User:ElNando888/Static Cloud Labs/CL-V.Zigzag1

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According to FRABASE, the first zigzag 5'-UUAA--UACA-3' seems to actually have some chances to fold in a way that may yield the wanted SHAPE reactivity.

Source: PDB accession 3J3C

 

I couldn't find a good candidate pattern for the other zigzag. The closest thing to a possible match seems to be the 5'-CAGG--CCUG-3'. Granted, it looks rather likely that this will actually form a stack composed of canonical pairs. But a number of entries in FRABASE do suggest that these bases would tend to bind in a different conformation... Out of curiosity, let's try it and see what comes out of it.

 

The hexaloop is once again one of the GURAYA sequence pattern I already used in a few other places.

 

Links

 

Results

Well, that went South...

It could be argued that the first zigzag may have had a measure of success (so I'll probably retry it somewhere else), but the SHAPE signals around bases 5-7, 33-38 and 44-46 are clearly indicative of a (or possibly a few) serious misfold(s). And it seems very hard to draw any conclusions here...

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