User:ElNando888/NF4 Discussion

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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:

 

  1. ................................................(((((..................)))))..
  2. ......(((((.......................................................))))).......

 

NF4.1.1.png NF4.2.1.png

 

b) Paste this sequence:

GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUAGUUAAAAAAAAAGGAGGAAAAAAAAAAAAAAAAAAAAAAAAA

 

NF4.1.2.png NF4.2.2.png

 

c) "Solve" the stacks.

Be careful not to touch the locked bases.

 

NF4.1.3.png NF4.2.3.png

 

d) Paste the "other" structure:

 

  1. ......(((((((((((((............))))))))..................(((...)))))))).......
  2. ...........((((((((............)))))))).........(((((....(((...))).....)))))..

 

NF4.1.4.png NF4.2.4.png

 

e) Again, "solve" the puzzle.

And again, be careful not to touch the locked bases, or the bases you mutated earlier

 

NF4.1.5.png NF4.2.5.png

 

f) Copy the sequence, and go paste it in the lab.

Then fix the details, barcode, long stretches of As, etc.

 

NF4.1.6.png NF4.2.6.png

 

 

One more possibility

Use

  • ..............(((((....................................................))))).., followed by
  • ......((((((((.................)))))))).........(((((....(((...)))))))).......

 

NF4.3.6.png