User:ElNando888/Static Cloud Labs/CL-IV.Single to Switch

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If you're reading this (which I don't expect many will do), you probably had a glance at my earlier blog entry about FRABASE. The lab results came out some time ago, and it's time to look at them and draw some conclusions, if possible.

 

Sequence information

Lab: http://eterna.cmu.edu/web/lab/2868155/

Design: http://eterna.cmu.edu/game/browse/2868155/?filter1_arg2=2962793&filter1_arg1=2962793&filter1=Id

 

Analysis

Blog frabase 10.png Blog frabase shape.png

So, I was expecting most of the bases in the multiloop, C32, C59, A60 and U61 to show up as protected, at least a little.

But it worked only partially... What happened?

 

A simple hypothesis is to say that only the multiloop folded differently, since the rest of the SHAPE data suggests that, globally, the design was successful (score 97 is quite ok, right?). Hard to draw any conclusions with this, so let's explore other possibilities, if any.

 

Now, if the multiloop actually did fold in a 3D conformation similar to the one presented in the structure published on PDB, then what can explain the discrepancies?

Blog frabase detail1.png

Blog frabase detail2.png

 

Let's observe those bases, and ponder for a while... see anything special about those nucleotides?

 

 

(to be continued)

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