EtBr in gel when run mRNA?

[wonder]

should i add EtBr in the gel solution, when i run the mRNA?

 

thanks!

[daisy]

I wouldn't....I used to stain and de-stain after running, because EtBr doesn't seem to "go" well with an RNA denaturing gel. If you're only running mRNA and not total you may only see a smear....are you going on to do a Northern?

[Guest BlueStone]

What's EtBr? Also, it would be nice if you could explain what you're doing, as it sounds interesting. What are you trying to do with mRNA? Staining? I don't undertand...I do understand that you are trying to make something more visable in a microscope perhaps, but I can understand little from what you are doing. Just curious...

 

~BS

[wonder]

hi daisy and bluestone,

 

we run the mRNA in the agarose gel to test for the its' stability.

 

p.s in denaturing condition will the mRNA lose its' native configuration? i have not heard about it, hope you will explain.

 

 

thanks!

[daisy]

If you run a denaturing gel you are ensuring that you have no secondary structure problems which would interfere with sizeing. I'm not sure I understand what you mean by testing mRNA stability (do you mean quality?)...I only run RNA gels to test for degradation (or to do Northerns), but you can really only do that if you run total RNA when you see obvious 18s and 28s RNA bands which should be clear and distinct in good quality RNA preps.