Difference between revisions of "User:Omei/Reversed motor - Step 4"

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<p>I'm going to use this lab as a test of my theory that the barcode interdference can be indirect.&nbsp; That is, f the barcode aligns anti-parallel with the neck, it will throw the trailer back over the hairpin.</p>
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<p style="padding-left: 30px;">I'm going to use this lab as a test of my theory that the barcode interference can be indirect.&nbsp; That is, f the barcode aligns anti-parallel with the neck, it will throw the trailer back over the hairpin.</p>
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
 
<p>I started with garydfisher's design that looks very good in the dot plot and has several mods already.&nbsp; But it looked to me like a case where we might well see tail interference.&nbsp; So I ran it through RNA Composer, and the antiparallel alignment did occur.&nbsp; So I than ran the Minimize Structure routine with the default parameters, to improve the estimate of the local interactions.&nbsp; (This takes an hour or so of CPU-bound computation.)&nbsp; Here's a screen shot of what it produced:</p>
 
<p>I started with garydfisher's design that looks very good in the dot plot and has several mods already.&nbsp; But it looked to me like a case where we might well see tail interference.&nbsp; So I ran it through RNA Composer, and the antiparallel alignment did occur.&nbsp; So I than ran the Minimize Structure routine with the default parameters, to improve the estimate of the local interactions.&nbsp; (This takes an hour or so of CPU-bound computation.)&nbsp; Here's a screen shot of what it produced:</p>
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<p>[[File:R3M4_3_(after_minimization).PNG|800px]]</p>
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
<p>&nbsp;</p>
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<p>Key to ribbon coloring:</p>
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<p style="padding-left: 30px;"><br />Magenta: trailer<br />Yellow: hairpin <br />White: neck<br />Orange: open loop around neck<br />Gray: All the other bases</p>
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<p style="padding-left: 30px;">The atom-level representation in <span style="color: #ff0000;">red</span> marks predicted base triples.</p>
 
<p>I then modified the two open loop bases adjacent to the neck and ran the mod through RNA Composer.&nbsp; This time, I didn't bother to do the mini,ization, because it predicted I had successfully moved the trailer away from the neck.</p>
 
<p>I then modified the two open loop bases adjacent to the neck and ran the mod through RNA Composer.&nbsp; This time, I didn't bother to do the mini,ization, because it predicted I had successfully moved the trailer away from the neck.</p>
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<p>[[File:R3M4_3_mod.PNG|800px]]</p>

Revision as of 04:49, 20 October 2013

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:

R3M4 3 (after minimization).PNG

 

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 mini,ization, because it predicted I had successfully moved the trailer away from the neck.

R3M4 3 mod.PNG

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