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Electrophoresis Stains: Difference between revisions

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Electrophoresis Stains (view source)

Revision as of 18:19, 3 August 2012

342 bytes added ,  3 August 2012
Reorganised into viable / nonviable
(Fixed SYBR Green in Taq discussion (it's a rt-pcr stain))
(Reorganised into viable / nonviable)
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= Errday I'm stainin' =
= Errday I'm stainin' =


==Option 0: Ethidium Bromide==
== Viable choices ==
 
===Ethidium Bromide===
* Cost of product: essentially nothing
* 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 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).
* Cost, total: 10p per gel, perhaps more realistically 15p-20p per per gel (since we'll want to put other stuff in the bins).
* Other considerations: possible mutagen, carcinogen, and teratogen.
* Why it's viable: We know it works. It's quite cheap. We have to organise professional hazardous waste disposal anyway.


== Option 1: SafeWhite ==
=== SafeWhite ===
* Info: http://nbsbio.co.uk/product.asp?pID=6241&cID=71
* 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 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.
* Cost, total: 8p per reaction, assuming 4 reactions per gel = 32p per gel.
* Other considerations: must be refrigerated (4C).  
* Other considerations: must be refrigerated (4C).  
* Why it's viable: Safe. Relatively cheap. Can be purchased in bulk for a saving of 1p per sample.
=== 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.
* Why it's viable: Expensive, but safe.


== Option 2: SafeWhite in bulk ==
== Non-viable options ==
* Info: http://nbsbio.co.uk/product.asp?pID=12207&cID=71
Often, these are stains which are not added to the sample and are mutagenic, placing them in the unenviable position of being as difficult to use as EtBr, but more expensive. They may also be nonviable for a variety of other reasons.
* 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 ==
=== SYBR Green ===
* Info: http://www.sigmaaldrich.com/catalog/product/sial/s9430?lang=en&region=GB
* 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 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.
* 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".
* Other considerations: must be frozen (-20C); must be used as a post-stain (20-40 minutes after electrophoresis has finished).  
* Why it's not viable: post-stain which produces hazardous waste.


== Option 4: SYBR Green, re-use of staining solution ==
=== SYBR Green, re-use of staining solution ===
* Info: As above.
* 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 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.
* 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).
* 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).
* Why it's not viable: post-stain which produces hazardous waste.


== Option 5: SYBR Green as part of a readymix ==
=== SYBR Green as part of a readymix ===
* Info: http://www.sigmaaldrich.com/catalog/product/sigma/s4438?lang=en&region=GB
* 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 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)
* Cost, total: This is a RT-PCR stain, which means the PCR vessel containing the stain would need to be disposed of as hazardous waste (I think).
* Other considerations: can't use it to visualise ladders.
* Why it's not viable: We're not doing RT-PCR yet, and we can't use it for traditional PCR, really.  
 
== 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 ==
=== 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
* 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 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.
* 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.
* Other considerations: About 100 times less sensitive than EtBr. Post-stain, which is annoying (and time consuming).
* Why it's not viable: Chances are we won't see anything with it, because it's not sensitive enough.


== Option 8: SYBR Safe ==
=== 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
* 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
* Cost of product: £44.50 for 400ul, 5ul per gel, so £0.55 per gel
* Total cost: 55p per gel.
* Total cost: 55p per gel.
* Why it's not viable: Invitrogen won't sell anything to us.


== Discussion ==
== Discussion ==
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