Biomod/2011/TUM/TNT/Results

(Difference between revisions)
 Revision as of 22:26, 2 November 2011 (view source)← Previous diff Revision as of 22:35, 2 November 2011 (view source)Next diff → Line 35: Line 35: {{-}} {{-}} - DNA binders were added in such concentrations, that a previously calculated fraction of binding sites should be occupied [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Calculation_of_intercalator_concentrations (see here for calculation)]. + DNA binders were added in such concentrations to theU, that a previously calculated fraction of binding sites should be occupied [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA/Calculation_of_intercalator_concentrations (see here for calculation)]. - We assumed to find a peak shift of the angles dependend on the added DNA binder concentration. The peaks for the tested DNA binding molecules spermine, ethidium bromide and DAPI as well as the negative control and the positive control (intrinsically twisted) are displayed in table 1. + We assumed to find a peak shift of the angles dependend on the added DNA binder concentration. The peaks for the tested DNA binding molecules spermine, ethidium bromide and DAPI as well as the negative control and the positive control (intrinsically twisted due to additional base pairs) are displayed in table 1. Line 78: Line 78: - The values in table 1 are based on the following histograms: + The values in table 1 are based on the following histograms (figure 4): [[Image:Negative control gaussian.png|390px]] [[Image:Negative control gaussian.png|390px]] Line 91: Line 91: [[Image:DAPI 7 histo gaussian.png|390px]] [[Image:DAPI 7 histo gaussian.png|390px]] - The measured angles are distributed in a gaussian manner around an angle $\phi_0$ with a width $\sigma$. 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 the 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].
+ 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°.
- The width of our measured angles can be explained by the following mechanism: + - when the grids for TEM are prepared, the structures are able to fluctuate around a certain mean position which - in our case - corresponds to $\phi_0$. So when the structures adhere to the carbon film of the grid and stain is added, they are fixed in one actual position. Since this fluctuation can be described by a Boltzmann distribution, we can easily calculate a theoretical value for the width of our angle measurements with some assumptions (for more details, please see: [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Methods/Data_Analysis Thermal fluctuation of the arms]). + - So we get a theoretical prediction of
+ - $\sigma = 4.4^{\circ}$
+ - which approximately explains the width of our measurements. +

Including Base-Twist Theory

Including Base-Twist Theory

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