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gels used for RNA detection


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3 replies to this topic

#1 vetticus3

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Posted 23 March 2005 - 06:54 PM

Hello,
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?
Thanks,
Vetticus :)

#2 fred_33

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Posted 24 March 2005 - 01:43 AM

hi
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.

#3 lula

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Posted 24 March 2005 - 11:16 AM

hello

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 ????????????)

#4 yongyk

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Posted 26 March 2005 - 02:00 AM

Dear Vetticus,

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.

Regards
yongyk




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