User:ElNando888/Static Cloud Labs/CL-VI.Modeled Impossible 2

 

Links

• Lab: http://eterna.cmu.edu/web/lab/3009949/
• Designs: 
  1. http://eterna.cmu.edu/game/browse/3009949/?filter1_arg2=3123119&filter1=Id&filter1_arg1=3123119
  2. http://eterna.cmu.edu/game/browse/3009949/?filter1_arg2=3123224&filter1=Id&filter1_arg1=3123224
  3. http://eterna.cmu.edu/game/browse/3009949/?filter1_arg2=3149035&filter1=Id&filter1_arg1=3149035

 

Details

 

Obviously, this one is a long shot. When FRABASE spitted that sequence out, I didn't even need to see the picture in the lab designer in natural mode, I immediately thought that this would fold into a GC pair supporting a GCGA tetraloop, which belongs to the famous GNRA-class, known to be very stable.

Surprisingly though, the 3D structure seems to support the idea that in this context, the Cytosine may tend to prefer to bind to the "other" Guanine. Worth experimenting I guess...

 

 

The other apical loop looks much more on target, with the bulged Uracil being literally kicked out of the stacking area.