ssRNA annealing

Use this category for the exchange of ideas, methodologies and references regarding the isolation, manipulation and analysis of RNA. (Extraction protocols, Northern Blot analysis, RNase Protection, Differential Display, In Vitro Transcription, etc.)

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ssRNA annealing

Postby nekameneka » Jul 05 2017 5:04 am

Hi guys,

I have another question about annealing RNA to get dsRNA. In my previous experience annealing ssRNA which will produce dsRNA bigger then 1kbp I used gel shift to check my annealing where dsRNA travels a little bit slower then it's ssRNA before annealing. So now I have question does the same rule apply for smaller RNAs?? Because I generated 50bp RNA and my "dsRNA" is traveling little bit faster then ss, what happened here?
Thanks!
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Re: ssRNA annealing

Postby 29yrsExperience » Sep 12 2017 9:11 am

I haven’t annealed RNA, but I have some experience with DNA annealing, and you have to be careful the oligo(s) will not self-anneal- in other words, form hairpins or stem-loop structures. On a gel the hairpins run ahead of the properly annealed band, so maybe that is what you saw. Just a guess, though.
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