I hate having to run MOPS PFA agarose gels with DEPC and everything just to verify my RNA integrity. I came across an alternative protocol that uses ordinary household bleach in the gel to inhibit RNases and was wondering if anyone here has tried it and what the success was like? Or any helpful insight is welcomed also.
here's a protocol I put together based on what was done in that paper.
For a 50ml gel IN a RNase-free 250ml Erlenmeyer flask Mix: 5 mls of 10x TAE that I gave you 42.5mls ultra purified water 0.5g of the agarose I gave you 2.5mls of household bleach (6% sodium hypochlorite, use clorox)
Incubate 5-10 minutes.
Microwave for the minim amount of time on the lowest heat setting that’s needed to completely solubilize the agarose, you don’t want evaporation adjusting your solutions volume Check your volume with a sterile 50ml serological pipette, if you have lost more than 5% volume I would redo, using less heat.
Add 3µl 10mg/ml ethidium bromide, swirl to mix. Pour in casting frame, allow to cool, submerge in 1xTAE
Combine 1µg of your total RNA, 2µg RNase free 6x loading dye and q.s to 12µl in RNAse feree water, you can use the water from the qiagen kit for this. Run at 100V, about 30 min, get good scanned image of it and use Photoshop to assess the band intensity. The 28S should be twice the brightness of the 18S in a sample with little to no fragmentation.