# Please review the proposed puzzles for the initial OpenCRISPR round
**URL:** https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861
**Category:** Uncategorized
**Created:** [August 14, 2017, 11:25pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861 "2017-08-14T23:25:00Z")
**Posts on this page:** 20
**Page:** 4
### Author:  [@Omei](https://forum.eternagame.org/u/Omei)
#### Post date: [August 19, 2017, 8:20pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/85 "2017-08-19T20:20:00Z")
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.)
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 19, 2017, 8:33pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/86 "2017-08-19T20:33:00Z")
**FMN 1a-ng - ON**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUCAUAGAAGGCAGGAUAUGAAAACAUGAGGAUCACCCAUGUUGACGGCAAAGCUGUCUGUGAUCGUCAGAAGGGCCGGUCUAUGAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@spvincent](https://forum.eternagame.org/u/spvincent)
#### Post date: [August 19, 2017, 9:19pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/87 "2017-08-19T21:19:00Z")
FMN 1a-ng-OFF
Vienna and NUPACK
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGUAGAAGAAAGGAUAUGCGUAACAUGAGGAUCACCCAUGUCGUUCGUGUAAAUGGUUUUCAAUGCAGAAGGUUCAAACCAAUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 19, 2017, 9:22pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/88 "2017-08-19T21:22:00Z")
**FMN 1a-ng - OFF**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUGUCUGAACGAAGGAUAUACAUGAGGAUCACCCAUGUAGAUCUAGAGCAUAUGUUCUAGAUCAUUGUAGAAGGUCGGGUCAGACAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 19, 2017, 10:18pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/89 "2017-08-19T22:18:00Z")
**FMN 1b-ng - ON**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAUCGCUACGUGAGAAGGCACUAAAACAUGAGGAUCACCCAUGUAAAGGCUAUUGUCAAAACCUGGGUGAGGAUAUCACAGUAGCGAUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 19, 2017, 10:42pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/90 "2017-08-19T22:42:00Z")
**FMN 1b-ng - OFF**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGACUAAGCAGAAGGACAUGAGGAUCACCCAUGUAAUAGUAGUCUCAUUUGAGACUACAAUAAUGUAGGAUAUGCGGUAGUCUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 19, 2017, 10:48pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/92 "2017-08-19T22:48:00Z")
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.
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### Author:  [@Omei](https://forum.eternagame.org/u/Omei)
#### Post date: [August 19, 2017, 11:16pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/94 "2017-08-19T23:16:00Z")
That doesn’t sound good. Can you post a pair of sequences that demonstrate this?
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 19, 2017, 11:27pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/95 "2017-08-19T23:27:00Z")
**FMN 2 - ON**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGUAGUAAGUACCAUUUGGUGCAACUUGGGAGAAGGGACGUAUUCGUCAGGAUAUUCAGACAUGAGGAUCACCCAUGUAAUACUACUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
---
### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 19, 2017, 11:43pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/97 "2017-08-19T23:43:00Z")
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
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 20, 2017, 1:06am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/98 "2017-08-20T01:06:00Z")
**FMN 2 - OFF**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGACUAGAUCAACAUGAGGAUCACCCAUGUAGAAGGCGUCAUUUGACGAGGAUAUACAGAUCACAUUUGUGAUCAAAGAUCUAGUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 20, 2017, 2:20am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/99 "2017-08-20T02:20:00Z")
**FMN 3 - ON**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGCAGAUCAGAAGGCGACAUUUGUCGAGGAUAUGAUCCUCAAACAUGAGGAUCACCCAUGUAGAUCUGACAUUGUUAGAUCAGCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@spvincent](https://forum.eternagame.org/u/spvincent)
#### Post date: [August 20, 2017, 3:00am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/100 "2017-08-20T03:00:00Z")
FMN 3 OFF
NUPACK only
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGAGUAUGUAGAAGGGUUGAAGAUAGCAGGAUAUACAAUAUAAACAUGAGGAUCACCCAUGUAAAUACAUGUGGAAUAGUUAACUCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 20, 2017, 3:26am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/101 "2017-08-20T03:26:00Z")
**FMN 3 - OFF**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGACAUGUAGAAGGCGACAUUUGUCGAGGAUAUACAUGAGGAUCACCCAUGUAAAAGAUCUAGUCAUUUGACUAGAUCAAAGUCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@Omei](https://forum.eternagame.org/u/Omei)
#### Post date: [August 20, 2017, 4:10am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/103 "2017-08-20T04:10:00Z")
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.
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 20, 2017, 4:13am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/104 "2017-08-20T04:13:00Z")
**FMN 4 - ON**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUAGGACAAAACAUGAGGAUCACCCAUGUAAUAGAUCAUUUGAUCAUAUAUGGGAAGAAGGCGACAUUUGUCGAGGAUAUUUCAGUCCUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 20, 2017, 4:33am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/105 "2017-08-20T04:33:00Z")
**FMN 4 - OFF**
GACGCAUAAAGAUGAGACGCGUUUGAGAGCUACGUCAAGAUGAGAGAUCAUUGAUCUCUUAUCAAACAUGAGGAUCACCCAUGUAGAAGGCGACAUUUGUCGAGGAUAUACAAGACGUAGCAAGUUCAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU
Solution works in all 3 models.
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### Author:  [@AndrewKae](https://forum.eternagame.org/u/AndrewKae)
#### Post date: [August 20, 2017, 4:36am UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/107 "2017-08-20T04:36:00Z")
Thanks Omei, had never noticed it before.
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### Author:  [@whbob](https://forum.eternagame.org/u/whbob)
#### Post date: [August 20, 2017, 2:32pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/109 "2017-08-20T14:32:00Z")
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.
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### Author:  [@whbob](https://forum.eternagame.org/u/whbob)
#### Post date: [August 20, 2017, 2:39pm UTC](https://forum.eternagame.org/t/please-review-the-proposed-puzzles-for-the-initial-opencrispr-round/2861/111 "2017-08-20T14:39:00Z")
There must be more that just history that I have to flush?
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