Biomod/2011/TUM/TNT/LabbookA/2011/08/29

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29th Aug 2011 <!-- sibboleth --><div id="m1" style="border:0px;"><div style="display:none;" id="id">m1</div><div style="display:none;" id="dtext"></div><div style="display:none;" id="page">Tnt - Labbook/20</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month">8</div><div style="display:none;" id="year">2011</div><div style="display:none;" id="readonly">Y</div></div> <!-- sibboleth --><div id="m2" style="border:0px;"><div style="display:none;" id="id">m2</div><div style="display:none;" id="dtext"></div><div style="display:none;" id="page">Tnt - Labbook/20</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month">9</div><div style="display:none;" id="year">2011</div><div style="display:none;" id="readonly">Y</div></div> <!-- sibboleth --><div id="m3" style="border:0px;"><div style="display:none;" id="id">m3</div><div style="display:none;" id="dtext"></div><div style="display:none;" id="page">Tnt - Labbook/20</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month">10</div><div style="display:none;" id="year">2011</div><div style="display:none;" id="readonly">Y</div></div>

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Purification of BM1 and BM2 folded with 2DH3ML and 5DH3ML via Agarose Gel Electrophoresis

File:2011.08.29 theU1kBlad-scaff-bm1-bm2.modified.tif

From left to right: 1kb ladder, p7560 scaffold, BM1 2D_H3_ML, BM2 2D_H3_ML, BM1 5D_H3_ML, BM2 5D_H3_ML (folding batches from 2011/08/23)

The BM2 2D_H3_ML lane displays unexpected intensities of the bands. We would have expected the lower band in this lane (correct folded structure) to have the highest intensity. Perhaps some error in the folding batch impaired the folding.
The gel displays no differences between the thermal ramps 15_65, 2D_H3_ML and 5D_H3_ML. As observed in the TEM, the major band of the gel with the 15_65 ramp consists of well folded origami structures, so we will use this fastest folding ramp for all further similar structures. The presence (BM1) or absence (BM2) of the polyT staples does not seem to affect folding. Therefore, further studies were based on BM2 and derivatives.