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

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The distribution of angles in the control has two populations, one where the two arms are exactly above each other which leads to very small angles and one where the two arms are considerably spread. This leads to a gaussian distribution around an finite angle. The width of this distribution is in good agreement with the calculated [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project/Theory#Fluctuation_of_the_measured_angles thermal fluctuations], which yield deviation of ca. 4.4°. <br>
The distribution of angles in the control has two populations, one where the two arms are exactly above each other which leads to very small angles and one where the two arms are considerably spread. This leads to a gaussian distribution around an finite angle. The width of this distribution is in good agreement with the calculated [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project/Theory#Fluctuation_of_the_measured_angles thermal fluctuations], which yield deviation of ca. 4.4°. <br>
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 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>
For small spermine concentrations, no significant peak shift can be observed. Only at higher concentration, the maximum of the distribution is shifted noticeably towards higher angles. For the series negative control - ethidium bromide every 21 bp - ethidium bromide every 7 bp, the data display no systematic shift, while for DAPI, the mean angle decreases continuously.


<h2>Including Base-Twist Theory</h2>
<h2>Including Base-Twist Theory</h2>

Revision as of 19:52, 2 November 2011

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