I noticed that designs with long stems that had a GU in the barcode often looked stabler than their counterparts without it.
I will like this strategy: In designs with with one or more stems of the length 8-9+ basepairs, give +1 if the (standard 7 nt barcode) contains a GU-basepair at least 2 basepairs away from the closing basepairs. I know that some GU’s outside this area will also do well, but since I can’t say which, I leave this one open. Feel free to add.
Eli: What was the status of this strategy? In a separate thread,
at the bottom, Omei suggested the use of G*U in barcodes as well.
The strategy Omei memtions is in the category scoop a good unused barcode, which is the not usual suspect. Ones that players which will normally avoid - due to we have seen many barcodes with GU’s as next pair or closing basepair break open.
However Omei saw that a GU at a particular spot actually did great in several designs and suggested such a strategy to get a good barcode when those one would normally preffered were already taken.
Omei can use it because he knows how to make the main design stable, however for an automated barcode generator, it could be risky buisiness putting in GU’s as next pair, in particar the one next to the closing basepair next to the gap. If the main design has some weaknesses in the neck, having a GU in the barcode at this position can create misfolds. This is why I particular made sure to exclude these cases from my strategy. I’m not saying it can’t be done. Omei surely showed it could, just say that it takes a more overall view of the design.
You asked what was the status of my strategy above. It is untested as many of its siblings, including some of your strategies too. Its a while since we have had our strategy market running.
Here is the list and the latest strategies from the forum have not made it there.
Additional note on this strategy. Small designs with generally short stems (In particular if most is 5 bp or less), generally don’t need or benefit from having GU’s added at all, rather the contrary. It easier hurts them and causes misfold.
Generally designs of this kind with GU added are not among the highest scoring. One can fine rare occasions. Sometimes a GU makes it when carried in the barcode.
However there was a case with a particular type of adjacent multiloops and mostly small stems, which actually seemed to want GU or AU as one of the closing base pairs in the multiloop. There were several incidences.