Say I have a target RNA strand:


I know that this strand will readily anneal to the sequence


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



In other words, can RNA form parallel helix structure?


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.

  • $\begingroup$ 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 Feb 8 '18 at 17:18
  • $\begingroup$ @charlesdarwin why is that? $\endgroup$ – Mike Flynn Feb 8 '18 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 Feb 8 '18 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 Feb 9 '18 at 3:29
  • $\begingroup$ @mike-flynn I think they do need to be parallel to pair up. $\endgroup$ – charlesdarwin Feb 9 '18 at 10:41

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