User:ElNando888/Static Cloud Labs/CL-VII.Find Z

Well, I tried to initiate collaboration, but it seems nobody is interested. So I guess I'll keep documenting for my own sake, without going into too many details.

Structural elements

Tetraloop

Just repeating the GUAA experiment for validation purposes.

Pentaloop

Inspection of a few PDB models shows that GUAAG is a GNRA-like shape, with an extruded G. Let's see what happens.

6-0 bulge

A little research on FRABASE returned a small number of hits. A specific one retained my attention.

I find it fascinating to see that a strand no less than 6 nucleotides long does actually not prevent coaxial stacking between the stems. That bulge looping on itself is just awesome.

It took me longer than it should, and it is probably a sign that I don't have yet mastered the art of searching for a motif on that website, but it turns out that this motif is cataloged on RNA 3D Hub as Motif IL_24546.4. Cool, I will be trying a few of them.

Links

Results

Loopy Bulge 2

As usual, the most interesting result is the most terrible failure.

Hmm, what the bloody hell happened here? The estimate makes some sense this time (who said I'm being sarcastic? :P):

But on the other hand, the open loop is slighty better "free-energy-wise":

So why would this stack form this way?

Now, if we consider the respective SHAPE signals of C33 and A53, another picture comes to mind:

(please ignore the paired CC, it doesn't change anything with the free energy, it just helps me picture a noncanonical interaction)

Now this is energetically more favorable and better than the open loop. But still, it doesn't explain why the MFE wouldn't form as predicted...

Maybe the global picture can help... The marked tetraloop is a GNRA family one. Those are known to have a potential to engage in tertiary interactions. And here, well, the SHAPE signature seems to indicate that something may indeed have happened... Coupled with the fact that it is uncertain whether the A22-U64 did form or not, one could very well hypothesize that the GUAA tetraloop found a favorable environment to "dock" with the other stack, and quite possibly, around the pairs 30-33, thereby stabilizing the alternate conformation and maybe preventing the MFE from appearing...

Well, that's my best shot so far anyway :)

Other

The GUAAG seems to have performed quite nicely.
Have we already done an intensive research on adjacent stacks in the hook? Could that be a good lab idea?