User:ElNando888/NF4 Discussion
Genesis of the lab
The pseudoknot I found in a database has following structure:
.(((((((((((((............)))))))).........[[[[[....(((...))))))))]]]]]..
Even before the results had come out, it was obvious that the setup of New Frontier 3 was quite confusing, so I was thinking of making things more understandable. The easiest way to morph it into a regular secondary structure was this:
.(((((((((((((............((((((((.........)))))....)))...)))))))))))))..
Then, in order to force designers to create a pseudoknot, all I had to do was to lock some of the bases, to make sure such a stack would be too weak to form properly.
Proposed solving methods
Beside the "natural" path to make it work (using the original pseudoknot as canvas), I found another way to attempt to solve the problem. Follow the (1) or (2) paths.
a) In the puzzlemaker, paste the structure:
- ................................................(((((..................)))))..
- ......(((((.......................................................))))).......
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b) Paste this sequence:
GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUAGUUAAAAAAAAAGGAGGAAAAAAAAAAAAAAAAAAAAAAAAA
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c) "Solve" the stacks.
Be careful not to touch the locked bases.
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d) Paste the "other" structure:
- ......(((((((((((((............))))))))..................(((...)))))))).......
- ...........((((((((............)))))))).........(((((....(((...))).....)))))..
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e) Again, "solve" the puzzle.
And again, be careful not to touch the locked bases, or the bases you mutated earlier
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f) Copy the sequence, and go paste it in the lab.
Then fix the details, barcode, long stretches of As, etc.
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One more possibility
Use
- ..............(((((....................................................))))).., followed by
- ......((((((((.................)))))))).........(((((....(((...)))))))).......
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