Biomod/2011/TUM/TNT/Project/Structure: Difference between revisions

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<h1>criteria for the structure</h1>
<h1>criteria for the structure</h1>
DNA binders should affect our structure in such a way, that local deformations are amplified to globally observable changes of the structure.  
In addition to the general requirements for a  structure as stated in the project idea & goals, there were some needs that should also be fulfilled by a candidate structure.
In the first place, such structure should allow for a simple observation of the twist by transmission electron microscopy so that changes in twist can easily be recognized. we considered a U-shaped DNA origami to be favorable, since it has two arms that can twist against each other. Also, if they were designed with a flattened cross section, their twist is more distinguished in TEM images. Most important, they allow for the placement of FRET dyes on different positions to measure their relative movement. Because of this, dimensions lie within fixed borders so that the linear FRET range can be fully exploited. Long arms are best suited for a good enhancement of the small structural changes imposed on DNA by the binding of a single DNA binder and for placing FRET dyes along their axes to measure elongation.<br>
Another important factor was flexibilty, since we wanted to measure deformations. A bulky structure would hinder this, as well as a maximal accessibility for DNA binders. Therefor, we decided for a lightweight structure whose arms consist of only a 10-helix bundle each. <br>
Considering time restraints, a proper and fast folding was preferable. So we decided against a multimeric structure where each assembly step would decrease the overall yield. Rapid folding is especially beneficial if certain modifications like the addition of different dyes or linker molecules to the structure are neccessary thus confering a significant operational freedom.
We considered the U-shape to be an elegant solution to the general design criteria and also the particular needs to be met.


<h1>caDNAno</h1>
<h1>caDNAno</h1>

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           <a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project#The_Idea">The Idea</a>|
           <a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project#Project_Specification">Project Specification</a>|
           <a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project#The_Structure">The Structure</a>|
           <a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project#Theoretical_Background">Theoretical Background</a>
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