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help needed with denaturing agarose gels for RNA

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#1 Andras



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Posted 15 November 2009 - 04:53 AM

Dear All,
I've been using the messenger kit for making a viral mRNA (and after transfection, hopefully, it would be translated into actual viral particles), and ran into a big problem: after spending a day cleaning assembling the whole gel-running apparatus, making the formaldehyde gel, bioling the samples with formamide, and all, I got nothing on the gel after I ran them. It seemed that the samples simply did not leave the wells -there was a very narrow, and very strong signal on one side of the wells. (And one component of the dye migrated to the + pole.)
When I ran the samples on a normal agarose gel, of course, I saw the samples, but not surprisingly, as many bands; so I have no clue if I have the desired size. So before I waste any more of my precious samples :), and a day for repeating the electrophoresis, I thought I'd ask if someone has any practical advice about it.
(I'm not even going into the question if I have caps on the mRNA...)
Any suggestions are greatly appreciated.

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