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

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<tr bgcolor="#f5f5f5"><td valign="top">The U structure was folded using the [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Setting_up_folding_reactions 15_65] ramp. This ramp was the fastest of the tested ones and also led to proper folded origamis as shown in figure 1. There is only one major band visible in the agarose gel, indicating that no significant amounts of byproducts (like dimers) have been formed. The results of the slower ramps 2D_H3_ML and 5D_H3_ML yielded similar results as the 15_65 ramp. </td><td>[[Image:2011.08.24 theU 1kBlad-scaff-bm1-bm2.jpg|400px |center | thumb | Fig. 1 From left: 1kb-ladder, scaffold p7560, (scaffold p7560),  [[http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Structure_page#BM1_.26_BM2:_Unlabeled_structures BM1, BM2]]]]</td></tr>
<tr bgcolor="#f5f5f5"><td valign="top">The U structure was folded using the [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Setting_up_folding_reactions 15_65] ramp. This ramp was the fastest of the tested ones and also led to proper folded origamis as shown in figure 1. There is only one major band visible in the agarose gel, indicating that no significant amounts of byproducts (like dimers) have been formed. The results of the slower ramps 2D_H3_ML and 5D_H3_ML yielded similar results as the 15_65 ramp. </td><td>[[Image:2011.08.24 theU 1kBlad-scaff-bm1-bm2.jpg|400x400px | thumb | Fig. 1 From left: 1kb-ladder, scaffold p7560, (scaffold p7560),  [[http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Structure_page#BM1_.26_BM2:_Unlabeled_structures BM1, BM2]]]]</td></tr>
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<tr bgcolor="#f5f5f5"><td valign="top">Most of the structures from the major band were folded correctly, which was proven by TEM images (figure 2).
<tr bgcolor="#f5f5f5"><td valign="top">Most of the structures from the major band were folded correctly, which was proven by TEM images (figure 2).
The purification of the structures was tried both with an agarose gel and with an Amicon size exclusion filter (molecular weight cutoff: 100kDa). According to general experience, the yield of purification via agarose gel is approximately 2 nM. The yield of the filter purification was definitively higher, since unexpected weak dilutions led to appropriate concentrations for TEM and fluorescence microscope. Therefore we estimate the yield to be roughly 10 nM. </td><td>[[Image:20111021controltheUBM2 2B7.png|400x400px|left|thumb|Fig. 2 The U structure (BM2_2B7)]]</td></tr>
The purification of the structures was tried both with an agarose gel and with an Amicon size exclusion filter (molecular weight cutoff: 100kDa). According to general experience, the yield of purification via agarose gel is approximately 2 nM. The yield of the filter purification was definitively higher, since unexpected weak dilutions led to appropriate concentrations for TEM and fluorescence microscope. Therefore we estimate the yield to be roughly 10 nM. </td><td>[[Image:20111021controltheUBM2 2B7.png|400px|thumb|Fig. 2 The U structure (BM2_2B7)]]</td></tr>
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