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Say I have a target RNA strand:

5'--AAUGGCCCUUUAAA-->3'

I know that this strand will readily anneal to the sequence

3'<--UUACCGGGAAAUUU--5'

which is the reverse-complement. I'm wondering if this strand will also anneal to it's "forward" complement, namely:

5'--UUACCGGGAAAUUU-->3'

?

In other words, can RNA form parallel helix structure?

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No. The 5' end has to anneal to the 3' end of the other strand. Here your 5' end is AAU and the 3' UUU, so you can see that U will not pair with U.

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  • $\begingroup$ It is, of course, a matter of opinion, but my opinion is that if this question can be answered in two lines it is a poor question for which the poster shows no evidence of having done any research himself. (It may even be a homework question.) I would say that this comes under the category of questions that should be ignored and the poster encouraged to do some research of his own as this site requires. $\endgroup$
    – David
    Commented Feb 8, 2018 at 17:18
  • $\begingroup$ @charlesdarwin why is that? $\endgroup$
    – Mike Flynn
    Commented Feb 8, 2018 at 19:52
  • $\begingroup$ @mike-flynn, I don't really understand your comment. In a double-stranded DNA helix, if you move along the helix, one strand goes in the 5'-3' direction and the other strands goes in the 3'-5' direction. So, if you want to pair 5'--AAUGGCCCUUUAAA-->3' and 5'--UUACCGGGAAAUUU-->3' you have to flip one over, align them and check that all nucleotides are complementary. When you flip over 5'--UUACCGGGAAAUUU-->3' you get 3'-UUU...5' and you can stop here because you see that the third U does not match the U in 5'--AAUGGCCCUUUAAA-->3'. $\endgroup$
    – charlesdarwin
    Commented Feb 8, 2018 at 20:48
  • $\begingroup$ @charlesdarwin, I'm talking about paring without flipping them over. Taking two free floating RNA strands that are complementary only in parallel direction (5' to 3'), will they form a helix. Can helices form with 5' ends going together towards 3' ends - or why not? That is my question. I don't think you have to "flip" them over as you say, I don't think that's chemically necessary. $\endgroup$
    – Mike Flynn
    Commented Feb 9, 2018 at 3:29
  • $\begingroup$ @mike-flynn I think they do need to be parallel to pair up. $\endgroup$
    – charlesdarwin
    Commented Feb 9, 2018 at 10:41

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