User:Omei/Reversed motor - Step 4

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I'm going to use this lab as a test of my theory that the barcode interference can be indirect. That is, f the barcode aligns anti-parallel with the neck, it will throw the trailer back over the hairpin.

I started with garydfisher's design that looks very good in the dot plot and has several mods already. But it looked to me like a case where we might well see tail interference. So I ran it through RNA Composer, and the antiparallel alignment did occur. So I than ran the Minimize Structure routine with the default parameters, to improve the estimate of the local interactions. (This takes an hour or so of CPU-bound computation.) Here's a screen shot of what it produced:

Key to ribbon coloring:

Magenta: trailer
Yellow: hairpin
White: neck
Orange: open loop around neck
Gray: All the other bases

The atom-level representation in red marks predicted base triples.

I then modified the two open loop bases adjacent to the neck and ran the mod through RNA Composer. This time, I didn't bother to do the minimization, because it predicted I had successfully moved the trailer away from the neck.