Electrophoresis Stains

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Revision as of 16:54, 3 August 2012 by Wzdd (talk | contribs) (Added SYBR Safe)

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

Option 2: SafeWhite in bulk

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

Option 8: SYBR Safe

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 twice as expensive as SafeWhite, but that's only a difference of 7p / gel. If we handle it properly and dispose of it correctly, we should be fine.
  3. For £40, we may as well check out SafeWhite. We can still 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.