FYI: There are four new puzzles in the FMN series; they have “ng” in the puzzle name. These are similar to the original 1 a/b series, the difference being fewer bases in the big loop. The main rationale for these is that we can take many of the previous NG (Next Generation) lab designs and map their switching areas directly into these puzzles. We can then compare the corresponding results and look for any big differences that show up. (For example, the 3D structure of the CRISPR complex might interfere with one or more states.)
FMN 1a-ng - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUCAUAGAAGGCAGGAUAUGAAAACAUGAGGAUCACCCAUGUUGACGGCAAAGCUGUCUGUGAUCGUCAGAAGGGCCGGUCUAUGAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
FMN 1a-ng-OFF
Vienna and NUPACK
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGUAGAAGAAAGGAUAUGCGUAACAUGAGGAUCACCCAUGUCGUUCGUGUAAAUGGUUUUCAAUGCAGAAGGUUCAAACCAAUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
FMN 1a-ng - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUGUCUGAACGAAGGAUAUACAUGAGGAUCACCCAUGUAGAUCUAGAGCAUAUGUUCUAGAUCAUUGUAGAAGGUCGGGUCAGACAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
FMN 1b-ng - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUCGCUACGUGAGAAGGCACUAAAACAUGAGGAUCACCCAUGUAAAGGCUAUUGUCAAAACCUGGGUGAGGAUAUCACAGUAGCGAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
FMN 1b-ng - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGACUAAGCAGAAGGACAUGAGGAUCACCCAUGUAAUAGUAGUCUCAUUUGAGACUACAAUAAUGUAGGAUAUGCGGUAGUCUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
I did notice some behavior in this puzzle that I don’t understand. In NuPACK while swapping bases in the static stem it would affect the pairing at the other end of the stem, without any sliding or loops involved.
That doesn’t sound good. Can you post a pair of sequences that demonstrate this?
FMN 2 - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGUAGUAAGUACCAUUUGGUGCAACUUGGGAGAAGGGACGUAUUCGUCAGGAUAUUCAGACAUGAGGAUCACCCAUGUAAUACUACUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
FMN 1b-ng - OFF
NuPACK - state 2 - in static stem GC pair 75-88 allows UA pair 70-93 to form
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGACUAAGCAGAAGGACAUGAGGAUCACCCAUGUAAUAGUAGACUCAUUUGAGUCUACAAAAAUGUAGGAUAUGCGGUAGUCUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Flip pair 75-88 to CG and UA pair 70-93 does not form
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGACUAAGCAGAAGGACAUGAGGAUCACCCAUGUAAUAGUACACUCAUUUGAGUGUACAAAAAUGUAGGAUAUGCGGUAGUCUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
FMN 2 - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGACUAGAUCAACAUGAGGAUCACCCAUGUAGAAGGCGUCAUUUGACGAGGAUAUACAGAUCACAUUUGUGAUCAAAGAUCUAGUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
FMN 3 - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGCAGAUCAGAAGGCGACAUUUGUCGAGGAUAUGAUCCUCAAACAUGAGGAUCACCCAUGUAGAUCUGACAUUGUUAGAUCAGCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
FMN 3 OFF
NUPACK only
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGUAUGUAGAAGGGUUGAAGAUAGCAGGAUAUACAAUAUAAACAUGAGGAUCACCCAUGUAAAUACAUGUGGAAUAGUUAACUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
FMN 3 - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGACAUGUAGAAGGCGACAUUUGUCGAGGAUAUACAUGAGGAUCACCCAUGUAAAAGAUCUAGUCAUUUGACUAGAUCAAAGUCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
Thanks. I was able to switch between the two configurations with other swaps as well. That’s a little surprising, but it has a plausible explanation.
Here’s a close-up of the local energy estimates for the two foldings.
Note that in both cases the total energy of the loops that are changing is 5.5. My guess is that in this case, these two are exactly equal, to whatever precision NUPACK is using. In the case two configurations tie exactly, which one NUPACK choses as the “minimum” is probably arbitrary.
FMN 4 - ON
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGACAAAACAUGAGGAUCACCCAUGUAAUAGAUCAUUUGAUCAUAUAUGGGAAGAAGGCGACAUUUGUCGAGGAUAUUUCAGUCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
FMN 4 - OFF
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACGUCAAGAUGAGAGAUCAUUGAUCUCUUAUCAAACAUGAGGAUCACCCAUGUAGAAGGCGACAUUUGUCGAGGAUAUACAAGACGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
Thanks Omei, had never noticed it before.
I’ve cleared my browsing history and reset the FMN 4-OFF and ON puzzles mentioned above, but when I pasted the above solutions, the MS2 is not present in State 2 using NUPACK. I’m using Chrome. FMN 4 - ON puzzle picture below.
There must be more that just history that I have to flush?