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

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<tr bgcolor="#f5f5f5"><td valign="top">Based on the cross section, we could begin routing the circular scaffold through the pattern of helices. The scaffold first goes through one 10 helix bundle and then changes over to the next 10 helix bundle as one can see in the fig. 3 (the red arrows indicate the direction of the scaffold path). It is commonly known that this enables easy folding of the structure. (refer to our results from [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Results#Folding_.26_Purification folding and purification]).
<tr bgcolor="#f5f5f5"><td valign="top"><font color="#555555">Based on the cross section, we could begin routing the circular scaffold through the pattern of helices. The scaffold first goes through one 10 helix bundle and then changes over to the next 10 helix bundle as one can see in the fig. 3 (the red arrows indicate the direction of the scaffold path). It is commonly known that this enables easy folding of the structure. (refer to our results from [http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Results#Folding_.26_Purification folding and purification]).
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<tr bgcolor="#f5f5f5"><td valign="top">The grey staples belong to the core of our structure and are needed to build the basic shape. The staples marked in red can be added to the folding reaction if uncontrolled aggregation arises (if included the single stranded poly-T domains build random coils which suppress the base stacking interaction with another structure). In our case basically no aggregation occurred and we did not need to add the extra poly-T staples.</td><td>[[Image:cadnano_design.tif|x330px | thumb | Fig. 4 caDNAno design. Grey staples: build the basic shape. Red staples: if uncontrolled aggregation arises.]]</td></tr>
<tr bgcolor="#f5f5f5"><td valign="top"><font color="#555555">The grey staples belong to the core of our structure and are needed to build the basic shape. The staples marked in red can be added to the folding reaction if uncontrolled aggregation arises (if included the single stranded poly-T domains build random coils which suppress the base stacking interaction with another structure). In our case basically no aggregation occurred and we did not need to add the extra poly-T staples.</font color="#555555"></td><td>[[Image:cadnano_design.tif|x330px | thumb | Fig. 4 caDNAno design. Grey staples: build the basic shape. Red staples: if uncontrolled aggregation arises.]]</td></tr>
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<tr bgcolor="#f5f5f5"><td valign="top">Since we also wanted to perform single molecule FRET measurements with our structure, we finally had to add adapter staples to the base of theU. We used biotin labeled staples to bind theU to the surface of a microscope slide.</td><td>[[Image:adaptors.png|right|x200px | thumb | Fig. 5 Adaptors]]</td></tr>
<tr bgcolor="#f5f5f5"><td valign="top"><font color="#555555">Since we also wanted to perform single molecule FRET measurements with our structure, we finally had to add adapter staples to the base of theU. We used biotin labeled staples to bind theU to the surface of a microscope slide.</font color="#555555"></td><td>[[Image:adaptors.png|right|x200px | thumb | Fig. 5 Adaptors]]</td></tr>
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<tr bgcolor="#f5f5f5"><td valign="top">In order to have a positive control, we designed a structure which has an internally induced twist. This was done by adding an extra base pair every 21 base pairs in every single helix of theU. Since there is a crossover to another helix every 7 base pairs, this additional base pairs induces a local torque which leads to a macroscopic twist in the structure. This conformational shift could later clearly be seen in finite elements computer simulations and TEM images. In fig. 6 the 21 base pair tokens are indicated by the 2 black dashed lines and the additional base pairs by the little loops with '1' inside the scaffold.</td><td>[[Image:loop.png|right|x200px | thumb | Fig. 6 Reference structure. 21 base pair tokens: 2 black dashed lines. Additional base pairs: loops with '1' inside the scaffold.]]</td></tr>
<tr bgcolor="#f5f5f5"><td valign="top"><font color="#555555">In order to have a positive control, we designed a structure which has an internally induced twist. This was done by adding an extra base pair every 21 base pairs in every single helix of theU. Since there is a crossover to another helix every 7 base pairs, this additional base pairs induces a local torque which leads to a macroscopic twist in the structure. This conformational shift could later clearly be seen in finite elements computer simulations and TEM images. In fig. 6 the 21 base pair tokens are indicated by the 2 black dashed lines and the additional base pairs by the little loops with '1' inside the scaffold.</font color="#555555"></td><td>[[Image:loop.png|right|x200px | thumb | Fig. 6 Reference structure. 21 base pair tokens: 2 black dashed lines. Additional base pairs: loops with '1' inside the scaffold.]]</td></tr>
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