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

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<h2>Length Measurements</h2>
<h2>Length Measurements</h2>
We also measured the lengths of the origami structures on the TEM images. Histograms of the length distributions display a gaussian shape (figure 5). For increasing concentrations of spermine, the length decreases steadily (figure 6a, for raw data see this file: [[Image:TEM length measurements raw data.xlsx]]). Surprisingly, for rising concentrations of ethidium bromide, the length decreases as well, although addition of ethidium bromide is known to increase the length of a simple double stranded DNA (figure 6b). It seems, that origami structures react here in another manner then single helices. <br>
We also measured the lengths of the origami structures on the TEM images. Histograms of the length distributions display a gaussian shape (figure 6). For increasing concentrations of spermine, the length decreases steadily (figure 6a, for raw data see this file: [[Image:TEM length measurements raw data.xlsx]]). Surprisingly, for rising concentrations of ethidium bromide, the length decreases as well, although addition of ethidium bromide is known to increase the length of a simple double stranded DNA (figure 6b). It seems, that origami structures react here in another manner then single helices. <br>


[[Image:Control length histo gaussian.png |390px|center|thumb|Fig. 5 Length distribution of theU negative control, with a gaussian fit, histogram based on 256 particles]]<br>
[[Image:Control length histo gaussian.png |390px|center|thumb|Fig. 6 Length distribution of theU negative control, with a gaussian fit, histogram based on 256 particles]]<br>
[[Image:Spermine length.png|375px|left|thumb|Fig. 6a: Gaussian fits of length distributions of spermine concentration series]]
[[Image:Spermine length.png|375px|left|thumb|Fig. 7a: Gaussian fits of length distributions of spermine concentration series]]
[[Image:Etbr length.png|375px|right|thumb|Fig. 6b: Gaussian fits of length distributions of ethidium bromide concentration series]]
[[Image:Etbr length.png|375px|right|thumb|Fig. 7b: Gaussian fits of length distributions of ethidium bromide concentration series]]
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The real time PCR, which is more sensitive, still did not deliver trustworthy data when using 50 µl samples with 10 nM Atto dyes. It could be shown that the reproducibility of the real time PCR setup was poor with deviations of up to 40 % between identical samples (figure 7). To assure the identity of the samples a 100 µl stock was divided into two 50 µl samples. Based on these results no experiments with theU structure were performed at all with this device as the concentration of theU structure is lower than the concentration of the here test structure.  
The real time PCR, which is more sensitive, still did not deliver trustworthy data when using 50 µl samples with 10 nM Atto dyes. It could be shown that the reproducibility of the real time PCR setup was poor with deviations of up to 40 % between identical samples (figure 7). To assure the identity of the samples a 100 µl stock was divided into two 50 µl samples. Based on these results no experiments with theU structure were performed at all with this device as the concentration of theU structure is lower than the concentration of the here test structure.  


<center>[[Image:FRET efficiency Spermine skal.PNG|x350px|left|thumb|Fig. 7a Bulk FRET with spermine]][[Image:FRET_efficiency_EtBr.PNG|x350px|right|thumb|Fig. 7b Bulk FRET with ethidium bromide]]</center>
<table cellspacing="0" cellpadding="2">
<tr bgcolor="#f5f5f5"><td valign="top">[[Image:FRET efficiency Spermine skal.PNG|385px|thumb|Fig. 8a Bulk FRET with spermine]]</td><td>[[Image:FRET_efficiency_EtBr.PNG|385px|thumb|Fig. 8b Bulk FRET with ethidium bromide]]</td></tr>
</table>




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