-Electrophoresis/DNA-Stains/SYBR-Safe.html
• Cost of product: £44.50 for 400ul, 5ul per gel, so £0.55 per gel
• Total cost: 55p per gel.

Discussion

Here is a Web page with more information and roughly similar costings to mine: http://bitesizebio.com/articles/ethidium-bromide-the-alternatives/

Three comments on all this:

1. Even though it's really cheap, I don't like SYBR Green in readymix. The problem is:
   1. I'm all about reducing the number of variables per reaction.
   2. We can't use SYBR Green + Taq to visualise ladders directly
   3. Because we won't be running a ladder mixed with the same dye (at best, we'd mix the ladder with SYBR green after PCR), we won't know if we screwed up the visualisation or if the reaction didn't work (this problem is what led us to ethidium bromide in the first place).
2. Even with disposal costs, ethidium bromide isn't that bad. It's less expensive than SafeWhite (for 2 or more reactions per gel), but, to be fair, that's still not a significant difference (10p or so). If we handle EtBr properly and dispose of it correctly, we should be fine.
3. For £40, we may as well check out SafeWhite. It's not particularly cheap, and we will still have to retain LabWaste for waste disposal, but we won't need them to dispose of gels, so we won't need them to come as frequently.