R80.New Frontier 3
The results for Round 80 took a long time to come out. And it seems to have been a very difficult batch. In many cases, there was a large amount of reactivity errors, and unfortunately, New Frontier 3 was no exception.
There are only a minority of designs that seem exempt of reactivity errors, or have relatively few. Observing those ones inspired me following thoughts.
A confusing presentation
Obviously, there was a lot of confusion associated with the way I had chosen to present the challenge.
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For instance, this design would probably have scored better if the pseudoknotting sequences had matched properly. So close... |
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In this case, I'm not sure whether it was confusion or deliberate choice, but the designer was consistently shooting for a slightly different target (which did work, apparently)
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Another case of mismatched sequences. |
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Mismatched again. The result is possibly interesting though, for a rather remarkable SHAPE signature, reminiscent of the Semicircle 2 bends lab. |
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Not mismatched, but I'm confused by the choice of poly(U)... |
Finally, the whole point of this confusing setup, was to force designers to create a pseudoknot in order to achieve success (score-wise), but the "fake" secondary structure I created for that goal was actually not impossible to solve directly (congratulations to JR), contrary to what I had expected.
One interesting case
This design had a subtle "flaw". The designer used a slightly different target, with the 5' strand of the pseudoknot shifted downstream by one nt, and the 3' strand shifted upstream also by 1 nt. The knotting sequences were a (rather) good match, so it could have worked just as well as the original target. But it didn't work too well.
I don't think that the presence of a UU mismatch in the pseudoknot could have presented a serious problem, but who knows? Maybe the 5' promoter (locked GG) interferred. Or possibly, the second shift caused the sequence to appear in a less convenient 3D position for an easy docking. And of course, all these factors may have played a role here.
It seems that it will soon be technically possible to create puzzles and labs with variable length segments. I think it will be specially interesting to use this new functionality in the context of pseudoknots.
No guarantees
A correct sequence was still not necessarily the promise of a winner though...
(tbc)
