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Question is rather self-explanatory. I'm looking for a non-cleavable RNA sequence to act as an RNA linker.

I mention 3- or 4-nucleotides only, but making such a sequence with 2 nucleotides is rather easy as seen below, but I've encountered some difficulties in transcription.

GAGGAAGGGAAAGGGGAAAAGGGGGAAAAA...

This also works for just about any random sequence of G's and A's.

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Used as a linker, I don't know if the second part of the question, "secondary structure" can be answered. This could be very dependent on the flanking regions. Using poly-A is nice for flexibility, but you will get slipping in your transcription. –  Atl LED Oct 18 '13 at 13:13
    
Question edited, thanks for the suggestion. –  LanceLafontaine Oct 18 '13 at 14:27
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I don't know the answer, but you could simply brute force the answer by generating all possible combinations of 3- or 4-nt length sequences, and comparing against the restriction enzyme database (REbase).

It would not take long to do. There are $ 3^4 $ and $ 4^4 $ combinations, respectively. Depending on your purpose, it might be possible when not considering engineered restriction enzymes (which are not likely to have recognition sequences found in nature).

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3 nucleotides are so short that many of them can be RE sites or not, depending on the other nucleotides around them. the brute force method here is the best shot, but the chance that an enzyme that includes your linker may later be discovered. some restriction enzymes do not cleave the sequence they bind to either. so not clear whether this is really possible at all. –  shigeta Oct 21 '13 at 0:43
    
Those are fair comments. I'm unclear why it's necessary to find such a sequence, unless it's just an exercise. If this is for expression in a particular system, then maybe only its restriction enzymes need to be avoided. –  leonardo Oct 21 '13 at 2:56
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