Catalog of close 2,2 loops in the lab

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  • Updated 8 years ago
The 2,2 loop has been a tough structure to get right in the lab. I wanted to make a list and call it "successful 2,2 loops", but, as I looked through the designs, I couldn't find any that are truly successful. So I'm making a list of the closest. Brourd's is the only one that has all 4 loop nucleotides unbonded. I added the other three, even though they have blue in the loop (in the experimental data view) because the blue is a lot lighter than in most designs. Otherwise it would've been a VERY short list.

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Posted 8 years ago

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Photo of Quasispecies


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Interesting idea.

I think the most stable 2-2 loops contain unusual base pairs that are detected by SHAPE but not by the EteRNA interface. Looking at the results from "Mat - things to test," it would seem that the G-G pair doesn't form in that structure's 2-2 loop or isn't detected by SHAPE.

The picture becomes murkier when you look at the results of "Mat - making it up as I go". Just as in previous labs, loops with symmetric A-A or GA mismatches appear to be paired. Freywa tried something new with the GG / AA mismatch, and the result was not what I would have guessed:

What is going on here? There is no way to know for sure, of course, but it might be worth looking at this 2-2 loop sequence again. Our results with other loop sequences have been very reproducible.
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Incidentally, I was the designer of that RNA.