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

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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|400px|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 gallery (BM2_2B7)]]</td></tr>
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<tr bgcolor="#f5f5f5"><td valign="top">The positive control with an internally induced twist by additional base pairs in each helix (these additional base pairs lead to a net torque in each helix and therefore a macroscopic deformation of the structure) displays much higher angles. The population around zero is maybe due to deformed structures which had no second arm and could not be excluded. This results in many angles around zero. The other population around the finite angle is now the more spread structure. Here the angle of the positive control is shifted to higher values by approximately a factor of 2 because of the induced twist. So in principle this way of measuring the deformation of our structure in dependence of induced stress works.</td><td>[[Image:Image:TUM theU twistcontrol galery.png | thumb | ]]</td></tr>
<tr bgcolor="#f5f5f5"><td valign="top">The positive control with an internally induced twist by additional base pairs in each helix (these additional base pairs lead to a net torque in each helix and therefore a macroscopic deformation of the structure) displays much higher angles. The population around zero is maybe due to deformed structures which had no second arm and could not be excluded. This results in many angles around zero. The other population around the finite angle is now the more spread structure. Here the angle of the positive control is shifted to higher values by approximately a factor of 2 because of the induced twist. So in principle this way of measuring the deformation of our structure in dependence of induced stress works.</td><td>[[Image:TUM theU twistcontrol galery.png | 400px|thumb |Fig. 5 twisted control structure gallery BM21 ]]</td></tr>
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The measured angles φ for negative and positive control, <math>\phi_{neg} \approx 9</math>° and <math>\phi_{pos} \approx 21</math>°, can be related to a torsion α of the base according to the [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project/Theory#Theoretical_considerations_2 theoretical considerations for the base twist]:
The measured angles φ for negative and positive control, <math>\phi_{neg} \approx 9</math>° and <math>\phi_{pos} \approx 21</math>°, can be related to a torsion α of the base according to the [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project/Theory#Theoretical_considerations_2 theoretical considerations for the base twist]:


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