Biomod/2013/StJohns/approaches: Difference between revisions
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As can be seen in the figure below, the IgG can be cleaved by an enzyme called ficin. The result yields two Fab fragments per IgG molecule. The sample gel on the right displays the relative mobilities and quantities of these fragments and IgG. Notice that the IgG shows up at around 150 kDa and Fab fragments show up at around 50 kDa. | As can be seen in the figure below, the IgG can be cleaved by an enzyme called ficin. The result yields two Fab fragments per IgG molecule. The sample gel on the right displays the relative mobilities and quantities of these fragments and IgG. Notice that the IgG shows up at around 150 kDa and Fab fragments show up at around 50 kDa. | ||
[[Image:Lukemanlab-2013-0008. | [[Image:Lukemanlab-2013-0008.jpg|thumb|600px|center]] | ||
=Triangles= | =Triangles= | ||
Revision as of 08:56, 26 October 2013
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<html><a href="http://lukemanlab.org"><img src="http://openwetware.org/images/thumb/f/f9/Lukemanlab-toehold-conga-nanny-header.jpg/180px-Lukemanlab-toehold-conga-nanny-header.jpg"></a></html>
Claw
(placeholder for explanation of Matt's project)
Selection
(Placeholder for explanation of Keshia's project)
Antibodies
In this approach, the goal is to generate small anti-Flag Fab fragments for potential use as binding elements in future claw designs (visualized as small red protrusions on our models of the claw). These anti-Flag Fab fragments are generated from a larger antibody protein molecule called Immunoglobulin G (IgG).
As can be seen in the figure below, the IgG can be cleaved by an enzyme called ficin. The result yields two Fab fragments per IgG molecule. The sample gel on the right displays the relative mobilities and quantities of these fragments and IgG. Notice that the IgG shows up at around 150 kDa and Fab fragments show up at around 50 kDa.
Triangles
The goal of this aspect project was to create precise DNA right triangles that could potentially serve as hinges for other DNA origami, more specifically DNA claws. These origami complexes can be utilized as hinges through their rigidity. We were successful in making these triangles by combining strands and their complementary strands in solution. After running several gels, we concluded that the solution that we had originally made was a DNA complex with specific configuration by the solid band that it expressed. However, we realized that the triangles were too small to image by themselves by AFM.
This is when we realized that we needed to add DNA to the ends to make them visible. We utilized the triangle’s sticky ends to attach DNA duplexes that would help to make them visible on AFM. We ran gels to see if a new complex was made compared to the triangle. We also added a DNA complex that included the triangle with each group of duplexes on the gel. We managed to successfully show that these different complexes all moved at different mobilities. Further analysis by AFM showed that these complexes with both extenders formed at specific angles. Although several of the angles were not the desired value (90 degrees), many of the angles of the complexes that we measured were precise.
Currently, we are working on creating and imaging origami triangles with modified ‘extenders’. We are conforming plasmid DNA into the modified ‘extenders’ and utilizing staple strands to hold the plasmid DNA in place. The triangle will be made of origami strands and their complementary strands. We expect that these modified extenders will allow us to easily see the angle that is made when the triangle forms.
