User:ElNando888/Static Cloud Labs/CL-V.Lonely Base Pair 1

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The multiloop

Based on PDB accession 2XZM



Multiloop 4-4-4.png Multiloop 4-4-4 Hbond.png



A fascinating structure. Compact, yet, comparatively few hydrogen-bonds. So it would seem that most of the global stability of this structure stems from the stacking interactions.


And a stack (incredibly) spinning outwards and back inwards around the backbone... quite unexpected.


Spinning stack.png


The 1-1 loop

Based on PDB accession 3ZEX



Internal loop 1-1.png


FRABASE fooled me again with this one. It said the C/U mismatch would be too far apart to form any hydrogen bond, but Chimera's calculations find that one is clearly possible... Well, this will be an interesting experiment. If everything goes like it did in Magic boosts, the prediction is that the Cytosine would appear somewhat protected, while the Uracil should appear largely reactive.



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