Biomod/2011/TUM/TNT/Methods: Difference between revisions

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<h2>Folding procedure</h2>
<h2>Folding procedure</h2>
For more detailed information, please consult the [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Setting_up_folding_reactions instruction] in the labbook.  
For more detailed information, please consult the [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Setting_up_folding_reactions instruction] in the labbook.  
<h2>Prestocks</h2>
<h3>Prestocks</h3>
Several hundreds of staples have to be mixed for a folding batch. Those staples, which are frequently used together for different variants of the structure, were mixed in prestocks. Later on, for small modifications of the structure, only the appropriate prestock needs to be remixed, while all other parts could be used again. Prestocks may vary in the number of included staples, but in one prestock, all staples are equally concentrated (usually 10µl 100µM staple are mixed).  
Several hundreds of staples have to be mixed for a folding batch. Those staples, which are frequently used together for different variants of the structure, were mixed in prestocks. Later on, for small modifications of the structure, only the appropriate prestock needs to be remixed, while all other parts could be used again. Prestocks may vary in the number of included staples, but in one prestock, all staples are equally concentrated (usually 10µl 100µM staple are mixed).  


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For this longest ramp, again the first part is cooling down from 65°C to 57°C by -1°C per 15 minutes. Then, the batch is cooled down by 1°C per 3 hours. Finally, temperature is set to 4°C.<br>
For this longest ramp, again the first part is cooling down from 65°C to 57°C by -1°C per 15 minutes. Then, the batch is cooled down by 1°C per 3 hours. Finally, temperature is set to 4°C.<br>


<h3>Validation of folding efficiency</h3>
<h2>Validation of folding efficiency</h2>
Success of folding was evaluated with agarose gel electrophoresis. Thereby, it could be investigated, whether additional bands besides the main structure do occur. Subsequently, these bands could be analyzed at the TEM. <br>
Success of folding was evaluated with agarose gel electrophoresis. Thereby, it could be investigated, whether additional bands besides the main structure do occur. Subsequently, these bands could be analyzed at the TEM. <br>


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