Difference between revisions of "Team:Warwick/Modelling5"
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| + | <p><img src="https://static.igem.org/mediawiki/2015/0/03/Warwickbubbles7.png" height="120px" width="800px" border="1px"></p> | ||
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| + | The tetrahedron construction model could only create sphere shaped 3D structures. The cells that bound to the outside couldn't be controlled as well as we hoped so we came up with a new model that could. This page discusses the use of cube shaped DNA to create a shape where the cells bonded to the outside could be chosen. | ||
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| + | <p>_______________________________________________________________________________________________________________________________________</p><h5>Cube Construction</h5> | ||
<p> One idea for a 3-D structure was, with the use of zinc fingers, small cubes of DNA (6 x 6 x 6nm) being bound together to form a megastructure large enough for E-coli cells (size: 2 x 0.5 x 0.5 µm) to bind to with reasonable rates of success. </p> | <p> One idea for a 3-D structure was, with the use of zinc fingers, small cubes of DNA (6 x 6 x 6nm) being bound together to form a megastructure large enough for E-coli cells (size: 2 x 0.5 x 0.5 µm) to bind to with reasonable rates of success. </p> | ||
<p> The first problem would be to form the cubes readily and make them stable enough to last for the combination processes. In 1991, a paper called ‘Synthesis from DNA of a molecule with the connectivity of a cube’ outlined a method to produce hollow DNA cubes using 10 Double stranded DNA sequences. | <p> The first problem would be to form the cubes readily and make them stable enough to last for the combination processes. In 1991, a paper called ‘Synthesis from DNA of a molecule with the connectivity of a cube’ outlined a method to produce hollow DNA cubes using 10 Double stranded DNA sequences. | ||
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| − | + | <p>_______________________________________________________________________________________________________________________________________</p> <h5>Sizing of Structure</h5> | |
<p> Using geometry, it is possible to determine the minimum size that the megastructure needs to be that will allow all the E-coli cells to bind to it without blocking each other off. This can be done using the idea of circle packing. | <p> Using geometry, it is possible to determine the minimum size that the megastructure needs to be that will allow all the E-coli cells to bind to it without blocking each other off. This can be done using the idea of circle packing. | ||
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| − | + | <p>_______________________________________________________________________________________________________________________________________</p> <h5>Manufacture of the structure</h5> | |
<p> For this shape to be manufactured, manual assembly will be needed. The way in which the cubes will be bound is illustrated by this picture. However due to the size of each cube, there will be significantly less zinc finger binding to each cube than in the picture. | <p> For this shape to be manufactured, manual assembly will be needed. The way in which the cubes will be bound is illustrated by this picture. However due to the size of each cube, there will be significantly less zinc finger binding to each cube than in the picture. | ||
<p><img src="https://static.igem.org/mediawiki/2015/d/d0/Zinc_finger_diagram.png" align="middle"> | <p><img src="https://static.igem.org/mediawiki/2015/d/d0/Zinc_finger_diagram.png" align="middle"> | ||
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| − | <h5 | + | <p>_______________________________________________________________________________________________________________________________________</p><h5>Problems with this model</h5> |
<p> The sizes are only approximations and they assume that the E-coli cells bind orthogonally to each other. They also only estimate the smallest size the structure could be to allow 6 cells to bind to it. In reality the structure would probably have to be much larger. The largest problem is that this method requires a lot of manual assembly which may be very expensive. | <p> The sizes are only approximations and they assume that the E-coli cells bind orthogonally to each other. They also only estimate the smallest size the structure could be to allow 6 cells to bind to it. In reality the structure would probably have to be much larger. The largest problem is that this method requires a lot of manual assembly which may be very expensive. | ||
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Latest revision as of 20:41, 17 September 2015
