RNA vs DNA migration rates

[Bluenoise]

Hey. So I was a bit of an idiot and forgot to digest away my template after transcription. Yeah figures. So as I've already added loading dye to my transcrption I can't exactley add DNase I to it now, so I got to run it on a gel first.

I guess my quesiton is: is there a significant enough difference in the migration rates of DNA and RNA on denaturing PAGE (urea) that I will be able to differentiate two peices of about equal length. Lets say the RNA is 350 bp and the DNA 22 bp longer than that. If I do get two bands differentiating between the two shouldn't be difficult since only my RNA is radio-labled.

 

Some one please say yes.

 

I really don't want to have to DNase I treat it after purifying my RNA from the gel... cuz phenonl:chloroform extraction is a pain in the ass.

[Bluenoise]

You know what. I decided that I'll just ignor the DNA. Hopefully it will just go away.

I'd be pretty freaken amazed if it interfere with what I'm doing downstream anyways lol.

[CharonY]

Ah, well too late to answer then. But if memory serves in denatured gels the speed is roughly equal (would make sense if both are linear ss, of course). However in PAGE (as opposed to agarose) 22bp can be resolved.

You can clean-up DNAseI treated RNA with columns w/o phenol extraction, btw.

[Bluenoise]

Ah, well too late to answer then. But if memory serves in denatured gels the speed is roughly equal (would make sense if both are linear ss, of course). However in PAGE (as opposed to agarose) 22bp can be resolved.

You can clean-up DNAseI treated RNA with columns w/o phenol extraction, btw.

 

Well in the end it didn't matter. The labled UTP i used was a bit old and didn't give a great signal.

Gave it another try. I DNase treated it. Purified on a QIAGEN nucl. removal kit., dephosphorylated, rephosphorylated.

Got a nice gel. a little degraded sample but good resolution. Was able to purify RNA from it.

 

The gel took 12 hours to run... lol