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

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<tr bgcolor="#f5f5f5"><td valign="top">[[Image:No twist control side view.png|385px |thumb|Figure 3a Side view of BM2 without DNA-binders.]]</td><td>[[Image:Twist_EtBr_7bp_side_view.png|385px|thumb|Figure 3b Side view of BM2 with one EtBr molecule every 7bp.]]</td></tr>
<tr bgcolor="#f5f5f5"><td valign="top">[[Image:No twist control side view.png|400px |thumb|Figure 3a Side view of BM2 without DNA-binders.]]</td><td>[[Image:Twist_EtBr_7bp_side_view.png|400px|thumb|Figure 3b Side view of BM2 with one EtBr molecule every 7bp.]]</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:TUM theU twistcontrol galery.png | 400px|thumb |Fig. 5 twisted control structure gallery BM21 ]]</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.<br>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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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]:


<math>
<math>
\frac{cos \alpha -1}{\alpha} = \frac{B L}{R (B - 2 L)} sin \frac{\phi}{2}
\frac{cos \alpha -1}{\alpha} = \frac{B L}{R (B - 2 L)} sin \frac{\phi}{2}
</math>
</math></td><td>[[Image:TUM theU twistcontrol galery.png | 400px|thumb |Fig. 5 twisted control structure gallery BM21 ]]</td></tr>
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The theory determines the torsion for these particular φ-values to <math>\alpha_{neg} \approx 33</math>° and <math>\alpha_{pos} \approx 93</math>°. This corresponds to a torsion of 5° per basepair in the base of theU. <br>
The theory determines the torsion for these particular φ-values to <math>\alpha_{neg} \approx 33</math>° and <math>\alpha_{pos} \approx 93</math>°. This corresponds to a torsion of 5° per basepair in the base of theU. <br>

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