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I have a question, maybe a naive one.

Let's assume that we isolated some RNA from a tissue. Do RNA molecules can bind each other if they have the complementary sequence? I know that some small RNA molecules can bind other RNAs and regulate them but I do not know it is possible in this case? It is like 2 different mRNA can bind each other or not?

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up vote 4 down vote accepted

The difference between RNA and DNA is rather small, and both can form a double-helix structure. So if you had two sequences of RNA complementary to each other they would basepair and form a helix.

There were also some ideas to use this for therapeutic purposes, antisense RNA, an RNA oligo complementary to a messenger RNA, can theoretically be used to silence gene expression by base-pairing to the mRNA.

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Thanks. But do they need to be completely complementary or not? And during the experiments, is there a way to prevent this issue? – golgicik Apr 30 '14 at 20:39
@golgicik Not completely, a certain amount of mismatches would be tolerated. There are various programs to calculate the likely secondary structure of RNA like MFold or the Vienna RNA package you could use to predict the structure of your specific RNA. – Mad Scientist Apr 30 '14 at 20:42
Thanks @Mad Scientist. I think 2-ME would prevent it, right? – golgicik Apr 30 '14 at 20:47
@golgicik 2'-OMe doesn't really affect base-pairing, it's a modification of the ribose. – Mad Scientist Apr 30 '14 at 20:50
I mean 2-Mercaptoethanol. – golgicik Apr 30 '14 at 20:55

@MadScientist answer is very good. I just want to add a detail that could not fit in a comment.

Double stranded RNA is nothing exceptional. You can see an RNA strand that binds to its antisense in tRNA and in RNAi for example.


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