Right. Are you OK with it by switching between modes as needed?
FMN 1a-on- GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUAGAGGAUAUAAAGUAAAAUAAAAUAAAACAUGAGGAUCACCCAUGUACAACAUGAGGAUCACCCAUGUCACCCUUAGAAGGUUGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU -vienna1
TEP-1-a-on- GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAAUGAUACCAGUGAAUAAUAAUAACAUGAGGAUCACCCAUGUCAUGUAAUAAAAUAAAUAAAAUAAAAUAACGCCCUUGGCAGCAUUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU -vienna1
Tep-1-a-on-venna2- GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAAUGAUACCAGUGAAUAAUAAUUACAUGAGGAUCACCCAUGUCAUGGAAUAAAAUAAAUAGUCUAAGAUAACGCCCUUGGCAGCAUUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
OK, I have a spreadsheet for keeping track of what has and hasn’t been solved - https://docs.google.com/spreadsheets/d/1DLUBU4LssU4HWyyFLqUi_LpfFyl8XP95W2xYUKQ-gps/edit?usp=sharing. You can consult it if you want to see which puzzles haven’t had any solutions submitted, or just to make sure that I have recorded your own. Feel free to leave comments in the spreadsheet if you see something in the spreadsheet that doesn’t seem right.
Thanks for all the quick responses!
CRISPR/Cas9 - Tetracycline - ON
It can be solved in blueprint style.
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACUAAAACAUACCUCAAUAAAUAAAACAUGAGGAUCACCCAUGUAAAAUAAUAAGAAAGGGAGAGGUGAAGAAUACGACCACCUAGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
http://www.eternagame.org/game/puzzle/8040919/
CRISPR/Cas9 - Tetracycline - OFF
Also the partnering lab can be solved in blueprint style
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACUAAAACAUACCACAUGAGGAUCACCCAUGUAAUAAAGAAAGGUGAUUACAAAAUAAAGGAGAGGUGAAGAAUACGACCACCUAGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Yes, a nice challenge.
FMN 1b - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACAAGAAGGUACAAAACAUGAGGAUCACCCAUGUAAUAGUAGAGUUAUGAAUUCAUAGCUCUAUAAGUUACAUAGUGAGGAUAUUGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Seems to have a lot of potential variability.
FMN 1b - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGCAGAAGGUAUAUAUUAAUUCUUAAGAUGUAGACUGUCUAUUGAUAGUCUACAUCAACAUGAGGAUCACCCAUGUAAGGAUAUGCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Again, appears to have a lot of potential variability.
Puzzle appears to be unsolvable in NuPACK, all in the locked portion.
1 Like
CRISPR/Cas9 - FMN 2 - ON
Ugly solve, not much blueprint here
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACCCAAAUAUAAAAUAAAAUAAAUCCUAAGAAGGAUAUCCGGAAACGGAGAAGGUCUCCUAGUAAAACAUGAGGAUCACCCAUGUGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
http://www.eternagame.org/game/puzzle/8038693/
CRISPR/Cas9 - FMN 2 - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACCCAAAAUAUAACAUGAGGAUCACCCAUGUAGGAUAUAGGAAAACCUAGAAGGACAAAACCUCAGACAAAAGUCUGAGGAAAGGGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
I too have noticed in Nupak the locked bases forming a structure breaks apart.
I was able to get designs with both vienna, and vienna2. Thanks
FMN 2 - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUGUCAAACAUGAGGAUCACCCAUGUAAAGAAGGAUAUGAGUAUUCUCAGAAGGUCUUCAUGUUAUUUAUUUAUAUUAUUUAGACAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Still seems to be plenty of potential variability.
FMN 2 - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUCGCAUUUAUAACAUGAGGAUCACCCAUGUAGGAUAUGCGUAUUCGCAGAAGGAUAUGGAAGUAGACUGAUUCAGUCUACAGCGAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Still seems to be plenty of potential variability.
FMN 3 - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGACAACAUGAGGAUAUGUGUAUUCACAGAAGGUAUAAGAUGAUGUAUUCAUCAUCAAUACAUGAGGAUCACCCAUGUUUUAUGUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Still seems to have plenty of variability.
Appears to be unsolvable with NuPACK, again the static locked bottom portion.
FMN 3 - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACUCAAAUGUAGGAUAUCUGUAUUCAGAGAAGGACAUGAGGAUCACCCAUGUAAGACUAGAGAUGAUUCAUCUCUAGUCAAAUGAGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
This puzzle seemed just a bit more difficult than the rest of the FMN series. Again with the state 2 not solvable with NuPACK. Seems to have a lot of potential variability.
FMN 4 - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGACAGAGGUUGCUCAACAUGAGGAUCACCCAUGUAGGAAAGCCUUAGGCAUCAAGGAUAUUGUUCCUACAAGAAGGUGAAUAGUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Ugly solution.
FMN 4 - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGACAAGAUGAUCGAGACUAUUGUCUCGAUCAUCAACAUGAGGAUCACCCAUGUAGGAUAUCUCUAUUGAGAGAAGGACAUAAGUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Thank you, @AndrewKae, for bringing up the issue with NUPACK predicting that the oligo will fall off. I’m going to bring up this up with the devs that designed the puzzles, but let me explain why it might be left just as it is.
In a real CRISPR system, what appears in the puzzle as an RNA oligo is actually a segment of genetic DNA. Base sequences 1-20 in the puzzle represent the CRISPR single stranded “guide” RNA strand that binds to the the DNA, which is what allows CRISPR to latch onto a specific segment of DNA. For the CRISPR mechanism to be effective, the guide RNA can’t be binding to some other part of the CRISPR mechanism (which includes our switching portion our designs) in preference to the DNA oligo. So falling off of the DNA is a real phenomenon that has to be taken into account.
What I don’t know, though, is whether the specific DNA segment in the puzzles was carefully chosen so that the guide sequence had a pretty strong tendency to pair with the other locked CRISPR bases, to ensure that this issue could and would show up in the in silico puzzles. I certainly suspect it was chosen with that in mind.
I also suspect that the puzzles can be solved, even in NUPACK, but that it may require starting over with a fresh approach. So if you’ve for the energy for it, keep trying. Meanwhile, I’ll talk with the devs and get back to you.
Thanks for the explanation Omei. If you find solutions for the ones I mentioned please let me know.
TEP 3 ON :
easily solved (ugly solve), not sure about further analysis
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAAACACAAUGAUACCAGAGAAACCACUCCCUUGGCAGCAUAAACAUGAGGAUCACCCAUGUAAACAUGGAAAUAACACAACACAAAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
TEP 3 OFF :
again, easily solved (ugly solve), not sure about further specs
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAACCAAAGUGAUACCAGAGUAAUAACUCCCUUGGCAGCACAUGAGGAUCACCCAUGUAAAUUUAUUUAAUUCUAACAAAACAACAAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Vienna btw
Vienna btw
TEP 4 ON
one of the requirements is “at most 4 A’s in a row”, the sequence below gives all green (= a solve) but between bases 155 and 160 there are 5 A’s in a row… Is this allowed because they are locked ? Or am I missing something else (newbie…)? Same for TEP 4 OFF…
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUAACAACAACUCACAUGAGGAUCACCCAUGUUACAGGGAACACACAACGAUACCAGAAACACAAUUCCCUUGGCAGCGUAGAACAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
And for completeness’ sake:
TEP 4 OFF :
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUAACAAAACUAAACAUGAGGAUCACCCAUGUUAGAGGGAAACAACAACGAUACCAGAAACACAAUUCCCUUGGCAGCGUAGAACAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Thank you, everyone. I think we have at least one solve for all the puzzles.
The major concern that has surfaced is that some puzzles seem difficult, or perhaps impossible, to solve for NUPACK. This is a concern, and we would like to get more information about how extensive this is before making a final decision on the puzzzles.
I’m going to add a new column to the spreadsheet to record solvability in NUPACK. Could you now specifically try for NUPACK solutions, posting either successful designs or unexpected inability to come up with one?