ssRNA annealing

Go to the profile of nekameneka
Jul 05, 2017

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?


Go to the profile of OldCloner
OldCloner 6 months ago

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.