Coaxial Stacking: Difference between revisions

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Coaxial stacking is a [[tertiary interaction]] where separate stacks in an RNA align along a common axis.
<p>[[File:Coaxial.jpg|thumb|300px|Coaxial stacking in a 4-branched multiloop.]] Coaxial stacking is a [[Tertiary Structure|tertiary interaction]] where separate [[stack]]s in an RNA align along a common axis.</p>
 
<p>&nbsp;</p>
 
<h2>Flush vs. Mismatch-Mediated Stacking</h2>
=== Flush vs. Mismatch-Mediated Stacking ===
<p>In flush stacking, the coaxially-stacked helices are not separated by any unpaired bases. This is depicted in panel C to the right. In [[Mismatch|mismatch]]-mediated stacking, the coaxially-stacked helices are separated by one or more unpaired bases. This is depicted in panels B and D in the figure at right.</p>
 
<p>&nbsp;</p>
In flush stacking, the coaxially-stacked helices are not separated by any unpaired bases. This is depicted in panel C to the right.
<h2>Treatment in EteRNA</h2>
 
<p>The energy model used by EteRNA accounts for coaxial stacking in [[Multiloop|multiloops]] and [[External Loop|external loops]] with closely-spaced stacks. GA and CA mismatches can be used to boost multiloops with mismatch-mediated coaxial stacking.</p>
In [[mismatch]]-mediated stacking, the coaxially-stacked helices are separated by one or more unpaired bases. This is depicted in panels B and D in the figure at right.
 
 
=== Treatment in EteRNA ===
 
The energy model used by EteRNA accounts for coaxial stacking in [[multiloops]] and [[external loops]] with closely-spaced stacks. GA and CA mismatches can be used to boost multiloops with mismatch-mediated coaxial stacking.

Revision as of 17:33, 16 April 2013

Coaxial stacking in a 4-branched multiloop.

Coaxial stacking is a tertiary interaction where separate stacks in an RNA align along a common axis.

 

Flush vs. Mismatch-Mediated Stacking

In flush stacking, the coaxially-stacked helices are not separated by any unpaired bases. This is depicted in panel C to the right. In mismatch-mediated stacking, the coaxially-stacked helices are separated by one or more unpaired bases. This is depicted in panels B and D in the figure at right.

 

Treatment in EteRNA

The energy model used by EteRNA accounts for coaxial stacking in multiloops and external loops with closely-spaced stacks. GA and CA mismatches can be used to boost multiloops with mismatch-mediated coaxial stacking.