gels used for RNA detection - (Mar/23/2005 )
just wondering which gel is best for looking at RNA. i've done some in vitro transcription to make some antisense probes, and the protocol i have suggests using an agarose/formaldehyde gel... but i've just been told that a 1% agarose gel works just as well without the smelly fumes (actual description).
what does everyone else use?
for RNA, the formaldehyde is a denaturer. So if ou run a simple agarose gel you will get strange results (abnormal migration) due to RNAs secondary structures.
for resolving small RNAs, less than 150pb, a 15% urea7m/ polyacrylamide gel will be ok.
i have been using 2% agarose gel to detect the presence of RNA prior to completing the RT_PCR protocol im using ( just o chek for the presence of RNA ) ,,,,It worked with me ( Fred : do u think that this is misleading ????????????)
Which gel to use is really depend to you RNA fragment size.
I was using acrylamide gel to purify my 46bp RNA probe. I follow protocol privide by Ambion Maxi Script kit. However, the method provided is using radioctive isotop detection.